Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 20:46:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vms_32037/04_2023/7vms_32037.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.007 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 Ca 4 9.91 5 Zn 4 6.06 5 S 720 5.16 5 C 78192 2.51 5 N 21544 2.21 5 O 23088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4079": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 123552 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "H" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "I" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 30067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4044, 30067 Classifications: {'peptide': 4044} Incomplete info: {'truncation_to_alanine': 775} Link IDs: {'CIS': 1, 'PTRANS': 116, 'TRANS': 3926} Chain breaks: 27 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1608 Unresolved non-hydrogen angles: 2379 Unresolved non-hydrogen dihedrals: 840 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'UNK:plan-1': 749, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 805 Chain: "J" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29421 SG CYS A4887 179.923 204.687 121.549 1.00 91.36 S ATOM 29446 SG CYS A4890 179.275 202.475 118.535 1.00 74.70 S ATOM 60307 SG CYS B4887 167.179 179.919 121.537 1.00 91.36 S ATOM 60332 SG CYS B4890 169.389 179.272 118.521 1.00 74.70 S ATOM 91193 SG CYS C4887 191.919 167.184 121.539 1.00 91.36 S ATOM 91218 SG CYS C4890 192.566 169.394 118.523 1.00 74.70 S ATOM A0H1B SG CYS D4887 204.655 191.918 121.539 1.00 91.36 S ATOM A0H20 SG CYS D4890 202.446 192.566 118.523 1.00 74.70 S Time building chain proxies: 45.29, per 1000 atoms: 0.37 Number of scatterers: 123552 At special positions: 0 Unit cell: (373.168, 373.168, 208.496, 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 4 29.99 Ca 4 19.99 S 720 16.00 O 23088 8.00 N 21544 7.00 C 78192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.46 Conformation dependent library (CDL) restraints added in 12.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4890 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4887 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4890 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4887 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4887 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4890 " pdb=" ZN D6002 " pdb="ZN ZN D6002 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D6002 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D6002 " - pdb=" SG CYS D4887 " pdb="ZN ZN D6002 " - pdb=" SG CYS D4890 " Number of angles added : 8 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31448 Finding SS restraints... Secondary structure from input PDB file: 648 helices and 104 sheets defined 68.1% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.04 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.212A pdb=" N VAL A 267 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG A 272 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 273 " --> pdb=" O HIS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 3.979A pdb=" N LYS A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.747A pdb=" N ARG A 383 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 removed outlier: 3.889A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.616A pdb=" N GLY A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 510 through 519 removed outlier: 3.645A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 517 " --> pdb=" O HIS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.955A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.546A pdb=" N ALA A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.677A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 582 through 589 removed outlier: 3.577A pdb=" N ALA A 585 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 607 through 619 removed outlier: 4.054A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 878 through 901 removed outlier: 3.976A pdb=" N LYS A 897 " --> pdb=" O TRP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 removed outlier: 4.131A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 931 " --> pdb=" O GLN A 927 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN A 932 " --> pdb=" O GLU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1012 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.141A pdb=" N VAL A1033 " --> pdb=" O PRO A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 removed outlier: 3.735A pdb=" N ASN A1046 " --> pdb=" O THR A1042 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA A1053 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 Processing helix chain 'A' and resid 1643 through 1647 Processing helix chain 'A' and resid 1648 through 1665 Processing helix chain 'A' and resid 1671 through 1682 removed outlier: 3.707A pdb=" N ALA A1676 " --> pdb=" O ARG A1672 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A1679 " --> pdb=" O HIS A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1692 Processing helix chain 'A' and resid 1697 through 1711 removed outlier: 3.677A pdb=" N HIS A1711 " --> pdb=" O LEU A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 4.569A pdb=" N TYR A1715 " --> pdb=" O HIS A1711 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A1722 " --> pdb=" O ALA A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.879A pdb=" N LEU A1788 " --> pdb=" O PRO A1784 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A1805 " --> pdb=" O LYS A1801 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A1806 " --> pdb=" O GLU A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1832 removed outlier: 3.633A pdb=" N LEU A1818 " --> pdb=" O THR A1814 " (cutoff:3.500A) Proline residue: A1821 - end of helix Processing helix chain 'A' and resid 1836 through 1848 removed outlier: 3.903A pdb=" N ILE A1847 " --> pdb=" O ILE A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1949 removed outlier: 3.594A pdb=" N GLN A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1907 " --> pdb=" O LEU A1903 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A1916 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A1930 " --> pdb=" O ALA A1926 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A1937 " --> pdb=" O ALA A1933 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A1938 " --> pdb=" O LYS A1934 " (cutoff:3.500A) Processing helix chain 'A' and resid 1955 through 1965 removed outlier: 4.573A pdb=" N ARG A1962 " --> pdb=" O ALA A1958 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLU A1963 " --> pdb=" O ARG A1959 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A1964 " --> pdb=" O LYS A1960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1967 through 1976 Processing helix chain 'A' and resid 1989 through 2006 removed outlier: 3.881A pdb=" N ASP A1993 " --> pdb=" O GLU A1989 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A1994 " --> pdb=" O GLU A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2072 removed outlier: 3.650A pdb=" N ALA A2069 " --> pdb=" O MET A2065 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A2072 " --> pdb=" O TRP A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2093 removed outlier: 3.674A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2101 removed outlier: 4.059A pdb=" N LEU A2097 " --> pdb=" O GLY A2093 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2130 Processing helix chain 'A' and resid 2134 through 2151 Processing helix chain 'A' and resid 2152 through 2157 removed outlier: 3.733A pdb=" N GLN A2156 " --> pdb=" O LYS A2152 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2165 removed outlier: 3.994A pdb=" N MET A2161 " --> pdb=" O HIS A2157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A2162 " --> pdb=" O PRO A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2179 Processing helix chain 'A' and resid 2188 through 2205 Processing helix chain 'A' and resid 2207 through 2221 removed outlier: 4.088A pdb=" N LYS A2211 " --> pdb=" O ARG A2207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS A2216 " --> pdb=" O ALA A2212 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER A2218 " --> pdb=" O PHE A2214 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A2219 " --> pdb=" O ASP A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2237 through 2246 Processing helix chain 'A' and resid 2249 through 2256 Processing helix chain 'A' and resid 2260 through 2274 Processing helix chain 'A' and resid 2276 through 2283 Processing helix chain 'A' and resid 2292 through 2305 Processing helix chain 'A' and resid 2312 through 2326 Processing helix chain 'A' and resid 2327 through 2330 Processing helix chain 'A' and resid 2341 through 2355 Processing helix chain 'A' and resid 2356 through 2359 removed outlier: 3.589A pdb=" N ASP A2359 " --> pdb=" O PRO A2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2356 through 2359' Processing helix chain 'A' and resid 2382 through 2402 Processing helix chain 'A' and resid 2413 through 2426 Processing helix chain 'A' and resid 2427 through 2436 Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.842A pdb=" N ALA A2465 " --> pdb=" O PRO A2461 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A2466 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A2467 " --> pdb=" O HIS A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2491 Processing helix chain 'A' and resid 2491 through 2500 Processing helix chain 'A' and resid 2508 through 2523 Processing helix chain 'A' and resid 2533 through 2547 Processing helix chain 'A' and resid 2553 through 2571 Processing helix chain 'A' and resid 2575 through 2589 Processing helix chain 'A' and resid 2594 through 2612 Processing helix chain 'A' and resid 2617 through 2635 removed outlier: 3.582A pdb=" N UNK A2621 " --> pdb=" O UNK A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2642 through 2650 Processing helix chain 'A' and resid 2652 through 2657 removed outlier: 3.692A pdb=" N UNK A2656 " --> pdb=" O UNK A2652 " (cutoff:3.500A) Processing helix chain 'A' and resid 2713 through 2739 removed outlier: 4.159A pdb=" N ASN A2721 " --> pdb=" O GLU A2717 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS A2722 " --> pdb=" O TYR A2718 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2769 removed outlier: 3.810A pdb=" N GLU A2768 " --> pdb=" O GLU A2764 " (cutoff:3.500A) Processing helix chain 'A' and resid 2772 through 2784 removed outlier: 4.316A pdb=" N GLU A2776 " --> pdb=" O TRP A2772 " (cutoff:3.500A) Processing helix chain 'A' and resid 2836 through 2863 removed outlier: 3.529A pdb=" N TRP A2851 " --> pdb=" O TYR A2847 " (cutoff:3.500A) Processing helix chain 'A' and resid 2877 through 2898 removed outlier: 3.916A pdb=" N ASP A2884 " --> pdb=" O GLU A2880 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A2887 " --> pdb=" O LYS A2883 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A2894 " --> pdb=" O ASP A2890 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A2895 " --> pdb=" O ILE A2891 " (cutoff:3.500A) Processing helix chain 'A' and resid 2917 through 2942 removed outlier: 3.748A pdb=" N UNK A2942 " --> pdb=" O UNK A2938 " (cutoff:3.500A) Processing helix chain 'A' and resid 2962 through 2982 removed outlier: 3.984A pdb=" N UNK A2975 " --> pdb=" O UNK A2971 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N UNK A2976 " --> pdb=" O UNK A2972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2992 through 3007 Processing helix chain 'A' and resid 3015 through 3029 Processing helix chain 'A' and resid 3105 through 3129 removed outlier: 3.789A pdb=" N UNK A3120 " --> pdb=" O UNK A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3137 through 3157 removed outlier: 4.227A pdb=" N UNK A3156 " --> pdb=" O UNK A3152 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK A3157 " --> pdb=" O UNK A3153 " (cutoff:3.500A) Processing helix chain 'A' and resid 3163 through 3182 Processing helix chain 'A' and resid 3183 through 3200 Processing helix chain 'A' and resid 3208 through 3220 removed outlier: 3.600A pdb=" N UNK A3219 " --> pdb=" O UNK A3215 " (cutoff:3.500A) Processing helix chain 'A' and resid 3232 through 3251 Processing helix chain 'A' and resid 3255 through 3269 Processing helix chain 'A' and resid 3271 through 3277 Processing helix chain 'A' and resid 3281 through 3296 removed outlier: 4.112A pdb=" N UNK A3285 " --> pdb=" O UNK A3281 " (cutoff:3.500A) Processing helix chain 'A' and resid 3301 through 3315 Processing helix chain 'A' and resid 3324 through 3355 Processing helix chain 'A' and resid 3362 through 3392 removed outlier: 4.211A pdb=" N UNK A3383 " --> pdb=" O UNK A3379 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N UNK A3389 " --> pdb=" O UNK A3385 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK A3390 " --> pdb=" O UNK A3386 " (cutoff:3.500A) Processing helix chain 'A' and resid 3400 through 3420 removed outlier: 4.114A pdb=" N UNK A3404 " --> pdb=" O UNK A3400 " (cutoff:3.500A) Processing helix chain 'A' and resid 3422 through 3434 removed outlier: 4.894A pdb=" N UNK A3428 " --> pdb=" O UNK A3424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N UNK A3429 " --> pdb=" O UNK A3425 " (cutoff:3.500A) Processing helix chain 'A' and resid 3478 through 3496 removed outlier: 4.011A pdb=" N UNK A3495 " --> pdb=" O UNK A3491 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N UNK A3496 " --> pdb=" O UNK A3492 " (cutoff:3.500A) Processing helix chain 'A' and resid 3503 through 3514 Processing helix chain 'A' and resid 3516 through 3527 removed outlier: 4.056A pdb=" N UNK A3527 " --> pdb=" O UNK A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3540 through 3548 removed outlier: 4.235A pdb=" N UNK A3544 " --> pdb=" O UNK A3540 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N UNK A3545 " --> pdb=" O UNK A3541 " (cutoff:3.500A) Processing helix chain 'A' and resid 3555 through 3579 Processing helix chain 'A' and resid 3612 through 3627 removed outlier: 4.010A pdb=" N VAL A3616 " --> pdb=" O ARG A3612 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3643 Processing helix chain 'A' and resid 3661 through 3676 Processing helix chain 'A' and resid 3684 through 3697 removed outlier: 4.233A pdb=" N ASP A3692 " --> pdb=" O MET A3688 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A3693 " --> pdb=" O ALA A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3732 removed outlier: 4.254A pdb=" N GLU A3719 " --> pdb=" O GLU A3715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A3720 " --> pdb=" O LYS A3716 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A3730 " --> pdb=" O GLN A3726 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A3732 " --> pdb=" O ALA A3728 " (cutoff:3.500A) Processing helix chain 'A' and resid 3734 through 3745 removed outlier: 3.672A pdb=" N LEU A3740 " --> pdb=" O ALA A3736 " (cutoff:3.500A) Processing helix chain 'A' and resid 3753 through 3765 removed outlier: 3.939A pdb=" N LYS A3759 " --> pdb=" O ALA A3755 " (cutoff:3.500A) Processing helix chain 'A' and resid 3769 through 3783 Processing helix chain 'A' and resid 3788 through 3797 Processing helix chain 'A' and resid 3803 through 3817 Processing helix chain 'A' and resid 3824 through 3828 Processing helix chain 'A' and resid 3831 through 3845 Processing helix chain 'A' and resid 3850 through 3857 Processing helix chain 'A' and resid 3868 through 3891 removed outlier: 3.648A pdb=" N SER A3872 " --> pdb=" O ASN A3868 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3923 removed outlier: 3.880A pdb=" N PHE A3905 " --> pdb=" O GLY A3901 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A3908 " --> pdb=" O ASN A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 Processing helix chain 'A' and resid 3938 through 3957 removed outlier: 3.784A pdb=" N ALA A3942 " --> pdb=" O ARG A3938 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A3952 " --> pdb=" O HIS A3948 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET A3955 " --> pdb=" O ALA A3951 " (cutoff:3.500A) Processing helix chain 'A' and resid 3963 through 3983 Processing helix chain 'A' and resid 3984 through 3986 No H-bonds generated for 'chain 'A' and resid 3984 through 3986' Processing helix chain 'A' and resid 3992 through 4005 removed outlier: 3.648A pdb=" N LYS A3996 " --> pdb=" O GLY A3992 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4021 Processing helix chain 'A' and resid 4022 through 4027 removed outlier: 4.071A pdb=" N SER A4027 " --> pdb=" O LYS A4023 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4034 Processing helix chain 'A' and resid 4045 through 4054 removed outlier: 3.931A pdb=" N HIS A4054 " --> pdb=" O ALA A4050 " (cutoff:3.500A) Processing helix chain 'A' and resid 4058 through 4068 Processing helix chain 'A' and resid 4078 through 4087 Processing helix chain 'A' and resid 4087 through 4108 removed outlier: 3.514A pdb=" N ASP A4092 " --> pdb=" O GLU A4088 " (cutoff:3.500A) Processing helix chain 'A' and resid 4111 through 4126 removed outlier: 4.050A pdb=" N PHE A4117 " --> pdb=" O ARG A4113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A4120 " --> pdb=" O THR A4116 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER A4123 " --> pdb=" O GLU A4119 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL A4124 " --> pdb=" O LEU A4120 " (cutoff:3.500A) Processing helix chain 'A' and resid 4128 through 4132 removed outlier: 3.793A pdb=" N LEU A4132 " --> pdb=" O GLN A4129 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4158 Processing helix chain 'A' and resid 4161 through 4177 Processing helix chain 'A' and resid 4183 through 4204 Processing helix chain 'A' and resid 4276 through 4284 removed outlier: 3.984A pdb=" N LEU A4280 " --> pdb=" O LYS A4276 " (cutoff:3.500A) Processing helix chain 'A' and resid 4286 through 4302 removed outlier: 3.752A pdb=" N THR A4292 " --> pdb=" O SER A4288 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A4300 " --> pdb=" O PHE A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4304 through 4309 removed outlier: 3.573A pdb=" N SER A4309 " --> pdb=" O PHE A4305 " (cutoff:3.500A) Processing helix chain 'A' and resid 4479 through 4496 removed outlier: 3.672A pdb=" N TYR A4485 " --> pdb=" O LYS A4481 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A4488 " --> pdb=" O ALA A4484 " (cutoff:3.500A) Processing helix chain 'A' and resid 4496 through 4515 Processing helix chain 'A' and resid 4567 through 4593 removed outlier: 3.624A pdb=" N LEU A4571 " --> pdb=" O MET A4567 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A4572 " --> pdb=" O GLU A4568 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A4590 " --> pdb=" O ILE A4586 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS A4591 " --> pdb=" O ILE A4587 " (cutoff:3.500A) Processing helix chain 'A' and resid 4593 through 4613 Processing helix chain 'A' and resid 4613 through 4618 Processing helix chain 'A' and resid 4625 through 4630 Processing helix chain 'A' and resid 4648 through 4657 Processing helix chain 'A' and resid 4661 through 4667 removed outlier: 3.813A pdb=" N SER A4666 " --> pdb=" O ARG A4662 " (cutoff:3.500A) Processing helix chain 'A' and resid 4671 through 4682 Processing helix chain 'A' and resid 4701 through 4713 Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 3.727A pdb=" N LEU A4721 " --> pdb=" O SER A4717 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4742 removed outlier: 3.552A pdb=" N HIS A4741 " --> pdb=" O PHE A4738 " (cutoff:3.500A) Processing helix chain 'A' and resid 4743 through 4748 Processing helix chain 'A' and resid 4752 through 4757 Processing helix chain 'A' and resid 4763 through 4788 removed outlier: 3.546A pdb=" N ALA A4774 " --> pdb=" O VAL A4770 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A4775 " --> pdb=" O GLY A4771 " (cutoff:3.500A) Processing helix chain 'A' and resid 4807 through 4819 Processing helix chain 'A' and resid 4840 through 4854 Processing helix chain 'A' and resid 4857 through 4886 removed outlier: 3.979A pdb=" N ILE A4861 " --> pdb=" O LEU A4857 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A4868 " --> pdb=" O LEU A4864 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A4869 " --> pdb=" O ILE A4865 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A4870 " --> pdb=" O ILE A4866 " (cutoff:3.500A) Processing helix chain 'A' and resid 4893 through 4898 removed outlier: 3.929A pdb=" N PHE A4897 " --> pdb=" O GLY A4893 " (cutoff:3.500A) Processing helix chain 'A' and resid 4902 through 4911 removed outlier: 4.132A pdb=" N THR A4906 " --> pdb=" O HIS A4902 " (cutoff:3.500A) Processing helix chain 'A' and resid 4913 through 4928 removed outlier: 4.646A pdb=" N ASP A4928 " --> pdb=" O LEU A4924 " (cutoff:3.500A) Processing helix chain 'A' and resid 4933 through 4946 Processing helix chain 'A' and resid 4956 through 4961 removed outlier: 3.578A pdb=" N TYR A4961 " --> pdb=" O PHE A4957 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 removed outlier: 4.048A pdb=" N GLY G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 264 through 273 removed outlier: 4.212A pdb=" N VAL B 267 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 271 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG B 272 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 273 " --> pdb=" O HIS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.979A pdb=" N LYS B 321 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.748A pdb=" N ARG B 383 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 438 removed outlier: 3.889A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 463 removed outlier: 3.616A pdb=" N GLY B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.645A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 517 " --> pdb=" O HIS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.955A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.546A pdb=" N ALA B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 562 removed outlier: 3.678A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 582 through 589 removed outlier: 3.577A pdb=" N ALA B 585 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 607 through 619 removed outlier: 4.054A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 612 " --> pdb=" O HIS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 822 through 826 Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 878 through 901 removed outlier: 3.975A pdb=" N LYS B 897 " --> pdb=" O TRP B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 removed outlier: 4.132A pdb=" N ASN B 930 " --> pdb=" O GLU B 926 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR B 931 " --> pdb=" O GLN B 927 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN B 932 " --> pdb=" O GLU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1012 Processing helix chain 'B' and resid 1029 through 1033 removed outlier: 4.142A pdb=" N VAL B1033 " --> pdb=" O PRO B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1060 removed outlier: 3.735A pdb=" N ASN B1046 " --> pdb=" O THR B1042 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B1052 " --> pdb=" O ASP B1048 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA B1053 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B1054 " --> pdb=" O LEU B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 Processing helix chain 'B' and resid 1643 through 1647 Processing helix chain 'B' and resid 1648 through 1665 Processing helix chain 'B' and resid 1671 through 1682 removed outlier: 3.707A pdb=" N ALA B1676 " --> pdb=" O ARG B1672 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B1679 " --> pdb=" O HIS B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1684 through 1692 Processing helix chain 'B' and resid 1697 through 1711 removed outlier: 3.676A pdb=" N HIS B1711 " --> pdb=" O LEU B1707 " (cutoff:3.500A) Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 4.569A pdb=" N TYR B1715 " --> pdb=" O HIS B1711 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B1722 " --> pdb=" O ALA B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.879A pdb=" N LEU B1788 " --> pdb=" O PRO B1784 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU B1805 " --> pdb=" O LYS B1801 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B1806 " --> pdb=" O GLU B1802 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1832 removed outlier: 3.633A pdb=" N LEU B1818 " --> pdb=" O THR B1814 " (cutoff:3.500A) Proline residue: B1821 - end of helix Processing helix chain 'B' and resid 1836 through 1848 removed outlier: 3.903A pdb=" N ILE B1847 " --> pdb=" O ILE B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1898 through 1949 removed outlier: 3.595A pdb=" N GLN B1904 " --> pdb=" O PRO B1900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B1916 " --> pdb=" O LEU B1912 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B1930 " --> pdb=" O ALA B1926 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP B1937 " --> pdb=" O ALA B1933 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B1938 " --> pdb=" O LYS B1934 " (cutoff:3.500A) Processing helix chain 'B' and resid 1955 through 1965 removed outlier: 4.572A pdb=" N ARG B1962 " --> pdb=" O ALA B1958 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLU B1963 " --> pdb=" O ARG B1959 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B1964 " --> pdb=" O LYS B1960 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1976 Processing helix chain 'B' and resid 1989 through 2006 removed outlier: 3.880A pdb=" N ASP B1993 " --> pdb=" O GLU B1989 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B1994 " --> pdb=" O GLU B1990 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2072 removed outlier: 3.650A pdb=" N ALA B2069 " --> pdb=" O MET B2065 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B2072 " --> pdb=" O TRP B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2093 removed outlier: 3.673A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2101 removed outlier: 4.060A pdb=" N LEU B2097 " --> pdb=" O GLY B2093 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2130 Processing helix chain 'B' and resid 2134 through 2151 Processing helix chain 'B' and resid 2152 through 2157 removed outlier: 3.732A pdb=" N GLN B2156 " --> pdb=" O LYS B2152 " (cutoff:3.500A) Processing helix chain 'B' and resid 2157 through 2165 removed outlier: 3.995A pdb=" N MET B2161 " --> pdb=" O HIS B2157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B2162 " --> pdb=" O PRO B2158 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2179 Processing helix chain 'B' and resid 2188 through 2205 Processing helix chain 'B' and resid 2207 through 2221 removed outlier: 4.088A pdb=" N LYS B2211 " --> pdb=" O ARG B2207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B2216 " --> pdb=" O ALA B2212 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B2218 " --> pdb=" O PHE B2214 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR B2219 " --> pdb=" O ASP B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2237 through 2246 Processing helix chain 'B' and resid 2249 through 2256 Processing helix chain 'B' and resid 2260 through 2274 Processing helix chain 'B' and resid 2276 through 2283 Processing helix chain 'B' and resid 2292 through 2305 Processing helix chain 'B' and resid 2312 through 2326 Processing helix chain 'B' and resid 2327 through 2330 Processing helix chain 'B' and resid 2341 through 2355 Processing helix chain 'B' and resid 2356 through 2359 removed outlier: 3.589A pdb=" N ASP B2359 " --> pdb=" O PRO B2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2356 through 2359' Processing helix chain 'B' and resid 2382 through 2402 Processing helix chain 'B' and resid 2413 through 2426 Processing helix chain 'B' and resid 2427 through 2436 Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.842A pdb=" N ALA B2465 " --> pdb=" O PRO B2461 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B2466 " --> pdb=" O ASP B2462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET B2467 " --> pdb=" O HIS B2463 " (cutoff:3.500A) Processing helix chain 'B' and resid 2479 through 2491 Processing helix chain 'B' and resid 2491 through 2500 Processing helix chain 'B' and resid 2508 through 2523 Processing helix chain 'B' and resid 2533 through 2547 Processing helix chain 'B' and resid 2553 through 2571 Processing helix chain 'B' and resid 2575 through 2589 Processing helix chain 'B' and resid 2594 through 2612 Processing helix chain 'B' and resid 2617 through 2635 removed outlier: 3.583A pdb=" N UNK B2621 " --> pdb=" O UNK B2617 " (cutoff:3.500A) Processing helix chain 'B' and resid 2642 through 2650 Processing helix chain 'B' and resid 2652 through 2657 removed outlier: 3.692A pdb=" N UNK B2656 " --> pdb=" O UNK B2652 " (cutoff:3.500A) Processing helix chain 'B' and resid 2713 through 2739 removed outlier: 4.159A pdb=" N ASN B2721 " --> pdb=" O GLU B2717 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS B2722 " --> pdb=" O TYR B2718 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2769 removed outlier: 3.810A pdb=" N GLU B2768 " --> pdb=" O GLU B2764 " (cutoff:3.500A) Processing helix chain 'B' and resid 2772 through 2784 removed outlier: 4.316A pdb=" N GLU B2776 " --> pdb=" O TRP B2772 " (cutoff:3.500A) Processing helix chain 'B' and resid 2836 through 2863 removed outlier: 3.528A pdb=" N TRP B2851 " --> pdb=" O TYR B2847 " (cutoff:3.500A) Processing helix chain 'B' and resid 2877 through 2898 removed outlier: 3.916A pdb=" N ASP B2884 " --> pdb=" O GLU B2880 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B2887 " --> pdb=" O LYS B2883 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B2894 " --> pdb=" O ASP B2890 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B2895 " --> pdb=" O ILE B2891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2917 through 2942 removed outlier: 3.748A pdb=" N UNK B2942 " --> pdb=" O UNK B2938 " (cutoff:3.500A) Processing helix chain 'B' and resid 2962 through 2982 removed outlier: 3.983A pdb=" N UNK B2975 " --> pdb=" O UNK B2971 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N UNK B2976 " --> pdb=" O UNK B2972 " (cutoff:3.500A) Processing helix chain 'B' and resid 2992 through 3007 Processing helix chain 'B' and resid 3015 through 3029 Processing helix chain 'B' and resid 3105 through 3129 removed outlier: 3.790A pdb=" N UNK B3120 " --> pdb=" O UNK B3116 " (cutoff:3.500A) Processing helix chain 'B' and resid 3137 through 3157 removed outlier: 4.228A pdb=" N UNK B3156 " --> pdb=" O UNK B3152 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N UNK B3157 " --> pdb=" O UNK B3153 " (cutoff:3.500A) Processing helix chain 'B' and resid 3163 through 3182 Processing helix chain 'B' and resid 3183 through 3200 Processing helix chain 'B' and resid 3208 through 3220 removed outlier: 3.601A pdb=" N UNK B3219 " --> pdb=" O UNK B3215 " (cutoff:3.500A) Processing helix chain 'B' and resid 3232 through 3251 Processing helix chain 'B' and resid 3255 through 3269 Processing helix chain 'B' and resid 3271 through 3277 Processing helix chain 'B' and resid 3281 through 3296 removed outlier: 4.111A pdb=" N UNK B3285 " --> pdb=" O UNK B3281 " (cutoff:3.500A) Processing helix chain 'B' and resid 3301 through 3315 Processing helix chain 'B' and resid 3324 through 3355 Processing helix chain 'B' and resid 3362 through 3392 removed outlier: 4.210A pdb=" N UNK B3383 " --> pdb=" O UNK B3379 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N UNK B3389 " --> pdb=" O UNK B3385 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK B3390 " --> pdb=" O UNK B3386 " (cutoff:3.500A) Processing helix chain 'B' and resid 3400 through 3420 removed outlier: 4.113A pdb=" N UNK B3404 " --> pdb=" O UNK B3400 " (cutoff:3.500A) Processing helix chain 'B' and resid 3422 through 3434 removed outlier: 4.894A pdb=" N UNK B3428 " --> pdb=" O UNK B3424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N UNK B3429 " --> pdb=" O UNK B3425 " (cutoff:3.500A) Processing helix chain 'B' and resid 3478 through 3496 removed outlier: 4.011A pdb=" N UNK B3495 " --> pdb=" O UNK B3491 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N UNK B3496 " --> pdb=" O UNK B3492 " (cutoff:3.500A) Processing helix chain 'B' and resid 3503 through 3514 Processing helix chain 'B' and resid 3516 through 3527 removed outlier: 4.056A pdb=" N UNK B3527 " --> pdb=" O UNK B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3540 through 3548 removed outlier: 4.236A pdb=" N UNK B3544 " --> pdb=" O UNK B3540 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N UNK B3545 " --> pdb=" O UNK B3541 " (cutoff:3.500A) Processing helix chain 'B' and resid 3555 through 3579 Processing helix chain 'B' and resid 3612 through 3627 removed outlier: 4.010A pdb=" N VAL B3616 " --> pdb=" O ARG B3612 " (cutoff:3.500A) Processing helix chain 'B' and resid 3637 through 3643 Processing helix chain 'B' and resid 3661 through 3676 Processing helix chain 'B' and resid 3684 through 3697 removed outlier: 4.232A pdb=" N ASP B3692 " --> pdb=" O MET B3688 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B3693 " --> pdb=" O ALA B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3732 removed outlier: 4.253A pdb=" N GLU B3719 " --> pdb=" O GLU B3715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B3720 " --> pdb=" O LYS B3716 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B3730 " --> pdb=" O GLN B3726 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B3732 " --> pdb=" O ALA B3728 " (cutoff:3.500A) Processing helix chain 'B' and resid 3734 through 3745 removed outlier: 3.672A pdb=" N LEU B3740 " --> pdb=" O ALA B3736 " (cutoff:3.500A) Processing helix chain 'B' and resid 3753 through 3765 removed outlier: 3.939A pdb=" N LYS B3759 " --> pdb=" O ALA B3755 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3783 Processing helix chain 'B' and resid 3788 through 3797 Processing helix chain 'B' and resid 3803 through 3817 Processing helix chain 'B' and resid 3824 through 3828 Processing helix chain 'B' and resid 3831 through 3845 Processing helix chain 'B' and resid 3850 through 3857 Processing helix chain 'B' and resid 3868 through 3891 removed outlier: 3.648A pdb=" N SER B3872 " --> pdb=" O ASN B3868 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3923 removed outlier: 3.880A pdb=" N PHE B3905 " --> pdb=" O GLY B3901 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B3908 " --> pdb=" O ASN B3904 " (cutoff:3.500A) Processing helix chain 'B' and resid 3927 through 3936 Processing helix chain 'B' and resid 3938 through 3957 removed outlier: 3.784A pdb=" N ALA B3942 " --> pdb=" O ARG B3938 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B3952 " --> pdb=" O HIS B3948 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET B3955 " --> pdb=" O ALA B3951 " (cutoff:3.500A) Processing helix chain 'B' and resid 3963 through 3983 Processing helix chain 'B' and resid 3984 through 3986 No H-bonds generated for 'chain 'B' and resid 3984 through 3986' Processing helix chain 'B' and resid 3992 through 4005 removed outlier: 3.649A pdb=" N LYS B3996 " --> pdb=" O GLY B3992 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4021 Processing helix chain 'B' and resid 4022 through 4027 removed outlier: 4.072A pdb=" N SER B4027 " --> pdb=" O LYS B4023 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4034 Processing helix chain 'B' and resid 4045 through 4054 removed outlier: 3.930A pdb=" N HIS B4054 " --> pdb=" O ALA B4050 " (cutoff:3.500A) Processing helix chain 'B' and resid 4058 through 4068 Processing helix chain 'B' and resid 4078 through 4087 Processing helix chain 'B' and resid 4087 through 4108 removed outlier: 3.514A pdb=" N ASP B4092 " --> pdb=" O GLU B4088 " (cutoff:3.500A) Processing helix chain 'B' and resid 4111 through 4126 removed outlier: 4.050A pdb=" N PHE B4117 " --> pdb=" O ARG B4113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B4120 " --> pdb=" O THR B4116 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER B4123 " --> pdb=" O GLU B4119 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL B4124 " --> pdb=" O LEU B4120 " (cutoff:3.500A) Processing helix chain 'B' and resid 4128 through 4132 removed outlier: 3.793A pdb=" N LEU B4132 " --> pdb=" O GLN B4129 " (cutoff:3.500A) Processing helix chain 'B' and resid 4152 through 4158 Processing helix chain 'B' and resid 4161 through 4177 Processing helix chain 'B' and resid 4183 through 4204 Processing helix chain 'B' and resid 4276 through 4284 removed outlier: 3.984A pdb=" N LEU B4280 " --> pdb=" O LYS B4276 " (cutoff:3.500A) Processing helix chain 'B' and resid 4286 through 4302 removed outlier: 3.752A pdb=" N THR B4292 " --> pdb=" O SER B4288 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B4300 " --> pdb=" O PHE B4296 " (cutoff:3.500A) Processing helix chain 'B' and resid 4304 through 4309 removed outlier: 3.573A pdb=" N SER B4309 " --> pdb=" O PHE B4305 " (cutoff:3.500A) Processing helix chain 'B' and resid 4479 through 4496 removed outlier: 3.672A pdb=" N TYR B4485 " --> pdb=" O LYS B4481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B4488 " --> pdb=" O ALA B4484 " (cutoff:3.500A) Processing helix chain 'B' and resid 4496 through 4515 Processing helix chain 'B' and resid 4567 through 4593 removed outlier: 3.625A pdb=" N LEU B4571 " --> pdb=" O MET B4567 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B4572 " --> pdb=" O GLU B4568 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B4590 " --> pdb=" O ILE B4586 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS B4591 " --> pdb=" O ILE B4587 " (cutoff:3.500A) Processing helix chain 'B' and resid 4593 through 4613 Processing helix chain 'B' and resid 4613 through 4618 Processing helix chain 'B' and resid 4625 through 4630 Processing helix chain 'B' and resid 4648 through 4657 Processing helix chain 'B' and resid 4661 through 4667 removed outlier: 3.813A pdb=" N SER B4666 " --> pdb=" O ARG B4662 " (cutoff:3.500A) Processing helix chain 'B' and resid 4671 through 4682 Processing helix chain 'B' and resid 4701 through 4713 Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 3.727A pdb=" N LEU B4721 " --> pdb=" O SER B4717 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4742 removed outlier: 3.552A pdb=" N HIS B4741 " --> pdb=" O PHE B4738 " (cutoff:3.500A) Processing helix chain 'B' and resid 4743 through 4748 Processing helix chain 'B' and resid 4752 through 4757 Processing helix chain 'B' and resid 4763 through 4788 removed outlier: 3.546A pdb=" N ALA B4774 " --> pdb=" O VAL B4770 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B4775 " --> pdb=" O GLY B4771 " (cutoff:3.500A) Processing helix chain 'B' and resid 4807 through 4819 Processing helix chain 'B' and resid 4840 through 4854 Processing helix chain 'B' and resid 4857 through 4886 removed outlier: 3.979A pdb=" N ILE B4861 " --> pdb=" O LEU B4857 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B4868 " --> pdb=" O LEU B4864 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B4869 " --> pdb=" O ILE B4865 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B4870 " --> pdb=" O ILE B4866 " (cutoff:3.500A) Processing helix chain 'B' and resid 4893 through 4898 removed outlier: 3.930A pdb=" N PHE B4897 " --> pdb=" O GLY B4893 " (cutoff:3.500A) Processing helix chain 'B' and resid 4902 through 4911 removed outlier: 4.132A pdb=" N THR B4906 " --> pdb=" O HIS B4902 " (cutoff:3.500A) Processing helix chain 'B' and resid 4913 through 4928 removed outlier: 4.646A pdb=" N ASP B4928 " --> pdb=" O LEU B4924 " (cutoff:3.500A) Processing helix chain 'B' and resid 4933 through 4946 Processing helix chain 'B' and resid 4956 through 4961 removed outlier: 3.577A pdb=" N TYR B4961 " --> pdb=" O PHE B4957 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 removed outlier: 4.047A pdb=" N GLY H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 264 through 273 removed outlier: 4.212A pdb=" N VAL C 267 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ALA C 271 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG C 272 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 273 " --> pdb=" O HIS C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.978A pdb=" N LYS C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 379 through 383 removed outlier: 3.747A pdb=" N ARG C 383 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 438 removed outlier: 3.889A pdb=" N LEU C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 removed outlier: 3.615A pdb=" N GLY C 461 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 Processing helix chain 'C' and resid 493 through 506 Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.646A pdb=" N ASP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 517 " --> pdb=" O HIS C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.955A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 552 removed outlier: 3.546A pdb=" N ALA C 549 " --> pdb=" O ARG C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 562 removed outlier: 3.678A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 580 Processing helix chain 'C' and resid 582 through 589 removed outlier: 3.577A pdb=" N ALA C 585 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 607 through 619 removed outlier: 4.055A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 612 " --> pdb=" O HIS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 822 through 826 Processing helix chain 'C' and resid 875 through 877 No H-bonds generated for 'chain 'C' and resid 875 through 877' Processing helix chain 'C' and resid 878 through 901 removed outlier: 3.975A pdb=" N LYS C 897 " --> pdb=" O TRP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 removed outlier: 4.131A pdb=" N ASN C 930 " --> pdb=" O GLU C 926 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR C 931 " --> pdb=" O GLN C 927 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASN C 932 " --> pdb=" O GLU C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1012 Processing helix chain 'C' and resid 1029 through 1033 removed outlier: 4.142A pdb=" N VAL C1033 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1060 removed outlier: 3.737A pdb=" N ASN C1046 " --> pdb=" O THR C1042 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C1052 " --> pdb=" O ASP C1048 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA C1053 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL C1054 " --> pdb=" O LEU C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 Processing helix chain 'C' and resid 1643 through 1647 Processing helix chain 'C' and resid 1648 through 1665 Processing helix chain 'C' and resid 1671 through 1682 removed outlier: 3.707A pdb=" N ALA C1676 " --> pdb=" O ARG C1672 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C1679 " --> pdb=" O HIS C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1684 through 1692 Processing helix chain 'C' and resid 1697 through 1711 removed outlier: 3.677A pdb=" N HIS C1711 " --> pdb=" O LEU C1707 " (cutoff:3.500A) Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 4.569A pdb=" N TYR C1715 " --> pdb=" O HIS C1711 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C1722 " --> pdb=" O ALA C1718 " (cutoff:3.500A) Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.880A pdb=" N LEU C1788 " --> pdb=" O PRO C1784 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C1805 " --> pdb=" O LYS C1801 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C1806 " --> pdb=" O GLU C1802 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1832 removed outlier: 3.633A pdb=" N LEU C1818 " --> pdb=" O THR C1814 " (cutoff:3.500A) Proline residue: C1821 - end of helix Processing helix chain 'C' and resid 1836 through 1848 removed outlier: 3.904A pdb=" N ILE C1847 " --> pdb=" O ILE C1843 " (cutoff:3.500A) Processing helix chain 'C' and resid 1898 through 1949 removed outlier: 3.595A pdb=" N GLN C1904 " --> pdb=" O PRO C1900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C1907 " --> pdb=" O LEU C1903 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C1916 " --> pdb=" O LEU C1912 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP C1930 " --> pdb=" O ALA C1926 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP C1937 " --> pdb=" O ALA C1933 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN C1938 " --> pdb=" O LYS C1934 " (cutoff:3.500A) Processing helix chain 'C' and resid 1955 through 1965 removed outlier: 4.572A pdb=" N ARG C1962 " --> pdb=" O ALA C1958 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU C1963 " --> pdb=" O ARG C1959 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE C1964 " --> pdb=" O LYS C1960 " (cutoff:3.500A) Processing helix chain 'C' and resid 1967 through 1976 Processing helix chain 'C' and resid 1989 through 2006 removed outlier: 3.881A pdb=" N ASP C1993 " --> pdb=" O GLU C1989 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C1994 " --> pdb=" O GLU C1990 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2072 removed outlier: 3.650A pdb=" N ALA C2069 " --> pdb=" O MET C2065 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C2072 " --> pdb=" O TRP C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2093 removed outlier: 3.673A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2101 removed outlier: 4.060A pdb=" N LEU C2097 " --> pdb=" O GLY C2093 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2130 Processing helix chain 'C' and resid 2134 through 2151 Processing helix chain 'C' and resid 2152 through 2157 removed outlier: 3.733A pdb=" N GLN C2156 " --> pdb=" O LYS C2152 " (cutoff:3.500A) Processing helix chain 'C' and resid 2157 through 2165 removed outlier: 3.995A pdb=" N MET C2161 " --> pdb=" O HIS C2157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C2162 " --> pdb=" O PRO C2158 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2179 Processing helix chain 'C' and resid 2188 through 2205 Processing helix chain 'C' and resid 2207 through 2221 removed outlier: 4.087A pdb=" N LYS C2211 " --> pdb=" O ARG C2207 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C2215 " --> pdb=" O LYS C2211 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS C2216 " --> pdb=" O ALA C2212 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER C2218 " --> pdb=" O PHE C2214 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR C2219 " --> pdb=" O ASP C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2237 through 2246 Processing helix chain 'C' and resid 2249 through 2256 Processing helix chain 'C' and resid 2260 through 2274 Processing helix chain 'C' and resid 2276 through 2283 Processing helix chain 'C' and resid 2292 through 2305 Processing helix chain 'C' and resid 2312 through 2326 Processing helix chain 'C' and resid 2327 through 2330 Processing helix chain 'C' and resid 2341 through 2355 Processing helix chain 'C' and resid 2356 through 2359 removed outlier: 3.589A pdb=" N ASP C2359 " --> pdb=" O PRO C2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2356 through 2359' Processing helix chain 'C' and resid 2382 through 2402 Processing helix chain 'C' and resid 2413 through 2426 Processing helix chain 'C' and resid 2427 through 2436 Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.842A pdb=" N ALA C2465 " --> pdb=" O PRO C2461 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C2466 " --> pdb=" O ASP C2462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET C2467 " --> pdb=" O HIS C2463 " (cutoff:3.500A) Processing helix chain 'C' and resid 2479 through 2491 Processing helix chain 'C' and resid 2491 through 2500 Processing helix chain 'C' and resid 2508 through 2523 Processing helix chain 'C' and resid 2533 through 2547 Processing helix chain 'C' and resid 2553 through 2571 Processing helix chain 'C' and resid 2575 through 2589 Processing helix chain 'C' and resid 2594 through 2612 Processing helix chain 'C' and resid 2617 through 2635 removed outlier: 3.582A pdb=" N UNK C2621 " --> pdb=" O UNK C2617 " (cutoff:3.500A) Processing helix chain 'C' and resid 2642 through 2650 Processing helix chain 'C' and resid 2652 through 2657 removed outlier: 3.692A pdb=" N UNK C2656 " --> pdb=" O UNK C2652 " (cutoff:3.500A) Processing helix chain 'C' and resid 2713 through 2739 removed outlier: 4.159A pdb=" N ASN C2721 " --> pdb=" O GLU C2717 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS C2722 " --> pdb=" O TYR C2718 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2769 removed outlier: 3.811A pdb=" N GLU C2768 " --> pdb=" O GLU C2764 " (cutoff:3.500A) Processing helix chain 'C' and resid 2772 through 2784 removed outlier: 4.316A pdb=" N GLU C2776 " --> pdb=" O TRP C2772 " (cutoff:3.500A) Processing helix chain 'C' and resid 2836 through 2863 removed outlier: 3.529A pdb=" N TRP C2851 " --> pdb=" O TYR C2847 " (cutoff:3.500A) Processing helix chain 'C' and resid 2877 through 2898 removed outlier: 3.917A pdb=" N ASP C2884 " --> pdb=" O GLU C2880 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C2887 " --> pdb=" O LYS C2883 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE C2894 " --> pdb=" O ASP C2890 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C2895 " --> pdb=" O ILE C2891 " (cutoff:3.500A) Processing helix chain 'C' and resid 2917 through 2942 removed outlier: 3.748A pdb=" N UNK C2942 " --> pdb=" O UNK C2938 " (cutoff:3.500A) Processing helix chain 'C' and resid 2962 through 2982 removed outlier: 3.983A pdb=" N UNK C2975 " --> pdb=" O UNK C2971 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N UNK C2976 " --> pdb=" O UNK C2972 " (cutoff:3.500A) Processing helix chain 'C' and resid 2992 through 3007 Processing helix chain 'C' and resid 3015 through 3029 Processing helix chain 'C' and resid 3105 through 3129 removed outlier: 3.789A pdb=" N UNK C3120 " --> pdb=" O UNK C3116 " (cutoff:3.500A) Processing helix chain 'C' and resid 3137 through 3157 removed outlier: 4.228A pdb=" N UNK C3156 " --> pdb=" O UNK C3152 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK C3157 " --> pdb=" O UNK C3153 " (cutoff:3.500A) Processing helix chain 'C' and resid 3163 through 3182 Processing helix chain 'C' and resid 3183 through 3200 Processing helix chain 'C' and resid 3208 through 3220 removed outlier: 3.601A pdb=" N UNK C3219 " --> pdb=" O UNK C3215 " (cutoff:3.500A) Processing helix chain 'C' and resid 3232 through 3251 Processing helix chain 'C' and resid 3255 through 3269 Processing helix chain 'C' and resid 3271 through 3277 Processing helix chain 'C' and resid 3281 through 3296 removed outlier: 4.112A pdb=" N UNK C3285 " --> pdb=" O UNK C3281 " (cutoff:3.500A) Processing helix chain 'C' and resid 3301 through 3315 Processing helix chain 'C' and resid 3324 through 3355 Processing helix chain 'C' and resid 3362 through 3392 removed outlier: 4.211A pdb=" N UNK C3383 " --> pdb=" O UNK C3379 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N UNK C3389 " --> pdb=" O UNK C3385 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N UNK C3390 " --> pdb=" O UNK C3386 " (cutoff:3.500A) Processing helix chain 'C' and resid 3400 through 3420 removed outlier: 4.114A pdb=" N UNK C3404 " --> pdb=" O UNK C3400 " (cutoff:3.500A) Processing helix chain 'C' and resid 3422 through 3434 removed outlier: 4.894A pdb=" N UNK C3428 " --> pdb=" O UNK C3424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N UNK C3429 " --> pdb=" O UNK C3425 " (cutoff:3.500A) Processing helix chain 'C' and resid 3478 through 3496 removed outlier: 4.012A pdb=" N UNK C3495 " --> pdb=" O UNK C3491 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK C3496 " --> pdb=" O UNK C3492 " (cutoff:3.500A) Processing helix chain 'C' and resid 3503 through 3514 Processing helix chain 'C' and resid 3516 through 3527 removed outlier: 4.056A pdb=" N UNK C3527 " --> pdb=" O UNK C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3540 through 3548 removed outlier: 4.235A pdb=" N UNK C3544 " --> pdb=" O UNK C3540 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N UNK C3545 " --> pdb=" O UNK C3541 " (cutoff:3.500A) Processing helix chain 'C' and resid 3555 through 3579 Processing helix chain 'C' and resid 3612 through 3627 removed outlier: 4.010A pdb=" N VAL C3616 " --> pdb=" O ARG C3612 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3643 Processing helix chain 'C' and resid 3661 through 3676 Processing helix chain 'C' and resid 3684 through 3697 removed outlier: 4.232A pdb=" N ASP C3692 " --> pdb=" O MET C3688 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C3693 " --> pdb=" O ALA C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3732 removed outlier: 4.254A pdb=" N GLU C3719 " --> pdb=" O GLU C3715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C3720 " --> pdb=" O LYS C3716 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C3730 " --> pdb=" O GLN C3726 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP C3732 " --> pdb=" O ALA C3728 " (cutoff:3.500A) Processing helix chain 'C' and resid 3734 through 3745 removed outlier: 3.672A pdb=" N LEU C3740 " --> pdb=" O ALA C3736 " (cutoff:3.500A) Processing helix chain 'C' and resid 3753 through 3765 removed outlier: 3.939A pdb=" N LYS C3759 " --> pdb=" O ALA C3755 " (cutoff:3.500A) Processing helix chain 'C' and resid 3769 through 3783 Processing helix chain 'C' and resid 3788 through 3797 Processing helix chain 'C' and resid 3803 through 3817 Processing helix chain 'C' and resid 3824 through 3828 Processing helix chain 'C' and resid 3831 through 3845 Processing helix chain 'C' and resid 3850 through 3857 Processing helix chain 'C' and resid 3868 through 3891 removed outlier: 3.648A pdb=" N SER C3872 " --> pdb=" O ASN C3868 " (cutoff:3.500A) Processing helix chain 'C' and resid 3898 through 3923 removed outlier: 3.880A pdb=" N PHE C3905 " --> pdb=" O GLY C3901 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C3908 " --> pdb=" O ASN C3904 " (cutoff:3.500A) Processing helix chain 'C' and resid 3927 through 3936 Processing helix chain 'C' and resid 3938 through 3957 removed outlier: 3.785A pdb=" N ALA C3942 " --> pdb=" O ARG C3938 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS C3952 " --> pdb=" O HIS C3948 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET C3955 " --> pdb=" O ALA C3951 " (cutoff:3.500A) Processing helix chain 'C' and resid 3963 through 3983 Processing helix chain 'C' and resid 3984 through 3986 No H-bonds generated for 'chain 'C' and resid 3984 through 3986' Processing helix chain 'C' and resid 3992 through 4005 removed outlier: 3.649A pdb=" N LYS C3996 " --> pdb=" O GLY C3992 " (cutoff:3.500A) Processing helix chain 'C' and resid 4005 through 4021 Processing helix chain 'C' and resid 4022 through 4027 removed outlier: 4.071A pdb=" N SER C4027 " --> pdb=" O LYS C4023 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4034 Processing helix chain 'C' and resid 4045 through 4054 removed outlier: 3.930A pdb=" N HIS C4054 " --> pdb=" O ALA C4050 " (cutoff:3.500A) Processing helix chain 'C' and resid 4058 through 4068 Processing helix chain 'C' and resid 4078 through 4087 Processing helix chain 'C' and resid 4087 through 4108 removed outlier: 3.513A pdb=" N ASP C4092 " --> pdb=" O GLU C4088 " (cutoff:3.500A) Processing helix chain 'C' and resid 4111 through 4126 removed outlier: 4.050A pdb=" N PHE C4117 " --> pdb=" O ARG C4113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C4120 " --> pdb=" O THR C4116 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER C4123 " --> pdb=" O GLU C4119 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL C4124 " --> pdb=" O LEU C4120 " (cutoff:3.500A) Processing helix chain 'C' and resid 4128 through 4132 removed outlier: 3.794A pdb=" N LEU C4132 " --> pdb=" O GLN C4129 " (cutoff:3.500A) Processing helix chain 'C' and resid 4152 through 4158 Processing helix chain 'C' and resid 4161 through 4177 Processing helix chain 'C' and resid 4183 through 4204 Processing helix chain 'C' and resid 4276 through 4284 removed outlier: 3.985A pdb=" N LEU C4280 " --> pdb=" O LYS C4276 " (cutoff:3.500A) Processing helix chain 'C' and resid 4286 through 4302 removed outlier: 3.751A pdb=" N THR C4292 " --> pdb=" O SER C4288 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL C4300 " --> pdb=" O PHE C4296 " (cutoff:3.500A) Processing helix chain 'C' and resid 4304 through 4309 removed outlier: 3.573A pdb=" N SER C4309 " --> pdb=" O PHE C4305 " (cutoff:3.500A) Processing helix chain 'C' and resid 4479 through 4496 removed outlier: 3.672A pdb=" N TYR C4485 " --> pdb=" O LYS C4481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C4488 " --> pdb=" O ALA C4484 " (cutoff:3.500A) Processing helix chain 'C' and resid 4496 through 4515 Processing helix chain 'C' and resid 4567 through 4593 removed outlier: 3.624A pdb=" N LEU C4571 " --> pdb=" O MET C4567 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C4572 " --> pdb=" O GLU C4568 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR C4590 " --> pdb=" O ILE C4586 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS C4591 " --> pdb=" O ILE C4587 " (cutoff:3.500A) Processing helix chain 'C' and resid 4593 through 4613 Processing helix chain 'C' and resid 4613 through 4618 Processing helix chain 'C' and resid 4625 through 4630 Processing helix chain 'C' and resid 4648 through 4657 Processing helix chain 'C' and resid 4661 through 4667 removed outlier: 3.813A pdb=" N SER C4666 " --> pdb=" O ARG C4662 " (cutoff:3.500A) Processing helix chain 'C' and resid 4671 through 4682 Processing helix chain 'C' and resid 4701 through 4713 Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 3.727A pdb=" N LEU C4721 " --> pdb=" O SER C4717 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4742 removed outlier: 3.552A pdb=" N HIS C4741 " --> pdb=" O PHE C4738 " (cutoff:3.500A) Processing helix chain 'C' and resid 4743 through 4748 Processing helix chain 'C' and resid 4752 through 4757 Processing helix chain 'C' and resid 4763 through 4788 removed outlier: 3.546A pdb=" N ALA C4774 " --> pdb=" O VAL C4770 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL C4775 " --> pdb=" O GLY C4771 " (cutoff:3.500A) Processing helix chain 'C' and resid 4807 through 4819 Processing helix chain 'C' and resid 4840 through 4854 Processing helix chain 'C' and resid 4857 through 4886 removed outlier: 3.979A pdb=" N ILE C4861 " --> pdb=" O LEU C4857 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C4868 " --> pdb=" O LEU C4864 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C4869 " --> pdb=" O ILE C4865 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C4870 " --> pdb=" O ILE C4866 " (cutoff:3.500A) Processing helix chain 'C' and resid 4893 through 4898 removed outlier: 3.929A pdb=" N PHE C4897 " --> pdb=" O GLY C4893 " (cutoff:3.500A) Processing helix chain 'C' and resid 4902 through 4911 removed outlier: 4.132A pdb=" N THR C4906 " --> pdb=" O HIS C4902 " (cutoff:3.500A) Processing helix chain 'C' and resid 4913 through 4928 removed outlier: 4.645A pdb=" N ASP C4928 " --> pdb=" O LEU C4924 " (cutoff:3.500A) Processing helix chain 'C' and resid 4933 through 4946 Processing helix chain 'C' and resid 4956 through 4961 removed outlier: 3.578A pdb=" N TYR C4961 " --> pdb=" O PHE C4957 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 removed outlier: 4.048A pdb=" N GLY I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 83 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 264 through 273 removed outlier: 4.212A pdb=" N VAL D 267 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA D 271 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG D 272 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER D 273 " --> pdb=" O HIS D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.979A pdb=" N LYS D 321 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 379 through 383 removed outlier: 3.747A pdb=" N ARG D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 438 removed outlier: 3.890A pdb=" N LEU D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 463 removed outlier: 3.615A pdb=" N GLY D 461 " --> pdb=" O GLN D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 Processing helix chain 'D' and resid 493 through 506 Processing helix chain 'D' and resid 510 through 519 removed outlier: 3.645A pdb=" N ASP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL D 517 " --> pdb=" O HIS D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.956A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.545A pdb=" N ALA D 549 " --> pdb=" O ARG D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 removed outlier: 3.677A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 580 Processing helix chain 'D' and resid 582 through 589 removed outlier: 3.577A pdb=" N ALA D 585 " --> pdb=" O SER D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 607 through 619 removed outlier: 4.054A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 822 through 826 Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 878 through 901 removed outlier: 3.976A pdb=" N LYS D 897 " --> pdb=" O TRP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 removed outlier: 4.131A pdb=" N ASN D 930 " --> pdb=" O GLU D 926 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN D 932 " --> pdb=" O GLU D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1012 Processing helix chain 'D' and resid 1029 through 1033 removed outlier: 4.141A pdb=" N VAL D1033 " --> pdb=" O PRO D1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1060 removed outlier: 3.736A pdb=" N ASN D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA D1053 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D1054 " --> pdb=" O LEU D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 Processing helix chain 'D' and resid 1643 through 1647 Processing helix chain 'D' and resid 1648 through 1665 Processing helix chain 'D' and resid 1671 through 1682 removed outlier: 3.708A pdb=" N ALA D1676 " --> pdb=" O ARG D1672 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER D1679 " --> pdb=" O HIS D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1684 through 1692 Processing helix chain 'D' and resid 1697 through 1711 removed outlier: 3.676A pdb=" N HIS D1711 " --> pdb=" O LEU D1707 " (cutoff:3.500A) Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 4.569A pdb=" N TYR D1715 " --> pdb=" O HIS D1711 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET D1722 " --> pdb=" O ALA D1718 " (cutoff:3.500A) Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.879A pdb=" N LEU D1788 " --> pdb=" O PRO D1784 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D1805 " --> pdb=" O LYS D1801 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS D1806 " --> pdb=" O GLU D1802 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1832 removed outlier: 3.633A pdb=" N LEU D1818 " --> pdb=" O THR D1814 " (cutoff:3.500A) Proline residue: D1821 - end of helix Processing helix chain 'D' and resid 1836 through 1848 removed outlier: 3.903A pdb=" N ILE D1847 " --> pdb=" O ILE D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1898 through 1949 removed outlier: 3.594A pdb=" N GLN D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D1907 " --> pdb=" O LEU D1903 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D1916 " --> pdb=" O LEU D1912 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D1930 " --> pdb=" O ALA D1926 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP D1937 " --> pdb=" O ALA D1933 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D1938 " --> pdb=" O LYS D1934 " (cutoff:3.500A) Processing helix chain 'D' and resid 1955 through 1965 removed outlier: 4.573A pdb=" N ARG D1962 " --> pdb=" O ALA D1958 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU D1963 " --> pdb=" O ARG D1959 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE D1964 " --> pdb=" O LYS D1960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1967 through 1976 Processing helix chain 'D' and resid 1989 through 2006 removed outlier: 3.880A pdb=" N ASP D1993 " --> pdb=" O GLU D1989 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D1994 " --> pdb=" O GLU D1990 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2072 removed outlier: 3.650A pdb=" N ALA D2069 " --> pdb=" O MET D2065 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D2072 " --> pdb=" O TRP D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2093 removed outlier: 3.674A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2101 removed outlier: 4.060A pdb=" N LEU D2097 " --> pdb=" O GLY D2093 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2130 Processing helix chain 'D' and resid 2134 through 2151 Processing helix chain 'D' and resid 2152 through 2157 removed outlier: 3.732A pdb=" N GLN D2156 " --> pdb=" O LYS D2152 " (cutoff:3.500A) Processing helix chain 'D' and resid 2157 through 2165 removed outlier: 3.995A pdb=" N MET D2161 " --> pdb=" O HIS D2157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D2162 " --> pdb=" O PRO D2158 " (cutoff:3.500A) Processing helix chain 'D' and resid 2165 through 2179 Processing helix chain 'D' and resid 2188 through 2205 Processing helix chain 'D' and resid 2207 through 2221 removed outlier: 4.088A pdb=" N LYS D2211 " --> pdb=" O ARG D2207 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D2215 " --> pdb=" O LYS D2211 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS D2216 " --> pdb=" O ALA D2212 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D2218 " --> pdb=" O PHE D2214 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR D2219 " --> pdb=" O ASP D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2237 through 2246 Processing helix chain 'D' and resid 2249 through 2256 Processing helix chain 'D' and resid 2260 through 2274 Processing helix chain 'D' and resid 2276 through 2283 Processing helix chain 'D' and resid 2292 through 2305 Processing helix chain 'D' and resid 2312 through 2326 Processing helix chain 'D' and resid 2327 through 2330 Processing helix chain 'D' and resid 2341 through 2355 Processing helix chain 'D' and resid 2356 through 2359 removed outlier: 3.589A pdb=" N ASP D2359 " --> pdb=" O PRO D2356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2356 through 2359' Processing helix chain 'D' and resid 2382 through 2402 Processing helix chain 'D' and resid 2413 through 2426 Processing helix chain 'D' and resid 2427 through 2436 Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.843A pdb=" N ALA D2465 " --> pdb=" O PRO D2461 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D2466 " --> pdb=" O ASP D2462 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D2467 " --> pdb=" O HIS D2463 " (cutoff:3.500A) Processing helix chain 'D' and resid 2479 through 2491 Processing helix chain 'D' and resid 2491 through 2500 Processing helix chain 'D' and resid 2508 through 2523 Processing helix chain 'D' and resid 2533 through 2547 Processing helix chain 'D' and resid 2553 through 2571 Processing helix chain 'D' and resid 2575 through 2589 Processing helix chain 'D' and resid 2594 through 2612 Processing helix chain 'D' and resid 2617 through 2635 removed outlier: 3.583A pdb=" N UNK D2621 " --> pdb=" O UNK D2617 " (cutoff:3.500A) Processing helix chain 'D' and resid 2642 through 2650 Processing helix chain 'D' and resid 2652 through 2657 removed outlier: 3.692A pdb=" N UNK D2656 " --> pdb=" O UNK D2652 " (cutoff:3.500A) Processing helix chain 'D' and resid 2713 through 2739 removed outlier: 4.159A pdb=" N ASN D2721 " --> pdb=" O GLU D2717 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS D2722 " --> pdb=" O TYR D2718 " (cutoff:3.500A) Processing helix chain 'D' and resid 2763 through 2769 removed outlier: 3.810A pdb=" N GLU D2768 " --> pdb=" O GLU D2764 " (cutoff:3.500A) Processing helix chain 'D' and resid 2772 through 2784 removed outlier: 4.315A pdb=" N GLU D2776 " --> pdb=" O TRP D2772 " (cutoff:3.500A) Processing helix chain 'D' and resid 2836 through 2863 removed outlier: 3.529A pdb=" N TRP D2851 " --> pdb=" O TYR D2847 " (cutoff:3.500A) Processing helix chain 'D' and resid 2877 through 2898 removed outlier: 3.917A pdb=" N ASP D2884 " --> pdb=" O GLU D2880 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D2887 " --> pdb=" O LYS D2883 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE D2894 " --> pdb=" O ASP D2890 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D2895 " --> pdb=" O ILE D2891 " (cutoff:3.500A) Processing helix chain 'D' and resid 2917 through 2942 removed outlier: 3.748A pdb=" N UNK D2942 " --> pdb=" O UNK D2938 " (cutoff:3.500A) Processing helix chain 'D' and resid 2962 through 2982 removed outlier: 3.984A pdb=" N UNK D2975 " --> pdb=" O UNK D2971 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N UNK D2976 " --> pdb=" O UNK D2972 " (cutoff:3.500A) Processing helix chain 'D' and resid 2992 through 3007 Processing helix chain 'D' and resid 3015 through 3029 Processing helix chain 'D' and resid 3105 through 3129 removed outlier: 3.789A pdb=" N UNK D3120 " --> pdb=" O UNK D3116 " (cutoff:3.500A) Processing helix chain 'D' and resid 3137 through 3157 removed outlier: 4.226A pdb=" N UNK D3156 " --> pdb=" O UNK D3152 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK D3157 " --> pdb=" O UNK D3153 " (cutoff:3.500A) Processing helix chain 'D' and resid 3163 through 3182 Processing helix chain 'D' and resid 3183 through 3200 Processing helix chain 'D' and resid 3208 through 3220 removed outlier: 3.601A pdb=" N UNK D3219 " --> pdb=" O UNK D3215 " (cutoff:3.500A) Processing helix chain 'D' and resid 3232 through 3251 Processing helix chain 'D' and resid 3255 through 3269 Processing helix chain 'D' and resid 3271 through 3277 Processing helix chain 'D' and resid 3281 through 3296 removed outlier: 4.112A pdb=" N UNK D3285 " --> pdb=" O UNK D3281 " (cutoff:3.500A) Processing helix chain 'D' and resid 3301 through 3315 Processing helix chain 'D' and resid 3324 through 3355 Processing helix chain 'D' and resid 3362 through 3392 removed outlier: 4.211A pdb=" N UNK D3383 " --> pdb=" O UNK D3379 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N UNK D3389 " --> pdb=" O UNK D3385 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N UNK D3390 " --> pdb=" O UNK D3386 " (cutoff:3.500A) Processing helix chain 'D' and resid 3400 through 3420 removed outlier: 4.114A pdb=" N UNK D3404 " --> pdb=" O UNK D3400 " (cutoff:3.500A) Processing helix chain 'D' and resid 3422 through 3434 removed outlier: 4.894A pdb=" N UNK D3428 " --> pdb=" O UNK D3424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N UNK D3429 " --> pdb=" O UNK D3425 " (cutoff:3.500A) Processing helix chain 'D' and resid 3478 through 3496 removed outlier: 4.011A pdb=" N UNK D3495 " --> pdb=" O UNK D3491 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK D3496 " --> pdb=" O UNK D3492 " (cutoff:3.500A) Processing helix chain 'D' and resid 3503 through 3514 Processing helix chain 'D' and resid 3516 through 3527 removed outlier: 4.056A pdb=" N UNK D3527 " --> pdb=" O UNK D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3540 through 3548 removed outlier: 4.235A pdb=" N UNK D3544 " --> pdb=" O UNK D3540 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N UNK D3545 " --> pdb=" O UNK D3541 " (cutoff:3.500A) Processing helix chain 'D' and resid 3555 through 3579 Processing helix chain 'D' and resid 3612 through 3627 removed outlier: 4.010A pdb=" N VAL D3616 " --> pdb=" O ARG D3612 " (cutoff:3.500A) Processing helix chain 'D' and resid 3637 through 3643 Processing helix chain 'D' and resid 3661 through 3676 Processing helix chain 'D' and resid 3684 through 3697 removed outlier: 4.232A pdb=" N ASP D3692 " --> pdb=" O MET D3688 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D3693 " --> pdb=" O ALA D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3732 removed outlier: 4.253A pdb=" N GLU D3719 " --> pdb=" O GLU D3715 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS D3720 " --> pdb=" O LYS D3716 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D3730 " --> pdb=" O GLN D3726 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP D3732 " --> pdb=" O ALA D3728 " (cutoff:3.500A) Processing helix chain 'D' and resid 3734 through 3745 removed outlier: 3.672A pdb=" N LEU D3740 " --> pdb=" O ALA D3736 " (cutoff:3.500A) Processing helix chain 'D' and resid 3753 through 3765 removed outlier: 3.939A pdb=" N LYS D3759 " --> pdb=" O ALA D3755 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3783 Processing helix chain 'D' and resid 3788 through 3797 Processing helix chain 'D' and resid 3803 through 3817 Processing helix chain 'D' and resid 3824 through 3828 Processing helix chain 'D' and resid 3831 through 3845 Processing helix chain 'D' and resid 3850 through 3857 Processing helix chain 'D' and resid 3868 through 3891 removed outlier: 3.648A pdb=" N SER D3872 " --> pdb=" O ASN D3868 " (cutoff:3.500A) Processing helix chain 'D' and resid 3898 through 3923 removed outlier: 3.880A pdb=" N PHE D3905 " --> pdb=" O GLY D3901 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D3908 " --> pdb=" O ASN D3904 " (cutoff:3.500A) Processing helix chain 'D' and resid 3927 through 3936 Processing helix chain 'D' and resid 3938 through 3957 removed outlier: 3.784A pdb=" N ALA D3942 " --> pdb=" O ARG D3938 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D3952 " --> pdb=" O HIS D3948 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET D3955 " --> pdb=" O ALA D3951 " (cutoff:3.500A) Processing helix chain 'D' and resid 3963 through 3983 Processing helix chain 'D' and resid 3984 through 3986 No H-bonds generated for 'chain 'D' and resid 3984 through 3986' Processing helix chain 'D' and resid 3992 through 4005 removed outlier: 3.649A pdb=" N LYS D3996 " --> pdb=" O GLY D3992 " (cutoff:3.500A) Processing helix chain 'D' and resid 4005 through 4021 Processing helix chain 'D' and resid 4022 through 4027 removed outlier: 4.071A pdb=" N SER D4027 " --> pdb=" O LYS D4023 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4034 Processing helix chain 'D' and resid 4045 through 4054 removed outlier: 3.931A pdb=" N HIS D4054 " --> pdb=" O ALA D4050 " (cutoff:3.500A) Processing helix chain 'D' and resid 4058 through 4068 Processing helix chain 'D' and resid 4078 through 4087 Processing helix chain 'D' and resid 4087 through 4108 removed outlier: 3.514A pdb=" N ASP D4092 " --> pdb=" O GLU D4088 " (cutoff:3.500A) Processing helix chain 'D' and resid 4111 through 4126 removed outlier: 4.049A pdb=" N PHE D4117 " --> pdb=" O ARG D4113 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D4120 " --> pdb=" O THR D4116 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER D4123 " --> pdb=" O GLU D4119 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N VAL D4124 " --> pdb=" O LEU D4120 " (cutoff:3.500A) Processing helix chain 'D' and resid 4128 through 4132 removed outlier: 3.793A pdb=" N LEU D4132 " --> pdb=" O GLN D4129 " (cutoff:3.500A) Processing helix chain 'D' and resid 4152 through 4158 Processing helix chain 'D' and resid 4161 through 4177 Processing helix chain 'D' and resid 4183 through 4204 Processing helix chain 'D' and resid 4276 through 4284 removed outlier: 3.984A pdb=" N LEU D4280 " --> pdb=" O LYS D4276 " (cutoff:3.500A) Processing helix chain 'D' and resid 4286 through 4302 removed outlier: 3.752A pdb=" N THR D4292 " --> pdb=" O SER D4288 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D4300 " --> pdb=" O PHE D4296 " (cutoff:3.500A) Processing helix chain 'D' and resid 4304 through 4309 removed outlier: 3.573A pdb=" N SER D4309 " --> pdb=" O PHE D4305 " (cutoff:3.500A) Processing helix chain 'D' and resid 4479 through 4496 removed outlier: 3.672A pdb=" N TYR D4485 " --> pdb=" O LYS D4481 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D4488 " --> pdb=" O ALA D4484 " (cutoff:3.500A) Processing helix chain 'D' and resid 4496 through 4515 Processing helix chain 'D' and resid 4567 through 4593 removed outlier: 3.625A pdb=" N LEU D4571 " --> pdb=" O MET D4567 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D4572 " --> pdb=" O GLU D4568 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D4590 " --> pdb=" O ILE D4586 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS D4591 " --> pdb=" O ILE D4587 " (cutoff:3.500A) Processing helix chain 'D' and resid 4593 through 4613 Processing helix chain 'D' and resid 4613 through 4618 Processing helix chain 'D' and resid 4625 through 4630 Processing helix chain 'D' and resid 4648 through 4657 Processing helix chain 'D' and resid 4661 through 4667 removed outlier: 3.813A pdb=" N SER D4666 " --> pdb=" O ARG D4662 " (cutoff:3.500A) Processing helix chain 'D' and resid 4671 through 4682 Processing helix chain 'D' and resid 4701 through 4713 Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 3.728A pdb=" N LEU D4721 " --> pdb=" O SER D4717 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4742 removed outlier: 3.552A pdb=" N HIS D4741 " --> pdb=" O PHE D4738 " (cutoff:3.500A) Processing helix chain 'D' and resid 4743 through 4748 Processing helix chain 'D' and resid 4752 through 4757 Processing helix chain 'D' and resid 4763 through 4788 removed outlier: 3.545A pdb=" N ALA D4774 " --> pdb=" O VAL D4770 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL D4775 " --> pdb=" O GLY D4771 " (cutoff:3.500A) Processing helix chain 'D' and resid 4807 through 4819 Processing helix chain 'D' and resid 4840 through 4854 Processing helix chain 'D' and resid 4857 through 4886 removed outlier: 3.979A pdb=" N ILE D4861 " --> pdb=" O LEU D4857 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D4868 " --> pdb=" O LEU D4864 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D4869 " --> pdb=" O ILE D4865 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D4870 " --> pdb=" O ILE D4866 " (cutoff:3.500A) Processing helix chain 'D' and resid 4893 through 4898 removed outlier: 3.930A pdb=" N PHE D4897 " --> pdb=" O GLY D4893 " (cutoff:3.500A) Processing helix chain 'D' and resid 4902 through 4911 removed outlier: 4.132A pdb=" N THR D4906 " --> pdb=" O HIS D4902 " (cutoff:3.500A) Processing helix chain 'D' and resid 4913 through 4928 removed outlier: 4.646A pdb=" N ASP D4928 " --> pdb=" O LEU D4924 " (cutoff:3.500A) Processing helix chain 'D' and resid 4933 through 4946 Processing helix chain 'D' and resid 4956 through 4961 removed outlier: 3.577A pdb=" N TYR D4961 " --> pdb=" O PHE D4957 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 removed outlier: 4.047A pdb=" N GLY J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.459A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.337A pdb=" N VAL A 147 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 203 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 299 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 246 removed outlier: 3.713A pdb=" N ARG A 389 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA7, first strand: chain 'A' and resid 645 through 650 Processing sheet with id=AA8, first strand: chain 'A' and resid 738 through 740 Processing sheet with id=AA9, first strand: chain 'A' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER A 756 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 672 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER A 756 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.944A pdb=" N PHE A1192 " --> pdb=" O MET A1173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1180 through 1181 Processing sheet with id=AB5, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 5.247A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1258 through 1260 Processing sheet with id=AB7, first strand: chain 'A' and resid 1269 through 1270 Processing sheet with id=AB8, first strand: chain 'A' and resid 1302 through 1303 Processing sheet with id=AB9, first strand: chain 'A' and resid 1302 through 1303 Processing sheet with id=AC1, first strand: chain 'A' and resid 1317 through 1318 removed outlier: 3.979A pdb=" N UNK A1440 " --> pdb=" O ASP A1362 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP A1362 " --> pdb=" O UNK A1440 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A1363 " --> pdb=" O ASP A1357 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1726 through 1728 removed outlier: 6.234A pdb=" N PHE A1726 " --> pdb=" O TYR A2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 2306 through 2307 Processing sheet with id=AC4, first strand: chain 'A' and resid 2741 through 2742 removed outlier: 5.817A pdb=" N ILE A2741 " --> pdb=" O GLN A2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 4135 through 4138 Processing sheet with id=AC6, first strand: chain 'A' and resid 4519 through 4520 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU G 107 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR G 22 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 51 removed outlier: 5.459A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 122 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU B 69 " --> pdb=" O ARG B 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 129 through 132 removed outlier: 4.338A pdb=" N VAL B 147 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 203 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 295 through 299 Processing sheet with id=AD3, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.713A pdb=" N ARG B 389 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 305 through 308 Processing sheet with id=AD5, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AD6, first strand: chain 'B' and resid 645 through 650 Processing sheet with id=AD7, first strand: chain 'B' and resid 738 through 740 Processing sheet with id=AD8, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER B 756 " --> pdb=" O ARG B 769 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS B 672 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER B 756 " --> pdb=" O ARG B 769 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AE2, first strand: chain 'B' and resid 850 through 851 removed outlier: 3.944A pdb=" N PHE B1192 " --> pdb=" O MET B1173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1180 through 1181 Processing sheet with id=AE4, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 5.248A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1258 through 1260 Processing sheet with id=AE6, first strand: chain 'B' and resid 1269 through 1270 Processing sheet with id=AE7, first strand: chain 'B' and resid 1302 through 1303 Processing sheet with id=AE8, first strand: chain 'B' and resid 1302 through 1303 Processing sheet with id=AE9, first strand: chain 'B' and resid 1317 through 1318 removed outlier: 3.979A pdb=" N UNK B1440 " --> pdb=" O ASP B1362 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP B1362 " --> pdb=" O UNK B1440 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B1363 " --> pdb=" O ASP B1357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1726 through 1728 removed outlier: 6.233A pdb=" N PHE B1726 " --> pdb=" O TYR B2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 2306 through 2307 Processing sheet with id=AF3, first strand: chain 'B' and resid 2741 through 2742 removed outlier: 5.817A pdb=" N ILE B2741 " --> pdb=" O GLN B2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 4135 through 4138 Processing sheet with id=AF5, first strand: chain 'B' and resid 4519 through 4520 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU H 107 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR H 22 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 51 removed outlier: 5.459A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG C 122 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU C 69 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 129 through 132 removed outlier: 4.337A pdb=" N VAL C 147 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 203 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 295 through 299 Processing sheet with id=AG2, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.712A pdb=" N ARG C 389 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AG4, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AG5, first strand: chain 'C' and resid 645 through 650 Processing sheet with id=AG6, first strand: chain 'C' and resid 738 through 740 Processing sheet with id=AG7, first strand: chain 'C' and resid 773 through 774 removed outlier: 3.589A pdb=" N SER C 756 " --> pdb=" O ARG C 769 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS C 672 " --> pdb=" O ALA C 820 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 773 through 774 removed outlier: 3.589A pdb=" N SER C 756 " --> pdb=" O ARG C 769 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 779 through 780 Processing sheet with id=AH1, first strand: chain 'C' and resid 850 through 851 removed outlier: 3.943A pdb=" N PHE C1192 " --> pdb=" O MET C1173 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1180 through 1181 Processing sheet with id=AH3, first strand: chain 'C' and resid 1149 through 1151 removed outlier: 5.247A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AH5, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AH6, first strand: chain 'C' and resid 1302 through 1303 Processing sheet with id=AH7, first strand: chain 'C' and resid 1302 through 1303 Processing sheet with id=AH8, first strand: chain 'C' and resid 1317 through 1318 removed outlier: 3.979A pdb=" N UNK C1440 " --> pdb=" O ASP C1362 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP C1362 " --> pdb=" O UNK C1440 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C1363 " --> pdb=" O ASP C1357 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1726 through 1728 removed outlier: 6.234A pdb=" N PHE C1726 " --> pdb=" O TYR C2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'C' and resid 2306 through 2307 Processing sheet with id=AI2, first strand: chain 'C' and resid 2741 through 2742 removed outlier: 5.817A pdb=" N ILE C2741 " --> pdb=" O GLN C2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'C' and resid 4135 through 4138 Processing sheet with id=AI4, first strand: chain 'C' and resid 4519 through 4520 Processing sheet with id=AI5, first strand: chain 'I' and resid 4 through 9 removed outlier: 6.477A pdb=" N ARG I 72 " --> pdb=" O ILE I 8 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 4 through 9 removed outlier: 6.477A pdb=" N ARG I 72 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL I 24 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU I 107 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR I 22 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 48 through 51 removed outlier: 5.460A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 129 through 132 removed outlier: 4.338A pdb=" N VAL D 147 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL D 203 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 295 through 299 Processing sheet with id=AJ1, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.712A pdb=" N ARG D 389 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 305 through 308 Processing sheet with id=AJ3, first strand: chain 'D' and resid 329 through 332 Processing sheet with id=AJ4, first strand: chain 'D' and resid 645 through 650 Processing sheet with id=AJ5, first strand: chain 'D' and resid 738 through 740 Processing sheet with id=AJ6, first strand: chain 'D' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER D 756 " --> pdb=" O ARG D 769 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS D 672 " --> pdb=" O ALA D 820 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 773 through 774 removed outlier: 3.590A pdb=" N SER D 756 " --> pdb=" O ARG D 769 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 779 through 780 Processing sheet with id=AJ9, first strand: chain 'D' and resid 850 through 851 removed outlier: 3.943A pdb=" N PHE D1192 " --> pdb=" O MET D1173 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 1180 through 1181 Processing sheet with id=AK2, first strand: chain 'D' and resid 1149 through 1151 removed outlier: 5.246A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 1258 through 1260 Processing sheet with id=AK4, first strand: chain 'D' and resid 1269 through 1270 Processing sheet with id=AK5, first strand: chain 'D' and resid 1302 through 1303 Processing sheet with id=AK6, first strand: chain 'D' and resid 1302 through 1303 Processing sheet with id=AK7, first strand: chain 'D' and resid 1317 through 1318 removed outlier: 3.979A pdb=" N UNK D1440 " --> pdb=" O ASP D1362 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP D1362 " --> pdb=" O UNK D1440 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D1363 " --> pdb=" O ASP D1357 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 1726 through 1728 removed outlier: 6.234A pdb=" N PHE D1726 " --> pdb=" O TYR D2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'D' and resid 2306 through 2307 Processing sheet with id=AL1, first strand: chain 'D' and resid 2741 through 2742 removed outlier: 5.817A pdb=" N ILE D2741 " --> pdb=" O GLN D2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL1 Processing sheet with id=AL2, first strand: chain 'D' and resid 4135 through 4138 Processing sheet with id=AL3, first strand: chain 'D' and resid 4519 through 4520 Processing sheet with id=AL4, first strand: chain 'J' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG J 72 " --> pdb=" O ILE J 8 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'J' and resid 4 through 9 removed outlier: 6.476A pdb=" N ARG J 72 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL J 24 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU J 107 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR J 22 " --> pdb=" O LEU J 107 " (cutoff:3.500A) 7180 hydrogen bonds defined for protein. 20580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 99.81 Time building geometry restraints manager: 42.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 39005 1.34 - 1.45: 17258 1.45 - 1.57: 68429 1.57 - 1.69: 0 1.69 - 1.81: 1168 Bond restraints: 125860 Sorted by residual: bond pdb=" C ALA C4606 " pdb=" N ARG C4607 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.31e-02 5.83e+03 3.22e+01 bond pdb=" C ALA D4606 " pdb=" N ARG D4607 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.31e-02 5.83e+03 3.18e+01 bond pdb=" C ALA A4606 " pdb=" N ARG A4607 " ideal model delta sigma weight residual 1.335 1.409 -0.074 1.31e-02 5.83e+03 3.18e+01 bond pdb=" C ALA B4606 " pdb=" N ARG B4607 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.31e-02 5.83e+03 3.14e+01 bond pdb=" N LEU D1255 " pdb=" CA LEU D1255 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.30e-02 5.92e+03 7.56e+00 ... (remaining 125855 not shown) Histogram of bond angle deviations from ideal: 96.43 - 103.97: 1499 103.97 - 111.51: 56472 111.51 - 119.05: 44936 119.05 - 126.59: 66192 126.59 - 134.13: 1549 Bond angle restraints: 170648 Sorted by residual: angle pdb=" N MET B4653 " pdb=" CA MET B4653 " pdb=" CB MET B4653 " ideal model delta sigma weight residual 110.16 117.24 -7.08 1.48e+00 4.57e-01 2.29e+01 angle pdb=" N MET A4653 " pdb=" CA MET A4653 " pdb=" CB MET A4653 " ideal model delta sigma weight residual 110.16 117.21 -7.05 1.48e+00 4.57e-01 2.27e+01 angle pdb=" N MET D4653 " pdb=" CA MET D4653 " pdb=" CB MET D4653 " ideal model delta sigma weight residual 110.16 117.21 -7.05 1.48e+00 4.57e-01 2.27e+01 angle pdb=" N MET C4653 " pdb=" CA MET C4653 " pdb=" CB MET C4653 " ideal model delta sigma weight residual 110.16 117.19 -7.03 1.48e+00 4.57e-01 2.26e+01 angle pdb=" C ALA C4606 " pdb=" N ARG C4607 " pdb=" CA ARG C4607 " ideal model delta sigma weight residual 120.28 114.25 6.03 1.34e+00 5.57e-01 2.03e+01 ... (remaining 170643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 69031 17.96 - 35.92: 5353 35.92 - 53.87: 852 53.87 - 71.83: 148 71.83 - 89.79: 80 Dihedral angle restraints: 75464 sinusoidal: 27060 harmonic: 48404 Sorted by residual: dihedral pdb=" CA UNK A2652 " pdb=" C UNK A2652 " pdb=" N UNK A2653 " pdb=" CA UNK A2653 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA UNK C2652 " pdb=" C UNK C2652 " pdb=" N UNK C2653 " pdb=" CA UNK C2653 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA UNK B2652 " pdb=" C UNK B2652 " pdb=" N UNK B2653 " pdb=" CA UNK B2653 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 75461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 14842 0.042 - 0.085: 3471 0.085 - 0.127: 939 0.127 - 0.170: 134 0.170 - 0.212: 18 Chirality restraints: 19404 Sorted by residual: chirality pdb=" CA ARG B 431 " pdb=" N ARG B 431 " pdb=" C ARG B 431 " pdb=" CB ARG B 431 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ARG D 431 " pdb=" N ARG D 431 " pdb=" C ARG D 431 " pdb=" CB ARG D 431 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ARG A 431 " pdb=" N ARG A 431 " pdb=" C ARG A 431 " pdb=" CB ARG A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 19401 not shown) Planarity restraints: 22256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1117 " -0.029 2.00e-02 2.50e+03 2.79e-02 1.95e+01 pdb=" CG TRP C1117 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP C1117 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP C1117 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1117 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C1117 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1117 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1117 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1117 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C1117 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1117 " 0.029 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP A1117 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP A1117 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A1117 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1117 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1117 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1117 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1117 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A1117 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1117 " 0.029 2.00e-02 2.50e+03 2.77e-02 1.92e+01 pdb=" CG TRP B1117 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B1117 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B1117 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1117 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B1117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1117 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1117 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1117 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B1117 " -0.001 2.00e-02 2.50e+03 ... (remaining 22253 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1446 2.64 - 3.20: 116147 3.20 - 3.77: 194551 3.77 - 4.33: 252950 4.33 - 4.90: 410589 Nonbonded interactions: 975683 Sorted by model distance: nonbonded pdb=" OG1 THR C 973 " pdb=" O TYR C 976 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR D 973 " pdb=" O TYR D 976 " model vdw 2.073 2.440 nonbonded pdb=" OG1 THR A 973 " pdb=" O TYR A 976 " model vdw 2.074 2.440 nonbonded pdb=" OG1 THR B 973 " pdb=" O TYR B 976 " model vdw 2.074 2.440 nonbonded pdb=" OH TYR C1094 " pdb=" OD2 ASP C1809 " model vdw 2.154 2.440 ... (remaining 975678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 4962) selection = (chain 'B' and resid 11 through 4962) selection = (chain 'C' and resid 11 through 4962) selection = (chain 'D' and resid 11 through 4962) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.070 Extract box with map and model: 15.080 Check model and map are aligned: 1.310 Set scattering table: 0.770 Process input model: 309.460 Find NCS groups from input model: 8.140 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 125860 Z= 0.190 Angle : 0.645 10.250 170648 Z= 0.335 Chirality : 0.040 0.212 19404 Planarity : 0.004 0.087 22256 Dihedral : 13.332 89.789 44016 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -2.49 (0.07), residues: 13424 helix: -0.36 (0.06), residues: 6380 sheet: -2.52 (0.12), residues: 1336 loop : -2.96 (0.07), residues: 5708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1156 time to evaluate : 9.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 1176 average time/residue: 1.0965 time to fit residues: 2288.1426 Evaluate side-chains 763 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 755 time to evaluate : 9.692 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 1.2213 time to fit residues: 29.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1398 optimal weight: 10.0000 chunk 1255 optimal weight: 20.0000 chunk 696 optimal weight: 40.0000 chunk 428 optimal weight: 20.0000 chunk 846 optimal weight: 0.6980 chunk 670 optimal weight: 50.0000 chunk 1297 optimal weight: 9.9990 chunk 502 optimal weight: 4.9990 chunk 789 optimal weight: 20.0000 chunk 966 optimal weight: 4.9990 chunk 1503 optimal weight: 40.0000 overall best weight: 6.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 299 HIS A 531 ASN A 669 GLN A 716 ASN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1685 GLN ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2290 ASN A2406 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3849 HIS ** A3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3900 GLN A4087 HIS ** A4619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4641 ASN A4642 ASN A4786 ASN B 150 GLN B 299 HIS B 531 ASN B 669 GLN B 716 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 ASN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1685 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2290 ASN B2406 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3849 HIS ** B3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3900 GLN B4008 ASN B4087 HIS B4177 ASN ** B4619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4642 ASN B4786 ASN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN C 299 HIS C 531 ASN C 669 GLN C 716 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1171 HIS ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1685 GLN ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2290 ASN C2406 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3849 HIS ** C3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3900 GLN C4008 ASN C4087 HIS C4177 ASN ** C4619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4642 ASN C4786 ASN D 150 GLN D 299 HIS D 531 ASN D 669 GLN D 716 ASN ** D 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 ASN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 HIS ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1685 GLN ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2290 ASN D2406 HIS ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3849 HIS ** D3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3900 GLN D4008 ASN D4087 HIS D4177 ASN ** D4619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4642 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 125860 Z= 0.344 Angle : 0.725 9.107 170648 Z= 0.371 Chirality : 0.043 0.221 19404 Planarity : 0.005 0.088 22256 Dihedral : 4.642 53.209 17656 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.85 (0.07), residues: 13424 helix: 0.07 (0.06), residues: 6384 sheet: -2.13 (0.13), residues: 1320 loop : -2.53 (0.07), residues: 5720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 814 time to evaluate : 9.233 Fit side-chains revert: symmetry clash outliers start: 190 outliers final: 91 residues processed: 935 average time/residue: 0.9610 time to fit residues: 1624.2319 Evaluate side-chains 793 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 702 time to evaluate : 8.742 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.8680 time to fit residues: 158.1838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 835 optimal weight: 20.0000 chunk 466 optimal weight: 0.0470 chunk 1251 optimal weight: 0.9990 chunk 1024 optimal weight: 1.9990 chunk 414 optimal weight: 20.0000 chunk 1506 optimal weight: 10.9990 chunk 1627 optimal weight: 5.9990 chunk 1341 optimal weight: 30.0000 chunk 1493 optimal weight: 30.0000 chunk 513 optimal weight: 20.0000 chunk 1208 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1616 GLN ** A1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN ** A4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4177 ASN A4619 GLN A4786 ASN A4894 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN ** B4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4619 GLN B4786 ASN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN ** C4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4619 GLN C4786 ASN C4894 ASN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN ** D4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4619 GLN D4786 ASN D4894 ASN ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 125860 Z= 0.165 Angle : 0.547 10.948 170648 Z= 0.278 Chirality : 0.037 0.173 19404 Planarity : 0.004 0.050 22256 Dihedral : 4.114 56.420 17656 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.44 (0.07), residues: 13424 helix: 0.49 (0.07), residues: 6448 sheet: -1.98 (0.13), residues: 1448 loop : -2.45 (0.08), residues: 5528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 783 time to evaluate : 9.772 Fit side-chains outliers start: 147 outliers final: 53 residues processed: 903 average time/residue: 0.9974 time to fit residues: 1639.1619 Evaluate side-chains 769 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 716 time to evaluate : 8.731 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.8068 time to fit residues: 93.4280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1488 optimal weight: 7.9990 chunk 1132 optimal weight: 6.9990 chunk 781 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 718 optimal weight: 5.9990 chunk 1011 optimal weight: 10.0000 chunk 1511 optimal weight: 50.0000 chunk 1600 optimal weight: 0.6980 chunk 789 optimal weight: 20.0000 chunk 1432 optimal weight: 0.0470 chunk 431 optimal weight: 20.0000 overall best weight: 3.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 57 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN ** A4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4786 ASN ** A4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS B 57 ASN ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN ** B4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4641 ASN B4786 ASN ** B4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 57 ASN ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN ** C4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4641 ASN C4786 ASN ** C4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 57 ASN ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN ** D4129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4641 ASN D4786 ASN ** D4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 125860 Z= 0.226 Angle : 0.573 9.206 170648 Z= 0.291 Chirality : 0.038 0.288 19404 Planarity : 0.004 0.047 22256 Dihedral : 4.199 58.918 17656 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.26 (0.07), residues: 13424 helix: 0.59 (0.07), residues: 6436 sheet: -1.75 (0.13), residues: 1388 loop : -2.34 (0.08), residues: 5600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 742 time to evaluate : 8.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 84 residues processed: 871 average time/residue: 0.9705 time to fit residues: 1546.4695 Evaluate side-chains 780 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 696 time to evaluate : 9.708 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.8603 time to fit residues: 151.6568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1333 optimal weight: 20.0000 chunk 908 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 1191 optimal weight: 9.9990 chunk 660 optimal weight: 0.9990 chunk 1365 optimal weight: 30.0000 chunk 1106 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 817 optimal weight: 7.9990 chunk 1436 optimal weight: 1.9990 chunk 403 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1627 GLN ** A1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN A4512 ASN A4786 ASN ** A4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS B 29 HIS ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1627 GLN ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN B4512 ASN B4786 ASN B4894 ASN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS C 29 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1627 GLN ** C1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN C4512 ASN C4786 ASN ** C4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS D 29 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1627 GLN ** D1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN D4512 ASN ** D4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 125860 Z= 0.265 Angle : 0.615 11.068 170648 Z= 0.314 Chirality : 0.039 0.278 19404 Planarity : 0.004 0.054 22256 Dihedral : 4.453 59.884 17656 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.29 (0.07), residues: 13424 helix: 0.51 (0.07), residues: 6448 sheet: -1.49 (0.14), residues: 1300 loop : -2.35 (0.08), residues: 5676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 745 time to evaluate : 9.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 228 outliers final: 111 residues processed: 937 average time/residue: 0.9837 time to fit residues: 1684.9825 Evaluate side-chains 792 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 681 time to evaluate : 9.748 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 0 residues processed: 111 average time/residue: 0.8978 time to fit residues: 204.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 538 optimal weight: 10.0000 chunk 1441 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 939 optimal weight: 20.0000 chunk 395 optimal weight: 9.9990 chunk 1602 optimal weight: 20.0000 chunk 1330 optimal weight: 9.9990 chunk 741 optimal weight: 0.8980 chunk 133 optimal weight: 40.0000 chunk 530 optimal weight: 9.9990 chunk 841 optimal weight: 10.0000 overall best weight: 7.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 HIS ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1837 ASN ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2726 HIS ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3948 HIS A4059 GLN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1837 ASN ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2726 HIS ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3948 HIS B4008 ASN B4059 GLN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1837 ASN ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2726 HIS ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3948 HIS C3997 GLN C4008 ASN C4059 GLN ** C4894 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1837 ASN ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2726 HIS ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3948 HIS D4008 ASN D4059 GLN ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 125860 Z= 0.381 Angle : 0.743 9.899 170648 Z= 0.380 Chirality : 0.043 0.202 19404 Planarity : 0.005 0.058 22256 Dihedral : 5.079 62.100 17656 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.11 % Favored : 90.86 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.62 (0.07), residues: 13424 helix: 0.25 (0.06), residues: 6372 sheet: -1.66 (0.15), residues: 1236 loop : -2.50 (0.07), residues: 5816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 724 time to evaluate : 9.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 87 residues processed: 925 average time/residue: 1.0120 time to fit residues: 1704.1383 Evaluate side-chains 773 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 686 time to evaluate : 8.706 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.8562 time to fit residues: 155.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1544 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 912 optimal weight: 50.0000 chunk 1170 optimal weight: 9.9990 chunk 906 optimal weight: 0.0270 chunk 1348 optimal weight: 0.0060 chunk 894 optimal weight: 20.0000 chunk 1596 optimal weight: 1.9990 chunk 998 optimal weight: 30.0000 chunk 973 optimal weight: 5.9990 chunk 736 optimal weight: 0.8980 overall best weight: 1.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 651 HIS ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN G 66 GLN B 79 GLN B 604 HIS ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN H 66 GLN C 79 GLN C 604 HIS ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN D 604 HIS D 651 HIS ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN J 66 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 125860 Z= 0.166 Angle : 0.574 10.413 170648 Z= 0.291 Chirality : 0.037 0.193 19404 Planarity : 0.004 0.058 22256 Dihedral : 4.459 60.156 17656 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.18 (0.07), residues: 13424 helix: 0.66 (0.07), residues: 6392 sheet: -1.55 (0.14), residues: 1336 loop : -2.33 (0.08), residues: 5696 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 764 time to evaluate : 9.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 60 residues processed: 879 average time/residue: 1.0177 time to fit residues: 1617.0464 Evaluate side-chains 750 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 690 time to evaluate : 9.758 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.9407 time to fit residues: 119.5156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 987 optimal weight: 0.5980 chunk 637 optimal weight: 40.0000 chunk 953 optimal weight: 30.0000 chunk 480 optimal weight: 20.0000 chunk 313 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 1014 optimal weight: 9.9990 chunk 1087 optimal weight: 30.0000 chunk 789 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 1254 optimal weight: 10.0000 overall best weight: 6.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1836 HIS ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3997 GLN A4059 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1836 HIS ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3997 GLN B4059 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1836 HIS ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3997 GLN D4059 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 125860 Z= 0.313 Angle : 0.668 12.795 170648 Z= 0.339 Chirality : 0.040 0.240 19404 Planarity : 0.005 0.058 22256 Dihedral : 4.756 61.151 17656 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.34 (0.07), residues: 13424 helix: 0.51 (0.07), residues: 6412 sheet: -1.52 (0.14), residues: 1284 loop : -2.41 (0.07), residues: 5728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 717 time to evaluate : 9.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 50 residues processed: 804 average time/residue: 1.0511 time to fit residues: 1537.5833 Evaluate side-chains 748 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 698 time to evaluate : 9.743 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.9417 time to fit residues: 102.0444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1451 optimal weight: 0.0270 chunk 1529 optimal weight: 50.0000 chunk 1395 optimal weight: 0.0010 chunk 1487 optimal weight: 20.0000 chunk 1528 optimal weight: 20.0000 chunk 895 optimal weight: 9.9990 chunk 647 optimal weight: 30.0000 chunk 1167 optimal weight: 1.9990 chunk 456 optimal weight: 8.9990 chunk 1344 optimal weight: 20.0000 chunk 1406 optimal weight: 0.8980 overall best weight: 2.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1680 HIS ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN B 531 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN I 66 GLN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1680 HIS ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 125860 Z= 0.177 Angle : 0.584 13.145 170648 Z= 0.294 Chirality : 0.037 0.291 19404 Planarity : 0.004 0.062 22256 Dihedral : 4.426 59.862 17656 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.07), residues: 13424 helix: 0.72 (0.07), residues: 6420 sheet: -1.40 (0.14), residues: 1288 loop : -2.29 (0.08), residues: 5716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 752 time to evaluate : 9.896 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 773 average time/residue: 1.0404 time to fit residues: 1452.8389 Evaluate side-chains 722 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 704 time to evaluate : 9.834 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.9002 time to fit residues: 44.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 1482 optimal weight: 30.0000 chunk 976 optimal weight: 8.9990 chunk 1572 optimal weight: 0.7980 chunk 959 optimal weight: 40.0000 chunk 746 optimal weight: 6.9990 chunk 1093 optimal weight: 50.0000 chunk 1649 optimal weight: 8.9990 chunk 1518 optimal weight: 40.0000 chunk 1313 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 1014 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 GLN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4059 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 971 GLN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1265 HIS ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN ** I 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 971 GLN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 HIS D1603 GLN ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 125860 Z= 0.311 Angle : 0.673 13.320 170648 Z= 0.341 Chirality : 0.040 0.241 19404 Planarity : 0.005 0.062 22256 Dihedral : 4.786 61.035 17656 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.95 % Favored : 91.02 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.33 (0.07), residues: 13424 helix: 0.51 (0.07), residues: 6412 sheet: -1.51 (0.14), residues: 1264 loop : -2.40 (0.08), residues: 5748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26848 Ramachandran restraints generated. 13424 Oldfield, 0 Emsley, 13424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 712 time to evaluate : 9.826 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 735 average time/residue: 1.0694 time to fit residues: 1422.7392 Evaluate side-chains 699 residues out of total 11928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 687 time to evaluate : 9.750 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.9506 time to fit residues: 34.6745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1656 random chunks: chunk 805 optimal weight: 0.9990 chunk 1043 optimal weight: 20.0000 chunk 1399 optimal weight: 1.9990 chunk 402 optimal weight: 0.9990 chunk 1211 optimal weight: 0.0970 chunk 193 optimal weight: 8.9990 chunk 365 optimal weight: 5.9990 chunk 1315 optimal weight: 5.9990 chunk 550 optimal weight: 0.7980 chunk 1351 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4059 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2090 GLN B4059 GLN C 531 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4059 GLN D 531 ASN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4059 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.104773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.089068 restraints weight = 514608.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.087128 restraints weight = 598374.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.087669 restraints weight = 512712.723| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 125860 Z= 0.156 Angle : 0.582 13.151 170648 Z= 0.291 Chirality : 0.037 0.256 19404 Planarity : 0.004 0.064 22256 Dihedral : 4.373 58.785 17656 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.01 (0.07), residues: 13424 helix: 0.77 (0.07), residues: 6452 sheet: -1.33 (0.15), residues: 1280 loop : -2.25 (0.08), residues: 5692 =============================================================================== Job complete usr+sys time: 25546.23 seconds wall clock time: 449 minutes 50.82 seconds (26990.82 seconds total)