Starting phenix.real_space_refine on Tue Nov 19 05:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/11_2024/6rui_10006.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Zn 1 6.06 5 P 93 5.49 5 S 238 5.16 5 C 32426 2.51 5 N 8884 2.21 5 O 9883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51525 Number of models: 1 Model: "" Number of chains: 21 Chain: "T" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 958 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "U" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 965 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1465, 11565 Classifications: {'peptide': 1465} Link IDs: {'PTRANS': 59, 'TRANS': 1405} Chain breaks: 7 Chain: "B" Number of atoms: 9365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9365 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "O" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4139 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3936 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40069 SG CYS Q 29 64.350 77.582 61.343 1.00 96.26 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb=" P DG U 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG U 12 " occ=0.00 residue: pdb=" P DA U 19 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 19 " occ=0.00 residue: pdb=" P DA U 31 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 31 " occ=0.00 Time building chain proxies: 24.86, per 1000 atoms: 0.48 Number of scatterers: 51525 At special positions: 0 Unit cell: (159.12, 217.36, 190.32, 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) Zn 1 29.99 S 238 16.00 P 93 15.00 O 9883 8.00 N 8884 7.00 C 32426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.37 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 29 " 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11720 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 64 sheets defined 38.6% alpha, 15.4% beta 13 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 17.16 Creating SS restraints... Processing helix chain 'I' and resid 58 through 63 removed outlier: 3.585A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.777A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 3.638A pdb=" N LEU A 27 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.808A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.611A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.642A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.550A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.679A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 266' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.619A pdb=" N ASN A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.417A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.968A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.789A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.511A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.863A pdb=" N GLN A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.824A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.507A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.652A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.662A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.545A pdb=" N GLY A 761 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.541A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.747A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.718A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.501A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.544A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1010 removed outlier: 4.282A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.605A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.531A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 removed outlier: 3.675A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 3.589A pdb=" N LEU A1085 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1082 through 1086' Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.505A pdb=" N LYS A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.680A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.628A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.585A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.512A pdb=" N LYS A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.508A pdb=" N GLN A1314 " --> pdb=" O LYS A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1338 removed outlier: 3.557A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.525A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.219A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1516 " --> pdb=" O GLU A1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1516' Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.614A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.794A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1553 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.766A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.604A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.775A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.547A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.981A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.934A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.539A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.629A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.182A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.272A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.852A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.632A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.633A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.354A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.537A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.582A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.533A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 492 through 498 Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.532A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.637A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.541A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.665A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.540A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.591A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.948A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.639A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 839' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.649A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1040 through 1044 removed outlier: 3.952A pdb=" N LYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B1044 " --> pdb=" O ASN B1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1040 through 1044' Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1180 through 1191 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.976A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.559A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.557A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.703A pdb=" N GLN C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 177' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.020A pdb=" N PHE C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.567A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.534A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.689A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 47 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.526A pdb=" N ASP D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.513A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.520A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.518A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.646A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.814A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.555A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.971A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.844A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.587A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 61 removed outlier: 3.597A pdb=" N VAL O 56 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 removed outlier: 4.038A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.757A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP O 98 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 121 removed outlier: 4.045A pdb=" N ILE O 116 " --> pdb=" O GLY O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 5.084A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 160 removed outlier: 3.583A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.567A pdb=" N HIS O 173 " --> pdb=" O THR O 169 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 195 removed outlier: 3.715A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 221 removed outlier: 4.276A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR O 212 " --> pdb=" O LEU O 208 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER O 213 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 219 " --> pdb=" O LEU O 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 246 removed outlier: 3.801A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU O 244 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 347 removed outlier: 3.649A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER O 340 " --> pdb=" O LEU O 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU O 345 " --> pdb=" O THR O 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.530A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 Processing helix chain 'O' and resid 392 through 397 removed outlier: 3.515A pdb=" N MET O 396 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 408 Processing helix chain 'O' and resid 413 through 431 removed outlier: 3.687A pdb=" N LYS O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 431 " --> pdb=" O TYR O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 458 removed outlier: 3.890A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR O 445 " --> pdb=" O PHE O 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR O 447 " --> pdb=" O ALA O 443 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 458 " --> pdb=" O VAL O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.634A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 487 removed outlier: 4.104A pdb=" N ILE O 483 " --> pdb=" O ALA O 479 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 486 " --> pdb=" O TYR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 510 removed outlier: 3.764A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 535 removed outlier: 3.836A pdb=" N GLN O 534 " --> pdb=" O ARG O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 551 Processing helix chain 'O' and resid 582 through 587 Processing helix chain 'O' and resid 601 through 607 removed outlier: 4.466A pdb=" N LEU O 605 " --> pdb=" O ASN O 601 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET O 606 " --> pdb=" O TYR O 602 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 90 removed outlier: 3.867A pdb=" N SER Q 88 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 122 removed outlier: 3.779A pdb=" N LEU Q 105 " --> pdb=" O LYS Q 101 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU Q 112 " --> pdb=" O PHE Q 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG Q 114 " --> pdb=" O PHE Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 146 removed outlier: 4.365A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 141 " --> pdb=" O TRP Q 137 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE Q 144 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 172 removed outlier: 3.742A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.566A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 237 Processing helix chain 'Q' and resid 248 through 261 removed outlier: 4.009A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 3.700A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Q 277 " --> pdb=" O VAL Q 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.725A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET Q 311 " --> pdb=" O LEU Q 307 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR Q 313 " --> pdb=" O TYR Q 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE Q 314 " --> pdb=" O PHE Q 310 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 339 removed outlier: 3.670A pdb=" N SER Q 333 " --> pdb=" O LYS Q 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Q 339 " --> pdb=" O THR Q 335 " (cutoff:3.500A) Processing helix chain 'Q' and resid 346 through 357 removed outlier: 3.687A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Q 354 " --> pdb=" O ARG Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.635A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP Q 369 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 370 through 386 removed outlier: 3.776A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU Q 386 " --> pdb=" O GLU Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 417 removed outlier: 4.118A pdb=" N ARG Q 410 " --> pdb=" O GLN Q 406 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Q 412 " --> pdb=" O ILE Q 408 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 449 removed outlier: 4.250A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA Q 447 " --> pdb=" O GLN Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 476 through 490 removed outlier: 3.850A pdb=" N LEU Q 480 " --> pdb=" O ILE Q 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN Q 486 " --> pdb=" O HIS Q 482 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 514 removed outlier: 3.834A pdb=" N LEU Q 498 " --> pdb=" O SER Q 494 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER Q 503 " --> pdb=" O LYS Q 499 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA Q 508 " --> pdb=" O ARG Q 504 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS Q 511 " --> pdb=" O ASN Q 507 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG Q 512 " --> pdb=" O ALA Q 508 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET Q 513 " --> pdb=" O CYS Q 509 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 193 removed outlier: 3.511A pdb=" N LEU S 193 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 removed outlier: 3.870A pdb=" N ALA S 575 " --> pdb=" O HIS S 571 " (cutoff:3.500A) Processing helix chain 'S' and resid 585 through 612 removed outlier: 4.689A pdb=" N LEU S 592 " --> pdb=" O SER S 588 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL S 593 " --> pdb=" O ILE S 589 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS S 597 " --> pdb=" O VAL S 593 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU S 598 " --> pdb=" O SER S 594 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG S 603 " --> pdb=" O LYS S 599 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN S 608 " --> pdb=" O ILE S 604 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU S 610 " --> pdb=" O ARG S 606 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 639 removed outlier: 3.601A pdb=" N TYR S 628 " --> pdb=" O GLN S 624 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG S 629 " --> pdb=" O ASP S 625 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.593A pdb=" N PHE S 675 " --> pdb=" O SER S 671 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR S 685 " --> pdb=" O GLN S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 703 removed outlier: 3.761A pdb=" N LEU S 702 " --> pdb=" O LEU S 699 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE S 703 " --> pdb=" O LEU S 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 699 through 703' Processing helix chain 'S' and resid 711 through 720 removed outlier: 3.631A pdb=" N LEU S 718 " --> pdb=" O PHE S 714 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN S 720 " --> pdb=" O ASN S 716 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 744 removed outlier: 4.160A pdb=" N ILE S 741 " --> pdb=" O VAL S 737 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP S 742 " --> pdb=" O LYS S 738 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 3.529A pdb=" N ILE S 756 " --> pdb=" O LEU S 752 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG S 762 " --> pdb=" O ASN S 758 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER S 763 " --> pdb=" O GLU S 759 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU S 764 " --> pdb=" O ILE S 760 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.720A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR R 26 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 131 removed outlier: 3.773A pdb=" N LYS R 129 " --> pdb=" O LYS R 126 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR R 131 " --> pdb=" O TRP R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 166 removed outlier: 3.744A pdb=" N LYS R 164 " --> pdb=" O HIS R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 174 removed outlier: 3.817A pdb=" N GLU R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 180 removed outlier: 3.845A pdb=" N HIS R 179 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.618A pdb=" N LEU R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN R 223 " --> pdb=" O LEU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.580A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.894A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.790A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.939A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 322 removed outlier: 3.510A pdb=" N ASN R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 removed outlier: 3.570A pdb=" N THR R 355 " --> pdb=" O GLU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.758A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 421 removed outlier: 4.278A pdb=" N ASN R 402 " --> pdb=" O ASP R 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN R 403 " --> pdb=" O ILE R 399 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL R 404 " --> pdb=" O LYS R 400 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE R 405 " --> pdb=" O ILE R 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS R 421 " --> pdb=" O ILE R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 441 removed outlier: 3.704A pdb=" N GLU R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN R 434 " --> pdb=" O LEU R 430 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 441 " --> pdb=" O SER R 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.495A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A1471 " --> pdb=" O ASN A1461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'N' and resid 29 through 31 removed outlier: 4.836A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 80 through 82 removed outlier: 3.544A pdb=" N HIS N 85 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP N 86 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR M 76 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 86 removed outlier: 5.824A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.648A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 7.085A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.132A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.402A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB7, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.594A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.956A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.755A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.675A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.675A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 71 through 74 removed outlier: 7.082A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 71 through 74 removed outlier: 7.082A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.246A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.308A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.498A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.168A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.168A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD6, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 7.458A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.564A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD9, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AE1, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AE2, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AE3, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.638A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 87 through 88 removed outlier: 4.543A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.348A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE9, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AF1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.973A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 132 through 140 removed outlier: 3.689A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER G 244 " --> pdb=" O HIS G 237 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.711A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.542A pdb=" N ILE K 103 " --> pdb=" O PHE K 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 20 through 21 Processing sheet with id=AF8, first strand: chain 'Q' and resid 63 through 64 removed outlier: 4.114A pdb=" N THR Q 63 " --> pdb=" O SER Q 72 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 63 through 66 removed outlier: 7.561A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 173 through 174 removed outlier: 3.620A pdb=" N GLU R 196 " --> pdb=" O TRP S 174 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 184 through 187 removed outlier: 3.519A pdb=" N ILE S 202 " --> pdb=" O GLN S 185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 213 through 214 removed outlier: 3.709A pdb=" N LEU S 214 " --> pdb=" O ILE S 236 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.571A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER S 268 " --> pdb=" O THR S 265 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.571A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER S 268 " --> pdb=" O THR S 265 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 302 through 303 removed outlier: 3.723A pdb=" N VAL S 302 " --> pdb=" O ASP S 319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE S 318 " --> pdb=" O SER S 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER S 325 " --> pdb=" O ILE S 318 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE S 326 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU S 347 " --> pdb=" O ILE S 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 362 through 366 removed outlier: 4.038A pdb=" N LYS S 371 " --> pdb=" O PHE S 366 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 402 through 406 Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.563A pdb=" N SER S 495 " --> pdb=" O MET S 478 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY S 493 " --> pdb=" O VAL S 480 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER S 482 " --> pdb=" O SER S 491 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER S 491 " --> pdb=" O SER S 482 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 504 through 505 removed outlier: 3.750A pdb=" N THR S 504 " --> pdb=" O ARG S 542 " (cutoff:3.500A) 1788 hydrogen bonds defined for protein. 5004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 26.28 Time building geometry restraints manager: 13.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 16527 1.34 - 1.48: 13698 1.48 - 1.61: 22150 1.61 - 1.75: 7 1.75 - 1.89: 372 Bond restraints: 52754 Sorted by residual: bond pdb=" CA PRO B 28 " pdb=" C PRO B 28 " ideal model delta sigma weight residual 1.514 1.487 0.028 5.50e-03 3.31e+04 2.51e+01 bond pdb=" C LYS A1110 " pdb=" N GLU A1111 " ideal model delta sigma weight residual 1.329 1.250 0.079 1.86e-02 2.89e+03 1.81e+01 bond pdb=" CA LEU B 542 " pdb=" CB LEU B 542 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.38e-02 5.25e+03 1.19e+01 bond pdb=" CB ARG C 69 " pdb=" CG ARG C 69 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" N MET Q 35 " pdb=" CA MET Q 35 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.25e-02 6.40e+03 1.12e+01 ... (remaining 52749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 67843 2.21 - 4.41: 3283 4.41 - 6.62: 405 6.62 - 8.82: 111 8.82 - 11.03: 33 Bond angle restraints: 71675 Sorted by residual: angle pdb=" N PHE Q 125 " pdb=" CA PHE Q 125 " pdb=" C PHE Q 125 " ideal model delta sigma weight residual 109.42 98.55 10.87 1.48e+00 4.57e-01 5.39e+01 angle pdb=" N VAL J 14 " pdb=" CA VAL J 14 " pdb=" C VAL J 14 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" C GLY A1218 " pdb=" N ILE A1219 " pdb=" CA ILE A1219 " ideal model delta sigma weight residual 120.24 123.85 -3.61 6.30e-01 2.52e+00 3.28e+01 angle pdb=" C MET B 783 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C LEU R 354 " pdb=" N THR R 355 " pdb=" CA THR R 355 " ideal model delta sigma weight residual 120.09 126.98 -6.89 1.25e+00 6.40e-01 3.04e+01 ... (remaining 71670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.42: 30919 30.42 - 60.84: 833 60.84 - 91.26: 52 91.26 - 121.68: 0 121.68 - 152.11: 3 Dihedral angle restraints: 31807 sinusoidal: 13734 harmonic: 18073 Sorted by residual: dihedral pdb=" CA GLN S 728 " pdb=" C GLN S 728 " pdb=" N ALA S 729 " pdb=" CA ALA S 729 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LYS A 919 " pdb=" C LYS A 919 " pdb=" N PHE A 920 " pdb=" CA PHE A 920 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY I 90 " pdb=" C GLY I 90 " pdb=" N ASN I 91 " pdb=" CA ASN I 91 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 31804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 7425 0.112 - 0.224: 538 0.224 - 0.336: 24 0.336 - 0.448: 3 0.448 - 0.560: 4 Chirality restraints: 7994 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA PHE Q 125 " pdb=" N PHE Q 125 " pdb=" C PHE Q 125 " pdb=" CB PHE Q 125 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 7991 not shown) Planarity restraints: 8874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER O 239 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C SER O 239 " 0.068 2.00e-02 2.50e+03 pdb=" O SER O 239 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE O 240 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 368 " -0.033 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR R 368 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR R 368 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 368 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR R 368 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 368 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR O 221 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C TYR O 221 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR O 221 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS O 222 " 0.020 2.00e-02 2.50e+03 ... (remaining 8871 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1004 2.66 - 3.22: 45393 3.22 - 3.78: 78890 3.78 - 4.34: 110365 4.34 - 4.90: 178533 Nonbonded interactions: 414185 Sorted by model distance: nonbonded pdb=" OG1 THR Q 12 " pdb="ZN ZN Q 601 " model vdw 2.098 2.230 nonbonded pdb=" OG1 THR A1458 " pdb=" OE1 GLU A1475 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLN S 21 " pdb=" OG SER S 24 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU S 355 " pdb=" OH TYR R 131 " model vdw 2.249 3.040 nonbonded pdb=" O ILE R 257 " pdb=" OG SER R 264 " model vdw 2.261 3.040 ... (remaining 414180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 7.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 2.060 Process input model: 125.030 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.180 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.010 0.103 52754 Z= 0.674 Angle : 1.096 11.029 71675 Z= 0.605 Chirality : 0.064 0.560 7994 Planarity : 0.008 0.082 8874 Dihedral : 13.028 152.105 20087 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer: Outliers : 0.81 % Allowed : 3.06 % Favored : 96.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -4.42 (0.08), residues: 6079 helix: -3.98 (0.06), residues: 2069 sheet: -2.04 (0.17), residues: 746 loop : -2.41 (0.09), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B 143 HIS 0.018 0.003 HIS B 735 PHE 0.049 0.004 PHE B 35 TYR 0.065 0.004 TYR R 368 ARG 0.022 0.002 ARG A1105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1389 time to evaluate : 5.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 53 ASP cc_start: 0.6776 (p0) cc_final: 0.6509 (p0) REVERT: N 68 LYS cc_start: 0.6164 (mptt) cc_final: 0.5951 (mtmt) REVERT: N 89 ILE cc_start: 0.5401 (OUTLIER) cc_final: 0.5170 (pt) REVERT: M 28 LYS cc_start: 0.5973 (mmmm) cc_final: 0.5214 (mtmt) REVERT: M 99 LYS cc_start: 0.5685 (pttt) cc_final: 0.4498 (mtmm) REVERT: M 112 LYS cc_start: 0.4712 (ptmt) cc_final: 0.3754 (tppt) REVERT: A 43 HIS cc_start: 0.5291 (t-90) cc_final: 0.4323 (m-70) REVERT: A 59 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6420 (mtt90) REVERT: A 94 LEU cc_start: 0.7398 (pp) cc_final: 0.7019 (tt) REVERT: A 95 TYR cc_start: 0.5991 (t80) cc_final: 0.5705 (t80) REVERT: A 222 GLU cc_start: 0.6109 (tt0) cc_final: 0.5887 (tm-30) REVERT: A 238 MET cc_start: 0.5872 (mtm) cc_final: 0.5558 (mpp) REVERT: A 325 ASP cc_start: 0.6545 (t0) cc_final: 0.6199 (t0) REVERT: A 347 ARG cc_start: 0.6113 (ptp90) cc_final: 0.5747 (tpt170) REVERT: A 377 VAL cc_start: 0.6971 (t) cc_final: 0.6614 (p) REVERT: A 549 MET cc_start: 0.7861 (mtt) cc_final: 0.7637 (mtt) REVERT: A 601 MET cc_start: 0.8818 (mtm) cc_final: 0.8500 (mtm) REVERT: A 604 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7604 (mptp) REVERT: A 612 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7495 (pttt) REVERT: A 881 GLU cc_start: 0.7507 (tt0) cc_final: 0.7261 (tt0) REVERT: A 1099 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7599 (mmtp) REVERT: A 1201 THR cc_start: 0.7720 (t) cc_final: 0.7484 (m) REVERT: A 1234 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7375 (mmtt) REVERT: A 1455 ARG cc_start: 0.7005 (mtt-85) cc_final: 0.6403 (mtp180) REVERT: A 1495 LYS cc_start: 0.7997 (mtpm) cc_final: 0.7423 (mptt) REVERT: A 1588 MET cc_start: 0.8350 (tpt) cc_final: 0.8106 (tpt) REVERT: A 1601 GLN cc_start: 0.8274 (mp10) cc_final: 0.7404 (mp10) REVERT: A 1655 ASP cc_start: 0.8119 (m-30) cc_final: 0.7837 (m-30) REVERT: B 257 GLN cc_start: 0.7319 (mt0) cc_final: 0.7037 (mm110) REVERT: B 377 MET cc_start: 0.8860 (mtp) cc_final: 0.8316 (mtp) REVERT: B 519 LYS cc_start: 0.7573 (ttmm) cc_final: 0.7330 (ttpp) REVERT: B 542 LEU cc_start: 0.9200 (tp) cc_final: 0.8974 (tt) REVERT: B 591 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8329 (tttt) REVERT: B 720 GLN cc_start: 0.7534 (tt0) cc_final: 0.7280 (tp40) REVERT: B 810 ASP cc_start: 0.7919 (t0) cc_final: 0.7493 (t70) REVERT: B 865 THR cc_start: 0.6944 (p) cc_final: 0.6530 (t) REVERT: B 1106 GLU cc_start: 0.6707 (tt0) cc_final: 0.6267 (mm-30) REVERT: B 1160 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6021 (mp0) REVERT: C 124 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6044 (mm-30) REVERT: C 245 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7123 (mpt180) REVERT: C 296 ASN cc_start: 0.7831 (m-40) cc_final: 0.7111 (p0) REVERT: D 1 MET cc_start: 0.1592 (ptm) cc_final: 0.0496 (tmm) REVERT: D 29 GLN cc_start: 0.7808 (tt0) cc_final: 0.7010 (mp10) REVERT: E 25 ASP cc_start: 0.6940 (m-30) cc_final: 0.6724 (m-30) REVERT: E 32 GLN cc_start: 0.6486 (tp40) cc_final: 0.6273 (tp40) REVERT: E 52 ARG cc_start: 0.6298 (ptp-170) cc_final: 0.5443 (ppt90) REVERT: E 74 ASP cc_start: 0.6789 (m-30) cc_final: 0.6485 (m-30) REVERT: E 122 LYS cc_start: 0.6973 (mmmt) cc_final: 0.6718 (mmpt) REVERT: E 215 MET cc_start: 0.7143 (mmt) cc_final: 0.6889 (mmt) REVERT: F 66 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7505 (mtp180) REVERT: F 67 LYS cc_start: 0.7997 (ttpp) cc_final: 0.7188 (ttmm) REVERT: F 127 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7777 (mt-10) REVERT: G 72 LYS cc_start: 0.8399 (mttt) cc_final: 0.7943 (mtmm) REVERT: G 88 LYS cc_start: 0.7595 (ttpt) cc_final: 0.7329 (ptpp) REVERT: G 102 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6366 (mp0) REVERT: G 157 ILE cc_start: 0.7393 (mt) cc_final: 0.7083 (mm) REVERT: H 41 ASP cc_start: 0.8190 (m-30) cc_final: 0.7837 (m-30) REVERT: H 93 TYR cc_start: 0.8338 (m-80) cc_final: 0.7972 (m-80) REVERT: H 97 MET cc_start: 0.8327 (mtm) cc_final: 0.8015 (mtm) REVERT: J 26 GLN cc_start: 0.8392 (tp40) cc_final: 0.8072 (mm-40) REVERT: K 44 ARG cc_start: 0.6214 (ptp-170) cc_final: 0.6000 (mtp85) REVERT: K 48 LYS cc_start: 0.8139 (tttp) cc_final: 0.7922 (ttmt) REVERT: K 68 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7248 (mm-30) REVERT: K 122 LYS cc_start: 0.7614 (tttt) cc_final: 0.7131 (tptt) REVERT: K 126 ASP cc_start: 0.7931 (m-30) cc_final: 0.7537 (m-30) REVERT: L 39 SER cc_start: 0.8524 (t) cc_final: 0.8239 (p) REVERT: O 88 ILE cc_start: 0.4151 (tt) cc_final: 0.3780 (mm) REVERT: O 131 HIS cc_start: 0.4904 (m-70) cc_final: 0.4393 (t70) REVERT: O 142 ILE cc_start: 0.5893 (pp) cc_final: 0.5566 (pt) REVERT: O 173 HIS cc_start: 0.3938 (t70) cc_final: 0.3299 (m90) REVERT: O 311 MET cc_start: 0.2691 (ptp) cc_final: 0.2469 (mtm) REVERT: O 346 GLN cc_start: 0.6403 (mm-40) cc_final: 0.6018 (mp10) REVERT: O 369 LYS cc_start: 0.7767 (ptpt) cc_final: 0.7393 (ptmt) REVERT: O 433 LYS cc_start: 0.6615 (mmmt) cc_final: 0.6310 (mmpt) REVERT: O 438 GLN cc_start: 0.6725 (mt0) cc_final: 0.6208 (mm110) REVERT: O 441 PHE cc_start: 0.5209 (t80) cc_final: 0.4297 (m-80) REVERT: O 462 ASP cc_start: 0.6890 (m-30) cc_final: 0.6081 (t0) REVERT: O 464 ARG cc_start: 0.5888 (ttt-90) cc_final: 0.5023 (tpp-160) REVERT: O 468 GLU cc_start: 0.6357 (pm20) cc_final: 0.6035 (mt-10) REVERT: O 490 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4472 (mp) REVERT: O 501 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6424 (pm20) REVERT: O 507 GLN cc_start: 0.5900 (tp40) cc_final: 0.5278 (tt0) REVERT: O 527 MET cc_start: 0.5779 (ttm) cc_final: 0.5405 (tpt) REVERT: O 545 GLU cc_start: 0.5221 (tp30) cc_final: 0.5021 (tt0) REVERT: O 582 ARG cc_start: 0.6456 (tpt170) cc_final: 0.6148 (tpt170) REVERT: O 603 LYS cc_start: 0.6856 (ttmt) cc_final: 0.6009 (tptt) REVERT: Q 141 LEU cc_start: 0.6046 (tp) cc_final: 0.5572 (pp) REVERT: Q 190 MET cc_start: 0.7553 (ptt) cc_final: 0.6984 (ttp) REVERT: Q 222 PHE cc_start: 0.5681 (p90) cc_final: 0.4869 (p90) REVERT: Q 225 GLN cc_start: 0.6706 (tt0) cc_final: 0.5736 (mm-40) REVERT: Q 250 GLN cc_start: 0.5127 (mp10) cc_final: 0.4795 (mp10) REVERT: Q 360 LYS cc_start: 0.4825 (ptpt) cc_final: 0.4371 (ptmm) REVERT: Q 371 GLU cc_start: 0.6944 (tp30) cc_final: 0.6627 (pt0) REVERT: Q 445 ARG cc_start: 0.5515 (mtt-85) cc_final: 0.5249 (mmm-85) REVERT: Q 448 LYS cc_start: 0.5094 (tttp) cc_final: 0.4349 (mttt) REVERT: Q 507 ASN cc_start: 0.3887 (m110) cc_final: 0.3529 (t0) REVERT: S 35 LYS cc_start: 0.6637 (pttt) cc_final: 0.6266 (pttt) REVERT: S 241 PRO cc_start: 0.3981 (Cg_exo) cc_final: 0.3761 (Cg_endo) REVERT: S 283 ASP cc_start: 0.3276 (t0) cc_final: 0.2885 (p0) REVERT: S 293 TYR cc_start: 0.2992 (m-80) cc_final: 0.2552 (m-80) REVERT: S 324 TRP cc_start: 0.6050 (p-90) cc_final: 0.5607 (p-90) REVERT: S 329 ILE cc_start: 0.5086 (tt) cc_final: 0.4671 (mm) REVERT: S 365 TRP cc_start: 0.3862 (m-10) cc_final: 0.3378 (m100) REVERT: S 380 MET cc_start: 0.6861 (ttp) cc_final: 0.6609 (ttm) REVERT: S 386 MET cc_start: 0.4017 (tpp) cc_final: 0.3725 (ttt) REVERT: S 407 ARG cc_start: 0.5176 (tmt90) cc_final: 0.3923 (tmt170) REVERT: S 458 LYS cc_start: 0.4565 (mttm) cc_final: 0.4278 (tptt) REVERT: S 471 MET cc_start: 0.5797 (mtt) cc_final: 0.5536 (mtp) REVERT: S 474 LYS cc_start: 0.6521 (mtmt) cc_final: 0.5646 (mtmt) REVERT: S 478 MET cc_start: 0.5434 (ptp) cc_final: 0.5065 (ptp) REVERT: S 484 ARG cc_start: 0.5551 (mtt-85) cc_final: 0.4835 (ttt-90) REVERT: S 540 LYS cc_start: 0.5838 (tttm) cc_final: 0.5518 (tttt) REVERT: S 636 GLU cc_start: 0.4978 (tm-30) cc_final: 0.4534 (mm-30) REVERT: S 638 LEU cc_start: 0.4793 (mt) cc_final: 0.4488 (tp) REVERT: S 639 GLU cc_start: 0.5365 (mm-30) cc_final: 0.4843 (pp20) REVERT: S 674 GLU cc_start: 0.6506 (tp30) cc_final: 0.5645 (mt-10) REVERT: S 698 LYS cc_start: 0.4609 (pttm) cc_final: 0.4207 (tmmt) REVERT: S 700 LEU cc_start: 0.6359 (tp) cc_final: 0.6136 (mm) REVERT: S 742 TRP cc_start: 0.4306 (m100) cc_final: 0.3513 (m-10) REVERT: R 3 GLU cc_start: 0.7125 (tt0) cc_final: 0.6838 (tt0) REVERT: R 21 TYR cc_start: 0.5725 (m-80) cc_final: 0.5382 (m-80) REVERT: R 253 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6311 (pt) REVERT: R 312 TYR cc_start: 0.8541 (t80) cc_final: 0.8186 (t80) REVERT: R 408 ILE cc_start: 0.7070 (mm) cc_final: 0.6050 (tt) REVERT: R 437 SER cc_start: 0.6976 (t) cc_final: 0.6695 (p) REVERT: R 439 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5654 (pp20) REVERT: R 441 ARG cc_start: 0.5285 (mtt180) cc_final: 0.4710 (tpp-160) outliers start: 45 outliers final: 17 residues processed: 1415 average time/residue: 1.7438 time to fit residues: 3057.1062 Evaluate side-chains 787 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 767 time to evaluate : 5.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 490 ILE Chi-restraints excluded: chain O residue 543 ILE Chi-restraints excluded: chain Q residue 104 PHE Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 319 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 522 optimal weight: 0.9990 chunk 469 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 316 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 485 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 295 optimal weight: 0.2980 chunk 361 optimal weight: 0.6980 chunk 562 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 74 ASN A 106 HIS A 344 ASN A 590 ASN A 706 HIS A 795 HIS A 819 ASN A1062 HIS A1336 GLN A1487 ASN A1500 GLN A1648 ASN B 479 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN B 735 HIS B 770 ASN B1165 ASN C 330 ASN G 126 GLN G 150 HIS G 221 ASN H 35 GLN J 53 HIS O 117 GLN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Q 300 ASN Q 486 GLN S 259 ASN S 267 ASN S 430 ASN S 554 ASN S 656 HIS R 10 ASN R 153 ASN R 184 ASN R 189 GLN R 223 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 434 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 52754 Z= 0.208 Angle : 0.686 12.556 71675 Z= 0.367 Chirality : 0.045 0.236 7994 Planarity : 0.006 0.064 8874 Dihedral : 13.158 145.717 7752 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.24 % Allowed : 12.15 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.03 (0.09), residues: 6079 helix: -2.09 (0.09), residues: 2145 sheet: -1.63 (0.18), residues: 741 loop : -2.03 (0.10), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 380 HIS 0.013 0.001 HIS B 282 PHE 0.024 0.002 PHE B 862 TYR 0.028 0.002 TYR A1302 ARG 0.007 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 925 time to evaluate : 5.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 8 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6477 (tp) REVERT: I 101 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.6033 (mp) REVERT: N 56 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.6055 (mt) REVERT: N 68 LYS cc_start: 0.6066 (mptt) cc_final: 0.5794 (pttt) REVERT: M 28 LYS cc_start: 0.5979 (mmmm) cc_final: 0.5275 (mttm) REVERT: M 99 LYS cc_start: 0.5626 (pttt) cc_final: 0.4469 (mtmm) REVERT: M 101 VAL cc_start: 0.5572 (OUTLIER) cc_final: 0.5207 (p) REVERT: A 43 HIS cc_start: 0.5402 (t-90) cc_final: 0.4464 (m-70) REVERT: A 59 ARG cc_start: 0.6855 (mtm110) cc_final: 0.6567 (mtt90) REVERT: A 94 LEU cc_start: 0.7129 (pp) cc_final: 0.6874 (tt) REVERT: A 182 LYS cc_start: 0.7142 (mttt) cc_final: 0.6722 (mtmm) REVERT: A 218 LYS cc_start: 0.7661 (mmpt) cc_final: 0.7402 (mtpt) REVERT: A 238 MET cc_start: 0.5563 (mtm) cc_final: 0.5346 (mpp) REVERT: A 325 ASP cc_start: 0.6433 (t0) cc_final: 0.6194 (t0) REVERT: A 347 ARG cc_start: 0.6059 (ptp90) cc_final: 0.5755 (tpt170) REVERT: A 589 MET cc_start: 0.8502 (mmm) cc_final: 0.8052 (mmm) REVERT: A 604 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7704 (mptp) REVERT: A 881 GLU cc_start: 0.7405 (tt0) cc_final: 0.7202 (tt0) REVERT: A 1028 GLU cc_start: 0.7105 (tt0) cc_final: 0.6816 (tt0) REVERT: A 1163 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6987 (mp0) REVERT: A 1234 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7399 (mmtt) REVERT: A 1274 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.7009 (tt0) REVERT: A 1295 ARG cc_start: 0.7060 (mmt90) cc_final: 0.6792 (mmt90) REVERT: A 1455 ARG cc_start: 0.6750 (mtt-85) cc_final: 0.6215 (mtp180) REVERT: A 1495 LYS cc_start: 0.8008 (mtpm) cc_final: 0.7447 (mptt) REVERT: A 1542 THR cc_start: 0.7871 (m) cc_final: 0.7631 (p) REVERT: A 1587 ASP cc_start: 0.7483 (m-30) cc_final: 0.7282 (m-30) REVERT: A 1601 GLN cc_start: 0.7915 (mp10) cc_final: 0.7630 (mp10) REVERT: A 1624 LYS cc_start: 0.7956 (mttp) cc_final: 0.7639 (mtpt) REVERT: A 1655 ASP cc_start: 0.8095 (m-30) cc_final: 0.7690 (m-30) REVERT: B 16 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6541 (p90) REVERT: B 40 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: B 257 GLN cc_start: 0.7371 (mt0) cc_final: 0.7078 (mm110) REVERT: B 591 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8265 (tttt) REVERT: B 720 GLN cc_start: 0.7424 (tt0) cc_final: 0.7208 (tp40) REVERT: B 810 ASP cc_start: 0.7747 (t0) cc_final: 0.7424 (t70) REVERT: B 865 THR cc_start: 0.6876 (p) cc_final: 0.6484 (t) REVERT: B 1057 MET cc_start: 0.7564 (mmm) cc_final: 0.7220 (mmm) REVERT: B 1115 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: B 1199 ASN cc_start: 0.8350 (m-40) cc_final: 0.8004 (m110) REVERT: C 51 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: C 124 GLU cc_start: 0.6514 (mt-10) cc_final: 0.5946 (mm-30) REVERT: C 245 ARG cc_start: 0.7687 (tpp80) cc_final: 0.7192 (tpp-160) REVERT: C 296 ASN cc_start: 0.7862 (m-40) cc_final: 0.7205 (p0) REVERT: C 327 TYR cc_start: 0.8559 (t80) cc_final: 0.8311 (t80) REVERT: D 1 MET cc_start: 0.1428 (ptm) cc_final: 0.0655 (tpt) REVERT: D 29 GLN cc_start: 0.7733 (tt0) cc_final: 0.7332 (mp10) REVERT: D 91 ARG cc_start: 0.6531 (mtm180) cc_final: 0.6255 (mmt90) REVERT: E 36 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7391 (mp0) REVERT: E 41 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: E 122 LYS cc_start: 0.7218 (mmmt) cc_final: 0.6481 (mtmm) REVERT: E 215 MET cc_start: 0.7070 (mmt) cc_final: 0.6779 (mmt) REVERT: F 66 ARG cc_start: 0.7418 (mtp180) cc_final: 0.7136 (mtp180) REVERT: F 71 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7281 (pt0) REVERT: F 112 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5706 (pp20) REVERT: F 127 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7503 (mt-10) REVERT: F 129 LYS cc_start: 0.8386 (mmtp) cc_final: 0.7966 (mmmt) REVERT: G 72 LYS cc_start: 0.8319 (mttt) cc_final: 0.8031 (mtmm) REVERT: G 85 GLU cc_start: 0.6668 (tp30) cc_final: 0.6449 (tp30) REVERT: G 88 LYS cc_start: 0.7447 (ttpt) cc_final: 0.7215 (ptpp) REVERT: G 102 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6366 (mp0) REVERT: G 157 ILE cc_start: 0.7253 (mt) cc_final: 0.6871 (mm) REVERT: H 22 LYS cc_start: 0.8694 (mttm) cc_final: 0.8139 (mtpt) REVERT: H 97 MET cc_start: 0.8165 (mtm) cc_final: 0.7845 (mtm) REVERT: J 26 GLN cc_start: 0.8374 (tp40) cc_final: 0.8017 (mm-40) REVERT: J 28 ASP cc_start: 0.7862 (m-30) cc_final: 0.6922 (t0) REVERT: L 39 SER cc_start: 0.8513 (t) cc_final: 0.8264 (p) REVERT: L 56 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7916 (mm) REVERT: O 98 ASP cc_start: 0.4127 (m-30) cc_final: 0.3861 (OUTLIER) REVERT: O 127 GLU cc_start: 0.4743 (mt-10) cc_final: 0.3714 (pp20) REVERT: O 173 HIS cc_start: 0.4081 (t70) cc_final: 0.3381 (m90) REVERT: O 187 MET cc_start: 0.6673 (mtm) cc_final: 0.6468 (mtm) REVERT: O 369 LYS cc_start: 0.7784 (ptpt) cc_final: 0.7485 (ptmt) REVERT: O 424 LEU cc_start: 0.7058 (tp) cc_final: 0.6775 (tp) REVERT: O 438 GLN cc_start: 0.6526 (mt0) cc_final: 0.6235 (mm110) REVERT: O 449 TRP cc_start: 0.7096 (t60) cc_final: 0.6806 (t60) REVERT: O 456 GLU cc_start: 0.5702 (mt-10) cc_final: 0.4933 (mm-30) REVERT: O 462 ASP cc_start: 0.6817 (m-30) cc_final: 0.6157 (t0) REVERT: O 464 ARG cc_start: 0.5830 (ttt-90) cc_final: 0.4985 (tpp-160) REVERT: O 468 GLU cc_start: 0.6298 (pm20) cc_final: 0.6013 (mt-10) REVERT: O 490 ILE cc_start: 0.4853 (OUTLIER) cc_final: 0.4426 (mp) REVERT: O 501 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6452 (tp30) REVERT: O 507 GLN cc_start: 0.5882 (tp40) cc_final: 0.5376 (tt0) REVERT: O 543 ILE cc_start: 0.5630 (mt) cc_final: 0.5285 (mp) REVERT: O 603 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5910 (tptt) REVERT: O 604 ILE cc_start: 0.6675 (mm) cc_final: 0.6384 (mt) REVERT: Q 141 LEU cc_start: 0.6386 (tp) cc_final: 0.5729 (pp) REVERT: Q 317 MET cc_start: 0.4519 (mpt) cc_final: 0.3550 (ttp) REVERT: Q 346 GLU cc_start: 0.5318 (tm-30) cc_final: 0.5115 (mp0) REVERT: Q 360 LYS cc_start: 0.4615 (ptpt) cc_final: 0.4183 (ptmm) REVERT: Q 376 GLU cc_start: 0.6628 (tp30) cc_final: 0.6139 (mm-30) REVERT: Q 421 ARG cc_start: 0.5074 (ttt90) cc_final: 0.4666 (mtt180) REVERT: Q 448 LYS cc_start: 0.5314 (tttp) cc_final: 0.4495 (mttt) REVERT: Q 450 THR cc_start: 0.4792 (t) cc_final: 0.4481 (m) REVERT: S 283 ASP cc_start: 0.3342 (t0) cc_final: 0.2893 (p0) REVERT: S 293 TYR cc_start: 0.3166 (m-80) cc_final: 0.2631 (m-80) REVERT: S 324 TRP cc_start: 0.6279 (p-90) cc_final: 0.5941 (p-90) REVERT: S 329 ILE cc_start: 0.4887 (tt) cc_final: 0.4496 (mt) REVERT: S 365 TRP cc_start: 0.3825 (m-10) cc_final: 0.3430 (m100) REVERT: S 386 MET cc_start: 0.4353 (tpp) cc_final: 0.3953 (ttt) REVERT: S 407 ARG cc_start: 0.5193 (tmt90) cc_final: 0.4361 (tmt170) REVERT: S 421 ILE cc_start: 0.7348 (tt) cc_final: 0.7034 (tt) REVERT: S 458 LYS cc_start: 0.4355 (mttm) cc_final: 0.4094 (tptt) REVERT: S 474 LYS cc_start: 0.5997 (mtmt) cc_final: 0.5587 (mmmt) REVERT: S 478 MET cc_start: 0.5565 (ptp) cc_final: 0.5229 (ptp) REVERT: S 531 PHE cc_start: 0.2602 (p90) cc_final: 0.2232 (m-10) REVERT: S 540 LYS cc_start: 0.6114 (tttm) cc_final: 0.5818 (tttt) REVERT: S 628 TYR cc_start: 0.5550 (t80) cc_final: 0.5179 (t80) REVERT: S 636 GLU cc_start: 0.4609 (tm-30) cc_final: 0.4079 (mm-30) REVERT: S 674 GLU cc_start: 0.6009 (tp30) cc_final: 0.4911 (mt-10) REVERT: S 698 LYS cc_start: 0.4523 (pttm) cc_final: 0.4231 (tmmt) REVERT: S 700 LEU cc_start: 0.6388 (tp) cc_final: 0.6153 (mm) REVERT: S 742 TRP cc_start: 0.3385 (m100) cc_final: 0.3016 (m-10) REVERT: R 256 GLU cc_start: 0.6591 (mp0) cc_final: 0.6361 (mp0) REVERT: R 312 TYR cc_start: 0.8345 (t80) cc_final: 0.7924 (t80) REVERT: R 319 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7431 (t0) REVERT: R 324 MET cc_start: 0.4709 (mtm) cc_final: 0.3856 (ttt) REVERT: R 441 ARG cc_start: 0.5314 (mtt180) cc_final: 0.4708 (tpp-160) outliers start: 180 outliers final: 55 residues processed: 1031 average time/residue: 1.6628 time to fit residues: 2156.2758 Evaluate side-chains 781 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 714 time to evaluate : 5.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 74 ASN Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1274 GLU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 490 ILE Chi-restraints excluded: chain O residue 540 CYS Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 417 THR Chi-restraints excluded: chain S residue 491 SER Chi-restraints excluded: chain S residue 589 ILE Chi-restraints excluded: chain S residue 691 VAL Chi-restraints excluded: chain S residue 732 LEU Chi-restraints excluded: chain S residue 769 GLN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 23 TYR Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 319 ASN Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 312 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 467 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 563 optimal weight: 9.9990 chunk 608 optimal weight: 0.6980 chunk 501 optimal weight: 6.9990 chunk 558 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 451 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 224 HIS A 260 GLN A 344 ASN A 425 ASN A 580 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 ASN A1487 ASN A1620 GLN A1648 ASN B 168 ASN B 231 HIS B 235 GLN B 462 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN B 695 ASN B 770 ASN G 20 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN H 35 GLN O 549 ASN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN ** Q 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 486 GLN S 267 ASN S 595 GLN R 433 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 52754 Z= 0.354 Angle : 0.742 14.094 71675 Z= 0.390 Chirality : 0.048 0.290 7994 Planarity : 0.006 0.087 8874 Dihedral : 13.239 147.307 7735 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.34 % Allowed : 14.96 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.10), residues: 6079 helix: -1.26 (0.10), residues: 2165 sheet: -1.47 (0.18), residues: 770 loop : -1.80 (0.10), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 143 HIS 0.012 0.002 HIS A 673 PHE 0.027 0.003 PHE B 954 TYR 0.029 0.003 TYR A1302 ARG 0.010 0.001 ARG A 956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 725 time to evaluate : 5.595 Fit side-chains revert: symmetry clash REVERT: N 56 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6267 (mt) REVERT: N 68 LYS cc_start: 0.6050 (mptt) cc_final: 0.5766 (pttt) REVERT: M 96 LEU cc_start: 0.7385 (mt) cc_final: 0.7027 (mm) REVERT: A 43 HIS cc_start: 0.5533 (t-90) cc_final: 0.4703 (m-70) REVERT: A 59 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6640 (mtt90) REVERT: A 70 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7677 (ttpp) REVERT: A 94 LEU cc_start: 0.7358 (pp) cc_final: 0.7057 (tt) REVERT: A 184 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6845 (tptp) REVERT: A 238 MET cc_start: 0.5720 (mtm) cc_final: 0.5510 (mpp) REVERT: A 316 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6235 (pt) REVERT: A 325 ASP cc_start: 0.6488 (t0) cc_final: 0.6194 (t0) REVERT: A 347 ARG cc_start: 0.6240 (ptp90) cc_final: 0.5767 (tpt170) REVERT: A 422 ARG cc_start: 0.5945 (mmp-170) cc_final: 0.4348 (mmm-85) REVERT: A 481 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7593 (ptp-170) REVERT: A 589 MET cc_start: 0.8575 (mmm) cc_final: 0.8195 (mmm) REVERT: A 604 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7735 (mptp) REVERT: A 768 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: A 928 MET cc_start: 0.8833 (mtm) cc_final: 0.8181 (mtm) REVERT: A 1163 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6992 (mp0) REVERT: A 1234 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7527 (mmtt) REVERT: A 1337 LYS cc_start: 0.6538 (mttt) cc_final: 0.5615 (mmtm) REVERT: A 1455 ARG cc_start: 0.6812 (mtt-85) cc_final: 0.6301 (mtp180) REVERT: A 1495 LYS cc_start: 0.8163 (mtpm) cc_final: 0.7516 (mptt) REVERT: A 1542 THR cc_start: 0.7791 (m) cc_final: 0.7512 (p) REVERT: A 1624 LYS cc_start: 0.7920 (mttp) cc_final: 0.7661 (mtpt) REVERT: A 1655 ASP cc_start: 0.8174 (m-30) cc_final: 0.7764 (m-30) REVERT: B 16 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.6507 (p90) REVERT: B 40 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: B 257 GLN cc_start: 0.7312 (mt0) cc_final: 0.6958 (mm110) REVERT: B 268 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: B 328 GLN cc_start: 0.7225 (mp10) cc_final: 0.6980 (mp10) REVERT: B 352 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: B 372 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7900 (mtm180) REVERT: B 377 MET cc_start: 0.8829 (mtp) cc_final: 0.8249 (mtp) REVERT: B 593 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7887 (pp) REVERT: B 720 GLN cc_start: 0.7529 (tt0) cc_final: 0.7195 (tp40) REVERT: B 810 ASP cc_start: 0.7828 (t0) cc_final: 0.7552 (t70) REVERT: B 858 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 865 THR cc_start: 0.6663 (p) cc_final: 0.6311 (t) REVERT: B 1057 MET cc_start: 0.7595 (mmm) cc_final: 0.7327 (mmm) REVERT: B 1074 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6799 (mtm) REVERT: B 1114 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7173 (pp30) REVERT: B 1115 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7417 (mm-40) REVERT: B 1160 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6417 (mm-30) REVERT: C 51 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: C 124 GLU cc_start: 0.6553 (mt-10) cc_final: 0.5997 (mm-30) REVERT: C 245 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7086 (tpp-160) REVERT: C 296 ASN cc_start: 0.7819 (m-40) cc_final: 0.7090 (p0) REVERT: C 329 LYS cc_start: 0.8527 (ttpp) cc_final: 0.8215 (tttp) REVERT: D 1 MET cc_start: 0.1578 (ptm) cc_final: 0.0867 (tpp) REVERT: D 29 GLN cc_start: 0.7972 (tt0) cc_final: 0.7413 (mp10) REVERT: D 91 ARG cc_start: 0.6616 (mtm180) cc_final: 0.6383 (mtm180) REVERT: E 9 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7409 (mp) REVERT: E 41 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6678 (t0) REVERT: E 65 THR cc_start: 0.7747 (p) cc_final: 0.7437 (t) REVERT: E 81 GLU cc_start: 0.7479 (tp30) cc_final: 0.7111 (tp30) REVERT: E 122 LYS cc_start: 0.7290 (mmmt) cc_final: 0.6554 (mtmm) REVERT: F 66 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7198 (mtp180) REVERT: F 78 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: F 127 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7752 (mt-10) REVERT: G 72 LYS cc_start: 0.8357 (mttt) cc_final: 0.7929 (mtmm) REVERT: G 88 LYS cc_start: 0.7470 (ttpt) cc_final: 0.7250 (ptpp) REVERT: G 128 GLN cc_start: 0.5917 (mt0) cc_final: 0.5501 (mp10) REVERT: G 138 PHE cc_start: 0.5415 (OUTLIER) cc_final: 0.4994 (t80) REVERT: G 157 ILE cc_start: 0.7186 (mt) cc_final: 0.6778 (mm) REVERT: H 93 TYR cc_start: 0.8574 (m-80) cc_final: 0.8296 (m-80) REVERT: H 97 MET cc_start: 0.8131 (mtm) cc_final: 0.7775 (mtm) REVERT: H 100 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8841 (t) REVERT: J 28 ASP cc_start: 0.8022 (m-30) cc_final: 0.7022 (t0) REVERT: K 67 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: L 39 SER cc_start: 0.8549 (t) cc_final: 0.8283 (p) REVERT: L 56 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7838 (mt) REVERT: O 88 ILE cc_start: 0.4263 (tt) cc_final: 0.3924 (mm) REVERT: O 98 ASP cc_start: 0.3921 (m-30) cc_final: 0.3697 (t70) REVERT: O 127 GLU cc_start: 0.4839 (mt-10) cc_final: 0.3815 (pp20) REVERT: O 138 TYR cc_start: 0.6088 (t80) cc_final: 0.5753 (t80) REVERT: O 173 HIS cc_start: 0.4142 (t70) cc_final: 0.3400 (m90) REVERT: O 245 GLN cc_start: 0.4090 (tt0) cc_final: 0.3283 (mm-40) REVERT: O 369 LYS cc_start: 0.7798 (ptpt) cc_final: 0.7493 (ptmt) REVERT: O 424 LEU cc_start: 0.7075 (tp) cc_final: 0.6805 (tp) REVERT: O 438 GLN cc_start: 0.6494 (mt0) cc_final: 0.6167 (mm110) REVERT: O 449 TRP cc_start: 0.7196 (t60) cc_final: 0.6924 (t60) REVERT: O 456 GLU cc_start: 0.5441 (mt-10) cc_final: 0.4775 (mm-30) REVERT: O 459 GLU cc_start: 0.6581 (pt0) cc_final: 0.6304 (pp20) REVERT: O 462 ASP cc_start: 0.6889 (m-30) cc_final: 0.6102 (t0) REVERT: O 464 ARG cc_start: 0.5904 (ttt-90) cc_final: 0.4934 (tpp-160) REVERT: O 468 GLU cc_start: 0.6225 (pm20) cc_final: 0.5882 (mt-10) REVERT: O 485 CYS cc_start: 0.6740 (m) cc_final: 0.6320 (p) REVERT: O 490 ILE cc_start: 0.4771 (OUTLIER) cc_final: 0.4348 (mp) REVERT: O 501 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6404 (pm20) REVERT: O 507 GLN cc_start: 0.5691 (tp40) cc_final: 0.5422 (tt0) REVERT: O 543 ILE cc_start: 0.5957 (mt) cc_final: 0.5632 (mp) REVERT: O 603 LYS cc_start: 0.6801 (ttmt) cc_final: 0.5863 (tptt) REVERT: O 604 ILE cc_start: 0.6641 (mm) cc_final: 0.6349 (mt) REVERT: Q 20 TRP cc_start: 0.6010 (t60) cc_final: 0.5695 (t60) REVERT: Q 141 LEU cc_start: 0.6632 (tp) cc_final: 0.5738 (pp) REVERT: Q 142 LYS cc_start: 0.4728 (tmtm) cc_final: 0.3812 (mmmt) REVERT: Q 162 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6683 (tp) REVERT: Q 165 LEU cc_start: 0.5444 (mt) cc_final: 0.5182 (mt) REVERT: Q 317 MET cc_start: 0.4645 (mpt) cc_final: 0.3619 (ttp) REVERT: Q 346 GLU cc_start: 0.5681 (tm-30) cc_final: 0.5267 (mp0) REVERT: Q 360 LYS cc_start: 0.4716 (ptpt) cc_final: 0.4267 (ptmm) REVERT: Q 376 GLU cc_start: 0.6578 (tp30) cc_final: 0.6057 (mm-30) REVERT: Q 421 ARG cc_start: 0.5324 (ttt90) cc_final: 0.4925 (mtt-85) REVERT: Q 439 ILE cc_start: 0.4858 (pt) cc_final: 0.4500 (mp) REVERT: Q 448 LYS cc_start: 0.5455 (tttp) cc_final: 0.4380 (mttt) REVERT: Q 513 MET cc_start: 0.4248 (mpt) cc_final: 0.1262 (ptm) REVERT: S 30 GLU cc_start: 0.6967 (pm20) cc_final: 0.6709 (pm20) REVERT: S 187 ILE cc_start: 0.4726 (tt) cc_final: 0.4071 (mm) REVERT: S 283 ASP cc_start: 0.3493 (t0) cc_final: 0.2968 (p0) REVERT: S 293 TYR cc_start: 0.3055 (m-80) cc_final: 0.2549 (m-80) REVERT: S 324 TRP cc_start: 0.6295 (p-90) cc_final: 0.5888 (p-90) REVERT: S 329 ILE cc_start: 0.4463 (tt) cc_final: 0.3968 (mt) REVERT: S 364 GLU cc_start: 0.6228 (tp30) cc_final: 0.5407 (tp30) REVERT: S 365 TRP cc_start: 0.3899 (m-10) cc_final: 0.3563 (m100) REVERT: S 407 ARG cc_start: 0.5143 (tmt90) cc_final: 0.4320 (tmt170) REVERT: S 458 LYS cc_start: 0.4302 (mttm) cc_final: 0.4039 (tptt) REVERT: S 474 LYS cc_start: 0.5895 (mtmt) cc_final: 0.5452 (mmmt) REVERT: S 478 MET cc_start: 0.5354 (ptp) cc_final: 0.4978 (ptp) REVERT: S 540 LYS cc_start: 0.6355 (tttm) cc_final: 0.6105 (tttt) REVERT: S 542 ARG cc_start: 0.4974 (mtp-110) cc_final: 0.4695 (ptm160) REVERT: S 628 TYR cc_start: 0.5658 (t80) cc_final: 0.5271 (t80) REVERT: S 674 GLU cc_start: 0.6165 (tp30) cc_final: 0.4906 (mt-10) REVERT: S 698 LYS cc_start: 0.4639 (pttm) cc_final: 0.4176 (tmmt) REVERT: S 742 TRP cc_start: 0.3376 (m100) cc_final: 0.2981 (m-10) REVERT: R 156 LYS cc_start: 0.4803 (pttm) cc_final: 0.4383 (pptt) REVERT: R 256 GLU cc_start: 0.6849 (mp0) cc_final: 0.6526 (mp0) REVERT: R 260 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6277 (m-40) REVERT: R 312 TYR cc_start: 0.8490 (t80) cc_final: 0.8018 (t80) REVERT: R 441 ARG cc_start: 0.5492 (mtt180) cc_final: 0.4765 (tpp-160) outliers start: 241 outliers final: 116 residues processed: 891 average time/residue: 1.6193 time to fit residues: 1821.3634 Evaluate side-chains 814 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 673 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 582 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1219 ILE Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1115 GLN Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain O residue 204 THR Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 402 THR Chi-restraints excluded: chain O residue 405 ASP Chi-restraints excluded: chain O residue 490 ILE Chi-restraints excluded: chain O residue 531 ILE Chi-restraints excluded: chain O residue 540 CYS Chi-restraints excluded: chain O residue 546 ASN Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 224 THR Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 355 GLU Chi-restraints excluded: chain S residue 397 LYS Chi-restraints excluded: chain S residue 417 THR Chi-restraints excluded: chain S residue 431 ASP Chi-restraints excluded: chain S residue 462 ILE Chi-restraints excluded: chain S residue 491 SER Chi-restraints excluded: chain S residue 589 ILE Chi-restraints excluded: chain S residue 639 GLU Chi-restraints excluded: chain S residue 691 VAL Chi-restraints excluded: chain S residue 694 ILE Chi-restraints excluded: chain S residue 732 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 23 TYR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 246 GLN Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 419 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 556 optimal weight: 0.9990 chunk 423 optimal weight: 0.8980 chunk 292 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 378 optimal weight: 0.9990 chunk 565 optimal weight: 10.0000 chunk 598 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 535 optimal weight: 0.0040 chunk 161 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 74 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 590 ASN A1026 GLN A1487 ASN A1648 ASN B 166 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN B1157 GLN E 146 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN Q 33 HIS ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 301 HIS Q 486 GLN S 278 HIS S 387 ASN S 395 GLN R 10 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 52754 Z= 0.180 Angle : 0.606 13.182 71675 Z= 0.320 Chirality : 0.044 0.298 7994 Planarity : 0.004 0.068 8874 Dihedral : 12.997 147.376 7733 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.05 % Allowed : 16.20 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.10), residues: 6079 helix: -0.58 (0.11), residues: 2161 sheet: -1.27 (0.18), residues: 766 loop : -1.63 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 143 HIS 0.007 0.001 HIS B 282 PHE 0.018 0.001 PHE B 16 TYR 0.024 0.001 TYR A1302 ARG 0.009 0.000 ARG Q 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 740 time to evaluate : 5.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 18 GLU cc_start: 0.7621 (mp0) cc_final: 0.6698 (tp30) REVERT: I 101 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5961 (mp) REVERT: N 56 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6185 (mt) REVERT: N 89 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5619 (pt) REVERT: M 96 LEU cc_start: 0.7371 (mt) cc_final: 0.7067 (mm) REVERT: M 108 LEU cc_start: 0.4271 (OUTLIER) cc_final: 0.3940 (pt) REVERT: A 43 HIS cc_start: 0.5476 (t-90) cc_final: 0.4682 (m-70) REVERT: A 59 ARG cc_start: 0.7076 (mtm110) cc_final: 0.6604 (mtt90) REVERT: A 94 LEU cc_start: 0.7354 (pp) cc_final: 0.7078 (tt) REVERT: A 182 LYS cc_start: 0.7002 (mttt) cc_final: 0.6622 (mttm) REVERT: A 316 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6169 (pt) REVERT: A 325 ASP cc_start: 0.6454 (t0) cc_final: 0.6168 (t0) REVERT: A 347 ARG cc_start: 0.6218 (ptp90) cc_final: 0.5839 (tpt170) REVERT: A 399 LEU cc_start: 0.4794 (OUTLIER) cc_final: 0.4409 (mp) REVERT: A 422 ARG cc_start: 0.6021 (mmp-170) cc_final: 0.4490 (ttt180) REVERT: A 553 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: A 589 MET cc_start: 0.8512 (mmm) cc_final: 0.8065 (mmm) REVERT: A 944 MET cc_start: 0.8986 (mtp) cc_final: 0.8774 (mtt) REVERT: A 1028 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: A 1163 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7085 (mp0) REVERT: A 1234 LYS cc_start: 0.8237 (mtmt) cc_final: 0.7448 (mmtt) REVERT: A 1455 ARG cc_start: 0.6710 (mtt-85) cc_final: 0.6215 (mtp180) REVERT: A 1491 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 1495 LYS cc_start: 0.8120 (mtpm) cc_final: 0.7416 (mptt) REVERT: A 1506 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7337 (mtp-110) REVERT: A 1601 GLN cc_start: 0.8177 (mp10) cc_final: 0.7942 (mp10) REVERT: A 1624 LYS cc_start: 0.7921 (mttp) cc_final: 0.7319 (mtpt) REVERT: A 1655 ASP cc_start: 0.8103 (m-30) cc_final: 0.7674 (m-30) REVERT: B 16 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.6452 (p90) REVERT: B 40 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: B 169 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8244 (mmp80) REVERT: B 257 GLN cc_start: 0.7311 (mt0) cc_final: 0.6939 (mm110) REVERT: B 328 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6745 (mp10) REVERT: B 352 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: B 372 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7923 (mtm180) REVERT: B 377 MET cc_start: 0.8757 (mtp) cc_final: 0.8278 (mtp) REVERT: B 451 MET cc_start: 0.7536 (ttp) cc_final: 0.7297 (ttt) REVERT: B 593 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7676 (pp) REVERT: B 620 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 720 GLN cc_start: 0.7524 (tt0) cc_final: 0.7269 (tp40) REVERT: B 810 ASP cc_start: 0.7728 (t0) cc_final: 0.7453 (t70) REVERT: B 858 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7617 (tp) REVERT: B 865 THR cc_start: 0.6836 (p) cc_final: 0.6496 (t) REVERT: B 957 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.6392 (mpt180) REVERT: B 1057 MET cc_start: 0.7598 (mmm) cc_final: 0.7286 (mmm) REVERT: B 1074 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6779 (mtm) REVERT: B 1114 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7259 (pp30) REVERT: B 1160 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6397 (mm-30) REVERT: C 51 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: C 124 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6015 (mm-30) REVERT: C 245 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7037 (tpp-160) REVERT: C 258 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6521 (pp) REVERT: C 281 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6972 (ptt90) REVERT: C 296 ASN cc_start: 0.7861 (m-40) cc_final: 0.7157 (p0) REVERT: D 1 MET cc_start: 0.1652 (ptm) cc_final: 0.0764 (tpp) REVERT: D 29 GLN cc_start: 0.7900 (tt0) cc_final: 0.7459 (mp10) REVERT: E 7 ARG cc_start: 0.7032 (ttp-110) cc_final: 0.6436 (mpt90) REVERT: E 9 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.6985 (mp) REVERT: E 41 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: E 65 THR cc_start: 0.7837 (p) cc_final: 0.7470 (t) REVERT: E 122 LYS cc_start: 0.7295 (mmmt) cc_final: 0.6555 (mtmm) REVERT: F 66 ARG cc_start: 0.7415 (mtp180) cc_final: 0.7121 (mtp180) REVERT: F 112 GLU cc_start: 0.6554 (mt-10) cc_final: 0.5888 (pp20) REVERT: F 127 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7648 (mt-10) REVERT: G 72 LYS cc_start: 0.8290 (mttt) cc_final: 0.7919 (mtmm) REVERT: G 128 GLN cc_start: 0.5761 (mt0) cc_final: 0.5361 (mp10) REVERT: G 134 GLU cc_start: 0.6697 (pm20) cc_final: 0.6175 (mm-30) REVERT: G 138 PHE cc_start: 0.5485 (OUTLIER) cc_final: 0.5077 (t80) REVERT: G 157 ILE cc_start: 0.7172 (mt) cc_final: 0.6753 (mm) REVERT: H 22 LYS cc_start: 0.8721 (mttm) cc_final: 0.8377 (mttt) REVERT: H 97 MET cc_start: 0.8121 (mtm) cc_final: 0.7753 (mtm) REVERT: J 19 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: J 28 ASP cc_start: 0.7870 (m-30) cc_final: 0.6978 (t0) REVERT: L 39 SER cc_start: 0.8509 (t) cc_final: 0.8250 (p) REVERT: L 56 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7822 (mt) REVERT: O 88 ILE cc_start: 0.4216 (tt) cc_final: 0.3870 (mm) REVERT: O 127 GLU cc_start: 0.4760 (mt-10) cc_final: 0.3735 (pp20) REVERT: O 173 HIS cc_start: 0.4122 (t70) cc_final: 0.3396 (m90) REVERT: O 245 GLN cc_start: 0.4041 (tt0) cc_final: 0.3267 (mm-40) REVERT: O 326 LYS cc_start: 0.4248 (mtpt) cc_final: 0.3887 (ptmm) REVERT: O 369 LYS cc_start: 0.7532 (ptpt) cc_final: 0.7284 (ptmt) REVERT: O 438 GLN cc_start: 0.6408 (mt0) cc_final: 0.6147 (mm110) REVERT: O 449 TRP cc_start: 0.7102 (t60) cc_final: 0.6859 (t60) REVERT: O 456 GLU cc_start: 0.5475 (mt-10) cc_final: 0.4801 (mm-30) REVERT: O 459 GLU cc_start: 0.6634 (pt0) cc_final: 0.6364 (pp20) REVERT: O 462 ASP cc_start: 0.6889 (m-30) cc_final: 0.6158 (t0) REVERT: O 464 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.4843 (tpp-160) REVERT: O 468 GLU cc_start: 0.6242 (pm20) cc_final: 0.5913 (mt-10) REVERT: O 485 CYS cc_start: 0.6685 (m) cc_final: 0.6326 (p) REVERT: O 490 ILE cc_start: 0.4666 (OUTLIER) cc_final: 0.4266 (mp) REVERT: O 501 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6580 (tp30) REVERT: O 507 GLN cc_start: 0.5833 (tp40) cc_final: 0.5431 (tt0) REVERT: O 511 ILE cc_start: 0.7694 (pt) cc_final: 0.7358 (tt) REVERT: O 540 CYS cc_start: 0.6095 (OUTLIER) cc_final: 0.4896 (m) REVERT: O 543 ILE cc_start: 0.5869 (mt) cc_final: 0.5584 (mp) REVERT: O 603 LYS cc_start: 0.6664 (ttmt) cc_final: 0.5798 (tptt) REVERT: O 604 ILE cc_start: 0.6398 (mm) cc_final: 0.6097 (mt) REVERT: Q 141 LEU cc_start: 0.6616 (tp) cc_final: 0.5704 (pp) REVERT: Q 142 LYS cc_start: 0.4666 (tmtm) cc_final: 0.3739 (mmmt) REVERT: Q 346 GLU cc_start: 0.5839 (tm-30) cc_final: 0.5397 (mp0) REVERT: Q 360 LYS cc_start: 0.4638 (ptpt) cc_final: 0.4223 (ptmm) REVERT: Q 376 GLU cc_start: 0.6620 (tp30) cc_final: 0.6119 (mm-30) REVERT: Q 421 ARG cc_start: 0.5212 (ttt90) cc_final: 0.4850 (mtt180) REVERT: Q 439 ILE cc_start: 0.4640 (pt) cc_final: 0.4348 (mp) REVERT: Q 448 LYS cc_start: 0.5559 (tttp) cc_final: 0.4461 (mttt) REVERT: Q 513 MET cc_start: 0.4269 (mpt) cc_final: 0.1576 (ptm) REVERT: S 187 ILE cc_start: 0.4683 (tt) cc_final: 0.3960 (mm) REVERT: S 188 GLN cc_start: 0.4856 (tt0) cc_final: 0.4537 (mt0) REVERT: S 202 ILE cc_start: 0.5684 (pt) cc_final: 0.5463 (mp) REVERT: S 283 ASP cc_start: 0.3481 (t0) cc_final: 0.3013 (p0) REVERT: S 293 TYR cc_start: 0.3006 (m-80) cc_final: 0.2510 (m-80) REVERT: S 324 TRP cc_start: 0.6439 (p-90) cc_final: 0.6064 (p-90) REVERT: S 364 GLU cc_start: 0.6057 (tp30) cc_final: 0.5462 (tp30) REVERT: S 365 TRP cc_start: 0.3888 (m-10) cc_final: 0.3553 (m100) REVERT: S 407 ARG cc_start: 0.5159 (tmt90) cc_final: 0.4327 (tmt170) REVERT: S 469 TYR cc_start: 0.7830 (p90) cc_final: 0.7361 (p90) REVERT: S 471 MET cc_start: 0.5823 (mtp) cc_final: 0.5512 (mtp) REVERT: S 474 LYS cc_start: 0.5945 (mtmt) cc_final: 0.5469 (mmmt) REVERT: S 478 MET cc_start: 0.5308 (ptp) cc_final: 0.5098 (ptp) REVERT: S 531 PHE cc_start: 0.2712 (p90) cc_final: 0.2180 (m-10) REVERT: S 540 LYS cc_start: 0.6192 (tttm) cc_final: 0.5958 (tttt) REVERT: S 542 ARG cc_start: 0.4972 (mtp-110) cc_final: 0.4661 (ptm160) REVERT: S 628 TYR cc_start: 0.5626 (t80) cc_final: 0.5291 (t80) REVERT: S 674 GLU cc_start: 0.6121 (tp30) cc_final: 0.4892 (mt-10) REVERT: S 742 TRP cc_start: 0.3405 (m100) cc_final: 0.2937 (m-10) REVERT: R 156 LYS cc_start: 0.4753 (pttm) cc_final: 0.4352 (pptt) REVERT: R 246 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5737 (mm110) REVERT: R 256 GLU cc_start: 0.6892 (mp0) cc_final: 0.6564 (mp0) REVERT: R 260 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6380 (m-40) REVERT: R 286 GLN cc_start: 0.7343 (tp40) cc_final: 0.7137 (tp40) REVERT: R 312 TYR cc_start: 0.8432 (t80) cc_final: 0.8055 (t80) REVERT: R 324 MET cc_start: 0.4415 (mtm) cc_final: 0.3863 (ttt) REVERT: R 441 ARG cc_start: 0.5372 (mtt180) cc_final: 0.4744 (tpp-160) outliers start: 225 outliers final: 90 residues processed: 890 average time/residue: 1.6147 time to fit residues: 1812.5820 Evaluate side-chains 792 residues out of total 5567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 671 time to evaluate : 5.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 1028 GLU Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1119 LYS Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1289 SER Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1506 ARG Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 328 GLN Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 859 CYS Chi-restraints excluded: chain B residue 887 LEU Chi-restraints excluded: chain B residue 957 ARG Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1102 SER Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 281 ARG Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 490 ILE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 531 ILE Chi-restraints excluded: chain O residue 540 CYS Chi-restraints excluded: chain O residue 546 ASN Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain S residue 295 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 355 GLU Chi-restraints excluded: chain S residue 417 THR Chi-restraints excluded: chain S residue 431 ASP Chi-restraints excluded: chain S residue 453 VAL Chi-restraints excluded: chain S residue 491 SER Chi-restraints excluded: chain S residue 589 ILE Chi-restraints excluded: chain S residue 691 VAL Chi-restraints excluded: chain S residue 732 LEU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 23 TYR Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 246 GLN Chi-restraints excluded: chain R residue 251 TRP Chi-restraints excluded: chain R residue 253 ILE Chi-restraints excluded: chain R residue 260 ASN Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 374 LEU Chi-restraints excluded: chain R residue 419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9772 > 50: distance: 25 - 30: 19.393 distance: 30 - 31: 15.264 distance: 31 - 32: 13.687 distance: 32 - 33: 38.888 distance: 32 - 37: 5.736 distance: 34 - 35: 5.656 distance: 34 - 36: 30.810 distance: 37 - 38: 8.239 distance: 38 - 39: 25.531 distance: 38 - 41: 7.104 distance: 39 - 40: 19.456 distance: 39 - 44: 22.954 distance: 41 - 42: 23.767 distance: 41 - 43: 29.462 distance: 44 - 45: 8.337 distance: 45 - 46: 4.031 distance: 45 - 48: 17.883 distance: 46 - 47: 13.330 distance: 46 - 52: 7.120 distance: 48 - 49: 39.643 distance: 48 - 50: 41.397 distance: 49 - 51: 31.106 distance: 52 - 53: 5.388 distance: 52 - 181: 28.475 distance: 53 - 54: 4.397 distance: 54 - 55: 3.629 distance: 54 - 62: 15.688 distance: 55 - 178: 26.594 distance: 56 - 57: 10.639 distance: 57 - 58: 22.844 distance: 57 - 59: 33.038 distance: 58 - 60: 37.085 distance: 59 - 61: 33.483 distance: 60 - 61: 25.112 distance: 63 - 64: 3.724 distance: 63 - 66: 29.737 distance: 64 - 65: 32.527 distance: 67 - 68: 31.819 distance: 68 - 69: 18.053 distance: 68 - 71: 31.256 distance: 69 - 70: 4.026 distance: 69 - 74: 30.299 distance: 71 - 72: 46.701 distance: 71 - 73: 3.793 distance: 74 - 75: 10.854 distance: 75 - 76: 32.423 distance: 75 - 78: 14.535 distance: 76 - 77: 23.856 distance: 76 - 83: 23.049 distance: 78 - 79: 8.349 distance: 79 - 80: 4.440 distance: 80 - 81: 14.846 distance: 80 - 82: 25.623 distance: 83 - 84: 10.258 distance: 84 - 85: 16.341 distance: 84 - 87: 17.650 distance: 85 - 86: 11.982 distance: 85 - 91: 29.207 distance: 87 - 88: 10.160 distance: 88 - 89: 30.624 distance: 88 - 90: 10.928 distance: 91 - 92: 21.592 distance: 91 - 97: 55.942 distance: 93 - 98: 39.955 distance: 95 - 96: 44.086 distance: 96 - 97: 46.492 distance: 98 - 99: 24.107 distance: 98 - 157: 32.919 distance: 99 - 100: 11.223 distance: 99 - 102: 15.386 distance: 100 - 101: 25.154 distance: 100 - 107: 26.299 distance: 101 - 154: 27.203 distance: 102 - 103: 7.678 distance: 103 - 104: 9.148 distance: 104 - 105: 24.834 distance: 104 - 106: 32.977