Starting phenix.real_space_refine on Sat Dec 16 09:45:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/12_2023/6l7e_0843_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 305 5.16 5 C 61665 2.51 5 N 16555 2.21 5 O 18875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1616": "NH1" <-> "NH2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1616": "NH1" <-> "NH2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1616": "NH1" <-> "NH2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1616": "NH1" <-> "NH2" Residue "D PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1616": "NH1" <-> "NH2" Residue "E PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 97400 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "B" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "C" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "D" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "E" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Time building chain proxies: 39.09, per 1000 atoms: 0.40 Number of scatterers: 97400 At special positions: 0 Unit cell: (202.038, 189.996, 262.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 305 16.00 O 18875 8.00 N 16555 7.00 C 61665 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: 29.22 Conformation dependent library (CDL) restraints added in 15.0 seconds 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23260 Finding SS restraints... Secondary structure from input PDB file: 435 helices and 105 sheets defined 47.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.47 Creating SS restraints... Processing helix chain 'A' and resid 42 through 70 removed outlier: 3.646A pdb=" N HIS A 50 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.140A pdb=" N GLY A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.573A pdb=" N MET A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.846A pdb=" N THR A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.808A pdb=" N VAL A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.551A pdb=" N ASN A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.660A pdb=" N LYS A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.640A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.582A pdb=" N LYS A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.583A pdb=" N ILE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 removed outlier: 3.685A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY A 787 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 removed outlier: 3.527A pdb=" N ALA A 838 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 855 removed outlier: 3.701A pdb=" N LEU A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 885 Processing helix chain 'A' and resid 890 through 899 removed outlier: 3.576A pdb=" N LEU A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS A 907 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 954 removed outlier: 3.557A pdb=" N ASN A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 944 " --> pdb=" O GLU A 940 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY A1033 " --> pdb=" O SER A1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1090 removed outlier: 3.557A pdb=" N VAL A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1084 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER A1258 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A1259 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A1260 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN A1261 " --> pdb=" O SER A1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1255 through 1261' Processing helix chain 'A' and resid 1279 through 1289 removed outlier: 3.949A pdb=" N VAL A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1289 " --> pdb=" O VAL A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1294 Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU A1329 " --> pdb=" O ASP A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU A1374 " --> pdb=" O ASN A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1467 Processing helix chain 'A' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN A1612 " --> pdb=" O LEU A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN A1630 " --> pdb=" O SER A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1773 Processing helix chain 'A' and resid 1773 through 1786 Processing helix chain 'A' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG A1794 " --> pdb=" O ASP A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1836 through 1844 removed outlier: 3.521A pdb=" N VAL A1840 " --> pdb=" O ASP A1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1869 Processing helix chain 'A' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU A1876 " --> pdb=" O GLU A1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1877 " --> pdb=" O ARG A1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1886 " --> pdb=" O TRP A1882 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 removed outlier: 3.617A pdb=" N LEU A1890 " --> pdb=" O ALA A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1912 through 1928 Processing helix chain 'A' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR A1959 " --> pdb=" O VAL A1955 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A1960 " --> pdb=" O MET A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2105 removed outlier: 3.900A pdb=" N GLU A2024 " --> pdb=" O PRO A2020 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A2032 " --> pdb=" O GLY A2028 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A2033 " --> pdb=" O MET A2029 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A2062 " --> pdb=" O ASN A2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A2064 " --> pdb=" O ALA A2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A2065 " --> pdb=" O ALA A2061 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A2072 " --> pdb=" O LEU A2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A2083 " --> pdb=" O ASP A2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A2094 " --> pdb=" O ALA A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN A2113 " --> pdb=" O ALA A2109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A2115 " --> pdb=" O GLU A2111 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2139 Processing helix chain 'A' and resid 2155 through 2244 removed outlier: 3.692A pdb=" N ASN A2170 " --> pdb=" O GLU A2166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A2199 " --> pdb=" O GLN A2195 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR A2251 " --> pdb=" O ASN A2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A2260 " --> pdb=" O GLY A2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A2268 " --> pdb=" O GLN A2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A2271 " --> pdb=" O ASP A2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A2272 " --> pdb=" O LEU A2268 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU A2312 " --> pdb=" O GLU A2308 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2342 Processing helix chain 'A' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A2363 " --> pdb=" O LYS A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR A2402 " --> pdb=" O ARG A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2503 Processing helix chain 'B' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.523A pdb=" N GLU B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.950A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.639A pdb=" N ILE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.539A pdb=" N VAL B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.549A pdb=" N GLY B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 594 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 595 " --> pdb=" O GLY B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP B 732 " --> pdb=" O GLU B 728 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.740A pdb=" N GLY B 787 " --> pdb=" O GLU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 817 through 827 removed outlier: 3.604A pdb=" N ALA B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA B 838 " --> pdb=" O GLN B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 855 removed outlier: 3.700A pdb=" N LEU B 846 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 885 Processing helix chain 'B' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU B 897 " --> pdb=" O GLY B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS B 907 " --> pdb=" O GLN B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 924 removed outlier: 3.604A pdb=" N LEU B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 940 " --> pdb=" O ALA B 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 944 " --> pdb=" O GLU B 940 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 948 " --> pdb=" O ALA B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1027 through 1040 removed outlier: 3.624A pdb=" N GLY B1033 " --> pdb=" O SER B1029 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B1038 " --> pdb=" O VAL B1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR B1039 " --> pdb=" O SER B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1044 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL B1074 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B1084 " --> pdb=" O SER B1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B1087 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1224 Processing helix chain 'B' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER B1258 " --> pdb=" O THR B1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B1259 " --> pdb=" O LEU B1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B1260 " --> pdb=" O ASP B1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B1261 " --> pdb=" O SER B1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1255 through 1261' Processing helix chain 'B' and resid 1279 through 1289 removed outlier: 3.950A pdb=" N VAL B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B1289 " --> pdb=" O VAL B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1294 Processing helix chain 'B' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU B1329 " --> pdb=" O ASP B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU B1374 " --> pdb=" O ASN B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1467 Processing helix chain 'B' and resid 1608 through 1613 removed outlier: 3.654A pdb=" N GLN B1612 " --> pdb=" O LEU B1608 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN B1630 " --> pdb=" O SER B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1773 Processing helix chain 'B' and resid 1773 through 1786 Processing helix chain 'B' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG B1794 " --> pdb=" O ASP B1790 " (cutoff:3.500A) Processing helix chain 'B' and resid 1818 through 1823 Processing helix chain 'B' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL B1840 " --> pdb=" O ASP B1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1841 " --> pdb=" O PRO B1837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1869 Processing helix chain 'B' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU B1876 " --> pdb=" O GLU B1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1877 " --> pdb=" O ARG B1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1886 " --> pdb=" O TRP B1882 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU B1890 " --> pdb=" O ALA B1886 " (cutoff:3.500A) Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1912 through 1928 Processing helix chain 'B' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR B1959 " --> pdb=" O VAL B1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B1960 " --> pdb=" O MET B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU B2024 " --> pdb=" O PRO B2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B2032 " --> pdb=" O GLY B2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B2033 " --> pdb=" O MET B2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B2035 " --> pdb=" O SER B2031 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B2062 " --> pdb=" O ASN B2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B2064 " --> pdb=" O ALA B2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B2065 " --> pdb=" O ALA B2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B2066 " --> pdb=" O GLU B2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B2072 " --> pdb=" O LEU B2068 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B2083 " --> pdb=" O ASP B2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B2094 " --> pdb=" O ALA B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2121 removed outlier: 3.715A pdb=" N GLN B2113 " --> pdb=" O ALA B2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B2115 " --> pdb=" O GLU B2111 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2139 Processing helix chain 'B' and resid 2155 through 2244 removed outlier: 3.690A pdb=" N ASN B2170 " --> pdb=" O GLU B2166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B2199 " --> pdb=" O GLN B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR B2251 " --> pdb=" O ASN B2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2260 " --> pdb=" O GLY B2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B2268 " --> pdb=" O GLN B2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B2271 " --> pdb=" O ASP B2267 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B2272 " --> pdb=" O LEU B2268 " (cutoff:3.500A) Processing helix chain 'B' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU B2312 " --> pdb=" O GLU B2308 " (cutoff:3.500A) Processing helix chain 'B' and resid 2337 through 2342 Processing helix chain 'B' and resid 2352 through 2363 removed outlier: 3.720A pdb=" N ASP B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B2362 " --> pdb=" O ASP B2358 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B2363 " --> pdb=" O LYS B2359 " (cutoff:3.500A) Processing helix chain 'B' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR B2402 " --> pdb=" O ARG B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2499 through 2503 Processing helix chain 'C' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS C 50 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.154A pdb=" N ALA C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.806A pdb=" N VAL C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.661A pdb=" N LYS C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 removed outlier: 3.634A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.638A pdb=" N ILE C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 556 removed outlier: 3.723A pdb=" N THR C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 594 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 595 " --> pdb=" O GLY C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE C 653 " --> pdb=" O PHE C 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL C 691 " --> pdb=" O ASP C 687 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 717 " --> pdb=" O LEU C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP C 732 " --> pdb=" O GLU C 728 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 769 removed outlier: 3.675A pdb=" N ILE C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY C 787 " --> pdb=" O GLU C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 813 removed outlier: 3.543A pdb=" N ILE C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET C 803 " --> pdb=" O LEU C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 816 No H-bonds generated for 'chain 'C' and resid 814 through 816' Processing helix chain 'C' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 839 removed outlier: 3.527A pdb=" N ALA C 838 " --> pdb=" O GLN C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 855 removed outlier: 3.702A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 885 Processing helix chain 'C' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU C 897 " --> pdb=" O GLY C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 907 removed outlier: 3.649A pdb=" N LYS C 907 " --> pdb=" O GLN C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 removed outlier: 3.604A pdb=" N LEU C 922 " --> pdb=" O ALA C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 940 " --> pdb=" O ALA C 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 944 " --> pdb=" O GLU C 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 945 " --> pdb=" O SER C 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG C 999 " --> pdb=" O LEU C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY C1033 " --> pdb=" O SER C1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C1038 " --> pdb=" O VAL C1034 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR C1039 " --> pdb=" O SER C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1064 Processing helix chain 'C' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL C1074 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C1084 " --> pdb=" O SER C1080 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1224 Processing helix chain 'C' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER C1258 " --> pdb=" O THR C1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C1259 " --> pdb=" O LEU C1256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C1260 " --> pdb=" O ASP C1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C1261 " --> pdb=" O SER C1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1255 through 1261' Processing helix chain 'C' and resid 1279 through 1289 removed outlier: 3.948A pdb=" N VAL C1285 " --> pdb=" O GLU C1281 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C1289 " --> pdb=" O VAL C1285 " (cutoff:3.500A) Processing helix chain 'C' and resid 1290 through 1294 Processing helix chain 'C' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU C1329 " --> pdb=" O ASP C1326 " (cutoff:3.500A) Processing helix chain 'C' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU C1374 " --> pdb=" O ASN C1370 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1467 Processing helix chain 'C' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN C1612 " --> pdb=" O LEU C1608 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN C1630 " --> pdb=" O SER C1626 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1773 Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG C1794 " --> pdb=" O ASP C1790 " (cutoff:3.500A) Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL C1840 " --> pdb=" O ASP C1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C1841 " --> pdb=" O PRO C1837 " (cutoff:3.500A) Processing helix chain 'C' and resid 1845 through 1869 Processing helix chain 'C' and resid 1872 through 1886 removed outlier: 3.654A pdb=" N LEU C1876 " --> pdb=" O GLU C1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C1877 " --> pdb=" O ARG C1873 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C1886 " --> pdb=" O TRP C1882 " (cutoff:3.500A) Processing helix chain 'C' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU C1890 " --> pdb=" O ALA C1886 " (cutoff:3.500A) Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1912 through 1928 Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR C1959 " --> pdb=" O VAL C1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2105 removed outlier: 3.900A pdb=" N GLU C2024 " --> pdb=" O PRO C2020 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C2032 " --> pdb=" O GLY C2028 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C2033 " --> pdb=" O MET C2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C2035 " --> pdb=" O SER C2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C2062 " --> pdb=" O ASN C2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C2064 " --> pdb=" O ALA C2060 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C2065 " --> pdb=" O ALA C2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR C2066 " --> pdb=" O GLU C2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C2072 " --> pdb=" O LEU C2068 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C2083 " --> pdb=" O ASP C2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C2094 " --> pdb=" O ALA C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN C2113 " --> pdb=" O ALA C2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C2115 " --> pdb=" O GLU C2111 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2139 Processing helix chain 'C' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN C2170 " --> pdb=" O GLU C2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C2199 " --> pdb=" O GLN C2195 " (cutoff:3.500A) Processing helix chain 'C' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR C2251 " --> pdb=" O ASN C2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C2260 " --> pdb=" O GLY C2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C2268 " --> pdb=" O GLN C2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C2271 " --> pdb=" O ASP C2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C2272 " --> pdb=" O LEU C2268 " (cutoff:3.500A) Processing helix chain 'C' and resid 2305 through 2323 removed outlier: 3.540A pdb=" N LEU C2312 " --> pdb=" O GLU C2308 " (cutoff:3.500A) Processing helix chain 'C' and resid 2337 through 2342 Processing helix chain 'C' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP C2358 " --> pdb=" O ALA C2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C2362 " --> pdb=" O ASP C2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C2363 " --> pdb=" O LYS C2359 " (cutoff:3.500A) Processing helix chain 'C' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR C2402 " --> pdb=" O ARG C2399 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2503 Processing helix chain 'D' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.521A pdb=" N GLU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 127 " --> pdb=" O TYR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.634A pdb=" N ARG D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 398 through 403 removed outlier: 3.639A pdb=" N ILE D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU D 498 " --> pdb=" O THR D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.705A pdb=" N GLY D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.723A pdb=" N THR D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 594 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 623 through 645 removed outlier: 3.525A pdb=" N SER D 639 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 643 " --> pdb=" O SER D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 656 removed outlier: 3.583A pdb=" N ILE D 653 " --> pdb=" O PHE D 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL D 691 " --> pdb=" O ASP D 687 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA D 708 " --> pdb=" O SER D 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 717 " --> pdb=" O LEU D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP D 732 " --> pdb=" O GLU D 728 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 removed outlier: 3.738A pdb=" N GLY D 787 " --> pdb=" O GLU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 816 No H-bonds generated for 'chain 'D' and resid 814 through 816' Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA D 838 " --> pdb=" O GLN D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 855 removed outlier: 3.702A pdb=" N LEU D 846 " --> pdb=" O ASP D 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D 854 " --> pdb=" O SER D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 885 Processing helix chain 'D' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU D 897 " --> pdb=" O GLY D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS D 907 " --> pdb=" O GLN D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU D 922 " --> pdb=" O ALA D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.557A pdb=" N ASN D 932 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 940 " --> pdb=" O ALA D 936 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 944 " --> pdb=" O GLU D 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 945 " --> pdb=" O SER D 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 948 " --> pdb=" O ALA D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 984 through 1001 removed outlier: 3.524A pdb=" N ARG D 999 " --> pdb=" O LEU D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1014 Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY D1033 " --> pdb=" O SER D1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D1038 " --> pdb=" O VAL D1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR D1039 " --> pdb=" O SER D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1044 Processing helix chain 'D' and resid 1054 through 1064 Processing helix chain 'D' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL D1074 " --> pdb=" O ASN D1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D1084 " --> pdb=" O SER D1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D1087 " --> pdb=" O THR D1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER D1258 " --> pdb=" O THR D1255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D1259 " --> pdb=" O LEU D1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D1260 " --> pdb=" O ASP D1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN D1261 " --> pdb=" O SER D1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1255 through 1261' Processing helix chain 'D' and resid 1279 through 1289 removed outlier: 3.948A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1294 Processing helix chain 'D' and resid 1325 through 1329 removed outlier: 3.655A pdb=" N LEU D1329 " --> pdb=" O ASP D1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 1368 through 1378 removed outlier: 3.669A pdb=" N LEU D1374 " --> pdb=" O ASN D1370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1467 Processing helix chain 'D' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN D1612 " --> pdb=" O LEU D1608 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1626 through 1631 removed outlier: 3.806A pdb=" N GLN D1630 " --> pdb=" O SER D1626 " (cutoff:3.500A) Processing helix chain 'D' and resid 1764 through 1773 Processing helix chain 'D' and resid 1773 through 1786 Processing helix chain 'D' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG D1794 " --> pdb=" O ASP D1790 " (cutoff:3.500A) Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL D1840 " --> pdb=" O ASP D1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D1841 " --> pdb=" O PRO D1837 " (cutoff:3.500A) Processing helix chain 'D' and resid 1845 through 1869 Processing helix chain 'D' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU D1876 " --> pdb=" O GLU D1872 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D1877 " --> pdb=" O ARG D1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D1886 " --> pdb=" O TRP D1882 " (cutoff:3.500A) Processing helix chain 'D' and resid 1886 through 1891 removed outlier: 3.617A pdb=" N LEU D1890 " --> pdb=" O ALA D1886 " (cutoff:3.500A) Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1912 through 1928 Processing helix chain 'D' and resid 1953 through 1972 removed outlier: 3.808A pdb=" N TYR D1959 " --> pdb=" O VAL D1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU D2024 " --> pdb=" O PRO D2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D2032 " --> pdb=" O GLY D2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D2033 " --> pdb=" O MET D2029 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D2035 " --> pdb=" O SER D2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D2062 " --> pdb=" O ASN D2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D2064 " --> pdb=" O ALA D2060 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D2065 " --> pdb=" O ALA D2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D2066 " --> pdb=" O GLU D2062 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D2072 " --> pdb=" O LEU D2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D2083 " --> pdb=" O ASP D2079 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D2094 " --> pdb=" O ALA D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2108 through 2121 removed outlier: 3.715A pdb=" N GLN D2113 " --> pdb=" O ALA D2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET D2115 " --> pdb=" O GLU D2111 " (cutoff:3.500A) Processing helix chain 'D' and resid 2124 through 2139 Processing helix chain 'D' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN D2170 " --> pdb=" O GLU D2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D2199 " --> pdb=" O GLN D2195 " (cutoff:3.500A) Processing helix chain 'D' and resid 2247 through 2284 removed outlier: 3.703A pdb=" N TYR D2251 " --> pdb=" O ASN D2247 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D2260 " --> pdb=" O GLY D2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D2268 " --> pdb=" O GLN D2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D2271 " --> pdb=" O ASP D2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D2272 " --> pdb=" O LEU D2268 " (cutoff:3.500A) Processing helix chain 'D' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU D2312 " --> pdb=" O GLU D2308 " (cutoff:3.500A) Processing helix chain 'D' and resid 2337 through 2342 Processing helix chain 'D' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP D2358 " --> pdb=" O ALA D2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D2362 " --> pdb=" O ASP D2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D2363 " --> pdb=" O LYS D2359 " (cutoff:3.500A) Processing helix chain 'D' and resid 2398 through 2402 removed outlier: 3.601A pdb=" N TYR D2402 " --> pdb=" O ARG D2399 " (cutoff:3.500A) Processing helix chain 'D' and resid 2499 through 2503 Processing helix chain 'E' and resid 43 through 70 removed outlier: 3.646A pdb=" N HIS E 50 " --> pdb=" O HIS E 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 4.154A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.140A pdb=" N GLY E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 157 removed outlier: 3.575A pdb=" N MET E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 181 through 192 removed outlier: 3.846A pdb=" N THR E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL E 210 " --> pdb=" O ASN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 398 through 403 removed outlier: 3.638A pdb=" N ILE E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 488 removed outlier: 3.584A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.707A pdb=" N GLY E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY E 591 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 594 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 595 " --> pdb=" O GLY E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 623 through 645 removed outlier: 3.525A pdb=" N SER E 639 " --> pdb=" O ASN E 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 643 " --> pdb=" O SER E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE E 653 " --> pdb=" O PHE E 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 678 removed outlier: 3.605A pdb=" N LEU E 670 " --> pdb=" O GLU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.579A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA E 708 " --> pdb=" O SER E 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 717 " --> pdb=" O LEU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP E 732 " --> pdb=" O GLU E 728 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE E 752 " --> pdb=" O THR E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG E 777 " --> pdb=" O GLU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY E 787 " --> pdb=" O GLU E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE E 802 " --> pdb=" O ALA E 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 816 No H-bonds generated for 'chain 'E' and resid 814 through 816' Processing helix chain 'E' and resid 817 through 827 removed outlier: 3.604A pdb=" N ALA E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA E 838 " --> pdb=" O GLN E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 855 removed outlier: 3.701A pdb=" N LEU E 846 " --> pdb=" O ASP E 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 854 " --> pdb=" O SER E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 885 Processing helix chain 'E' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU E 897 " --> pdb=" O GLY E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS E 907 " --> pdb=" O GLN E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU E 922 " --> pdb=" O ALA E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN E 932 " --> pdb=" O SER E 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 940 " --> pdb=" O ALA E 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 944 " --> pdb=" O GLU E 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 945 " --> pdb=" O SER E 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 948 " --> pdb=" O ALA E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG E 999 " --> pdb=" O LEU E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1014 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY E1033 " --> pdb=" O SER E1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E1038 " --> pdb=" O VAL E1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR E1039 " --> pdb=" O SER E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1064 Processing helix chain 'E' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL E1074 " --> pdb=" O ASN E1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER E1084 " --> pdb=" O SER E1080 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E1087 " --> pdb=" O THR E1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E1088 " --> pdb=" O SER E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1224 Processing helix chain 'E' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER E1258 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E1259 " --> pdb=" O LEU E1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E1260 " --> pdb=" O ASP E1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN E1261 " --> pdb=" O SER E1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1255 through 1261' Processing helix chain 'E' and resid 1279 through 1289 removed outlier: 3.950A pdb=" N VAL E1285 " --> pdb=" O GLU E1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E1289 " --> pdb=" O VAL E1285 " (cutoff:3.500A) Processing helix chain 'E' and resid 1290 through 1294 Processing helix chain 'E' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU E1329 " --> pdb=" O ASP E1326 " (cutoff:3.500A) Processing helix chain 'E' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU E1374 " --> pdb=" O ASN E1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 1463 through 1467 Processing helix chain 'E' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN E1612 " --> pdb=" O LEU E1608 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1626 through 1631 removed outlier: 3.806A pdb=" N GLN E1630 " --> pdb=" O SER E1626 " (cutoff:3.500A) Processing helix chain 'E' and resid 1764 through 1773 Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG E1794 " --> pdb=" O ASP E1790 " (cutoff:3.500A) Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL E1840 " --> pdb=" O ASP E1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E1841 " --> pdb=" O PRO E1837 " (cutoff:3.500A) Processing helix chain 'E' and resid 1845 through 1869 Processing helix chain 'E' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU E1876 " --> pdb=" O GLU E1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E1877 " --> pdb=" O ARG E1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E1886 " --> pdb=" O TRP E1882 " (cutoff:3.500A) Processing helix chain 'E' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU E1890 " --> pdb=" O ALA E1886 " (cutoff:3.500A) Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1912 through 1928 Processing helix chain 'E' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR E1959 " --> pdb=" O VAL E1955 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP E1960 " --> pdb=" O MET E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU E2024 " --> pdb=" O PRO E2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E2032 " --> pdb=" O GLY E2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E2033 " --> pdb=" O MET E2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN E2035 " --> pdb=" O SER E2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E2062 " --> pdb=" O ASN E2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E2064 " --> pdb=" O ALA E2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E2065 " --> pdb=" O ALA E2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E2066 " --> pdb=" O GLU E2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP E2072 " --> pdb=" O LEU E2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E2083 " --> pdb=" O ASP E2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E2094 " --> pdb=" O ALA E2090 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN E2113 " --> pdb=" O ALA E2109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E2115 " --> pdb=" O GLU E2111 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2139 Processing helix chain 'E' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN E2170 " --> pdb=" O GLU E2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E2199 " --> pdb=" O GLN E2195 " (cutoff:3.500A) Processing helix chain 'E' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR E2251 " --> pdb=" O ASN E2247 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E2260 " --> pdb=" O GLY E2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E2268 " --> pdb=" O GLN E2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E2271 " --> pdb=" O ASP E2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E2272 " --> pdb=" O LEU E2268 " (cutoff:3.500A) Processing helix chain 'E' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU E2312 " --> pdb=" O GLU E2308 " (cutoff:3.500A) Processing helix chain 'E' and resid 2337 through 2342 Processing helix chain 'E' and resid 2352 through 2363 removed outlier: 3.720A pdb=" N ASP E2358 " --> pdb=" O ALA E2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E2362 " --> pdb=" O ASP E2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN E2363 " --> pdb=" O LYS E2359 " (cutoff:3.500A) Processing helix chain 'E' and resid 2398 through 2402 removed outlier: 3.601A pdb=" N TYR E2402 " --> pdb=" O ARG E2399 " (cutoff:3.500A) Processing helix chain 'E' and resid 2499 through 2503 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS A 299 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 307 " --> pdb=" O LYS A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR A 315 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 423 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 367 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 368 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 380 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 370 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 1096 through 1098 Processing sheet with id=AA6, first strand: chain 'A' and resid 1122 through 1123 Processing sheet with id=AA7, first strand: chain 'A' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS A1135 " --> pdb=" O ASN A1132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL A1161 " --> pdb=" O TYR A1168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR A1239 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A1244 " --> pdb=" O TYR A1239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG A1300 " --> pdb=" O LEU A1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1584 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1585 " --> pdb=" O GLN A1597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1310 through 1311 removed outlier: 3.928A pdb=" N ALA A1557 " --> pdb=" O GLY A1566 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A1566 " --> pdb=" O ALA A1557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1310 through 1311 Processing sheet with id=AB4, first strand: chain 'A' and resid 1331 through 1332 Processing sheet with id=AB5, first strand: chain 'A' and resid 1340 through 1345 removed outlier: 3.527A pdb=" N LYS A1343 " --> pdb=" O LYS A1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A1348 " --> pdb=" O ALA A1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A1353 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1443 through 1450 removed outlier: 3.755A pdb=" N ASN A1449 " --> pdb=" O SER A1432 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A1432 " --> pdb=" O ASN A1449 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A1388 " --> pdb=" O PRO A1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A1488 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1386 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A1490 " --> pdb=" O LYS A1384 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A1384 " --> pdb=" O ASN A1490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1633 through 1635 Processing sheet with id=AB8, first strand: chain 'A' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE A1686 " --> pdb=" O ILE A1647 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A1642 " --> pdb=" O LEU A1750 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A1746 " --> pdb=" O VAL A1646 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1673 through 1680 removed outlier: 6.377A pdb=" N LEU A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A1678 " --> pdb=" O PHE A1661 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A1661 " --> pdb=" O SER A1678 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2144 through 2146 Processing sheet with id=AC2, first strand: chain 'A' and resid 2148 through 2150 Processing sheet with id=AC3, first strand: chain 'A' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE A2508 " --> pdb=" O VAL A2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A2417 " --> pdb=" O ILE A2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS A2510 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A2415 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A2512 " --> pdb=" O LYS A2413 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2369 through 2370 removed outlier: 3.717A pdb=" N SER A2370 " --> pdb=" O ASN A2373 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A2374 " --> pdb=" O SER A2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A2431 " --> pdb=" O VAL A2450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS B 299 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 307 " --> pdb=" O LYS B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR B 315 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 423 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 367 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 368 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 380 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 370 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 341 through 347 Processing sheet with id=AC9, first strand: chain 'B' and resid 1096 through 1098 Processing sheet with id=AD1, first strand: chain 'B' and resid 1122 through 1123 Processing sheet with id=AD2, first strand: chain 'B' and resid 1131 through 1132 removed outlier: 3.567A pdb=" N LYS B1135 " --> pdb=" O ASN B1132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL B1161 " --> pdb=" O TYR B1168 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1233 through 1239 removed outlier: 3.663A pdb=" N TYR B1239 " --> pdb=" O THR B1244 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B1244 " --> pdb=" O TYR B1239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG B1300 " --> pdb=" O LEU B1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B1584 " --> pdb=" O VAL B1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B1585 " --> pdb=" O GLN B1597 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA B1557 " --> pdb=" O GLY B1566 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY B1566 " --> pdb=" O ALA B1557 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1310 through 1311 Processing sheet with id=AD8, first strand: chain 'B' and resid 1331 through 1332 Processing sheet with id=AD9, first strand: chain 'B' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS B1343 " --> pdb=" O LYS B1350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B1348 " --> pdb=" O ALA B1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B1353 " --> pdb=" O LEU B1535 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1443 through 1450 removed outlier: 3.755A pdb=" N ASN B1449 " --> pdb=" O SER B1432 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B1432 " --> pdb=" O ASN B1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR B1388 " --> pdb=" O PRO B1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B1488 " --> pdb=" O ILE B1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B1386 " --> pdb=" O GLU B1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN B1490 " --> pdb=" O LYS B1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS B1384 " --> pdb=" O ASN B1490 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1633 through 1635 Processing sheet with id=AE3, first strand: chain 'B' and resid 1686 through 1693 removed outlier: 3.522A pdb=" N ILE B1686 " --> pdb=" O ILE B1647 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR B1642 " --> pdb=" O LEU B1750 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B1746 " --> pdb=" O VAL B1646 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU B1663 " --> pdb=" O ILE B1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B1678 " --> pdb=" O PHE B1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE B1661 " --> pdb=" O SER B1678 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2148 through 2150 Processing sheet with id=AE6, first strand: chain 'B' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE B2508 " --> pdb=" O VAL B2417 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B2417 " --> pdb=" O ILE B2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS B2510 " --> pdb=" O ILE B2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B2415 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B2512 " --> pdb=" O LYS B2413 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 2369 through 2370 removed outlier: 3.719A pdb=" N SER B2370 " --> pdb=" O ASN B2373 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B2373 " --> pdb=" O SER B2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B2374 " --> pdb=" O SER B2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B2431 " --> pdb=" O VAL B2450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AE9, first strand: chain 'C' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS C 299 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 307 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR C 315 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 423 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 367 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 368 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 370 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 341 through 347 Processing sheet with id=AF3, first strand: chain 'C' and resid 1096 through 1098 Processing sheet with id=AF4, first strand: chain 'C' and resid 1122 through 1123 Processing sheet with id=AF5, first strand: chain 'C' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS C1135 " --> pdb=" O ASN C1132 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL C1161 " --> pdb=" O TYR C1168 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR C1239 " --> pdb=" O THR C1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C1244 " --> pdb=" O TYR C1239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG C1300 " --> pdb=" O LEU C1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU C1584 " --> pdb=" O VAL C1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C1585 " --> pdb=" O GLN C1597 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA C1557 " --> pdb=" O GLY C1566 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY C1566 " --> pdb=" O ALA C1557 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1310 through 1311 Processing sheet with id=AG2, first strand: chain 'C' and resid 1331 through 1332 Processing sheet with id=AG3, first strand: chain 'C' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS C1343 " --> pdb=" O LYS C1350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C1348 " --> pdb=" O ALA C1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C1353 " --> pdb=" O LEU C1535 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1443 through 1450 removed outlier: 3.757A pdb=" N ASN C1449 " --> pdb=" O SER C1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER C1432 " --> pdb=" O ASN C1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C1388 " --> pdb=" O PRO C1486 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU C1488 " --> pdb=" O ILE C1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C1386 " --> pdb=" O GLU C1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN C1490 " --> pdb=" O LYS C1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C1384 " --> pdb=" O ASN C1490 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1633 through 1635 Processing sheet with id=AG6, first strand: chain 'C' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE C1686 " --> pdb=" O ILE C1647 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR C1642 " --> pdb=" O LEU C1750 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C1746 " --> pdb=" O VAL C1646 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU C1663 " --> pdb=" O ILE C1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C1678 " --> pdb=" O PHE C1661 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE C1661 " --> pdb=" O SER C1678 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 2148 through 2150 Processing sheet with id=AG9, first strand: chain 'C' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE C2508 " --> pdb=" O VAL C2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C2417 " --> pdb=" O ILE C2508 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS C2510 " --> pdb=" O ILE C2415 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C2415 " --> pdb=" O HIS C2510 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C2512 " --> pdb=" O LYS C2413 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 2369 through 2370 removed outlier: 3.717A pdb=" N SER C2370 " --> pdb=" O ASN C2373 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C2373 " --> pdb=" O SER C2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C2374 " --> pdb=" O SER C2390 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C2431 " --> pdb=" O VAL C2450 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AH3, first strand: chain 'D' and resid 299 through 300 removed outlier: 4.209A pdb=" N LYS D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 307 " --> pdb=" O LYS D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'D' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR D 315 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 423 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 367 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 368 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D 380 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 370 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 341 through 347 Processing sheet with id=AH6, first strand: chain 'D' and resid 1096 through 1098 Processing sheet with id=AH7, first strand: chain 'D' and resid 1122 through 1123 Processing sheet with id=AH8, first strand: chain 'D' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS D1135 " --> pdb=" O ASN D1132 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL D1161 " --> pdb=" O TYR D1168 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 1233 through 1239 removed outlier: 3.663A pdb=" N TYR D1239 " --> pdb=" O THR D1244 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D1244 " --> pdb=" O TYR D1239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG D1300 " --> pdb=" O LEU D1586 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D1584 " --> pdb=" O VAL D1302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D1585 " --> pdb=" O GLN D1597 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA D1557 " --> pdb=" O GLY D1566 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY D1566 " --> pdb=" O ALA D1557 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 1310 through 1311 Processing sheet with id=AI5, first strand: chain 'D' and resid 1331 through 1332 Processing sheet with id=AI6, first strand: chain 'D' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS D1343 " --> pdb=" O LYS D1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D1348 " --> pdb=" O ALA D1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D1353 " --> pdb=" O LEU D1535 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 1443 through 1450 removed outlier: 3.756A pdb=" N ASN D1449 " --> pdb=" O SER D1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER D1432 " --> pdb=" O ASN D1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR D1388 " --> pdb=" O PRO D1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU D1488 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D1386 " --> pdb=" O GLU D1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN D1490 " --> pdb=" O LYS D1384 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS D1384 " --> pdb=" O ASN D1490 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 1633 through 1635 Processing sheet with id=AI9, first strand: chain 'D' and resid 1686 through 1693 removed outlier: 3.522A pdb=" N ILE D1686 " --> pdb=" O ILE D1647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D1642 " --> pdb=" O LEU D1750 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D1746 " --> pdb=" O VAL D1646 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 1673 through 1680 removed outlier: 6.375A pdb=" N LEU D1663 " --> pdb=" O ILE D1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D1678 " --> pdb=" O PHE D1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE D1661 " --> pdb=" O SER D1678 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 2148 through 2150 Processing sheet with id=AJ3, first strand: chain 'D' and resid 2329 through 2336 removed outlier: 6.705A pdb=" N ILE D2508 " --> pdb=" O VAL D2417 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D2417 " --> pdb=" O ILE D2508 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS D2510 " --> pdb=" O ILE D2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D2415 " --> pdb=" O HIS D2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG D2512 " --> pdb=" O LYS D2413 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 2369 through 2370 removed outlier: 3.718A pdb=" N SER D2370 " --> pdb=" O ASN D2373 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D2373 " --> pdb=" O SER D2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D2374 " --> pdb=" O SER D2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D2431 " --> pdb=" O VAL D2450 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AJ6, first strand: chain 'E' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS E 299 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 307 " --> pdb=" O LYS E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'E' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR E 315 " --> pdb=" O TYR E 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 423 " --> pdb=" O THR E 335 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 367 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU E 368 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG E 380 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 370 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 341 through 347 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1096 through 1098 Processing sheet with id=AK1, first strand: chain 'E' and resid 1122 through 1123 Processing sheet with id=AK2, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS E1135 " --> pdb=" O ASN E1132 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL E1161 " --> pdb=" O TYR E1168 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR E1239 " --> pdb=" O THR E1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E1244 " --> pdb=" O TYR E1239 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG E1300 " --> pdb=" O LEU E1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E1584 " --> pdb=" O VAL E1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E1585 " --> pdb=" O GLN E1597 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA E1557 " --> pdb=" O GLY E1566 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY E1566 " --> pdb=" O ALA E1557 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 1310 through 1311 Processing sheet with id=AK8, first strand: chain 'E' and resid 1331 through 1332 Processing sheet with id=AK9, first strand: chain 'E' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS E1343 " --> pdb=" O LYS E1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E1348 " --> pdb=" O ALA E1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E1353 " --> pdb=" O LEU E1535 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 1443 through 1450 removed outlier: 3.756A pdb=" N ASN E1449 " --> pdb=" O SER E1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E1432 " --> pdb=" O ASN E1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR E1388 " --> pdb=" O PRO E1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU E1488 " --> pdb=" O ILE E1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE E1386 " --> pdb=" O GLU E1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN E1490 " --> pdb=" O LYS E1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS E1384 " --> pdb=" O ASN E1490 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'E' and resid 1633 through 1635 Processing sheet with id=AL3, first strand: chain 'E' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE E1686 " --> pdb=" O ILE E1647 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR E1642 " --> pdb=" O LEU E1750 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER E1746 " --> pdb=" O VAL E1646 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU E1663 " --> pdb=" O ILE E1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER E1678 " --> pdb=" O PHE E1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE E1661 " --> pdb=" O SER E1678 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'E' and resid 2329 through 2336 removed outlier: 6.705A pdb=" N ILE E2508 " --> pdb=" O VAL E2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL E2417 " --> pdb=" O ILE E2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS E2510 " --> pdb=" O ILE E2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE E2415 " --> pdb=" O HIS E2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG E2512 " --> pdb=" O LYS E2413 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'E' and resid 2369 through 2370 removed outlier: 3.718A pdb=" N SER E2370 " --> pdb=" O ASN E2373 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E2373 " --> pdb=" O SER E2370 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E2374 " --> pdb=" O SER E2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E2431 " --> pdb=" O VAL E2450 " (cutoff:3.500A) 4646 hydrogen bonds defined for protein. 13383 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: 64.16 Time building geometry restraints manager: 32.30 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: 31887 1.34 - 1.46: 17934 1.46 - 1.58: 49104 1.58 - 1.69: 0 1.69 - 1.81: 570 Bond restraints: 99495 Sorted by residual: bond pdb=" C THR B 198 " pdb=" N PRO B 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.51e+00 bond pdb=" C THR D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.38e+00 bond pdb=" C THR E 198 " pdb=" N PRO E 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.35e+00 bond pdb=" C THR A 198 " pdb=" N PRO A 199 " ideal model delta sigma weight residual 1.334 1.401 -0.068 2.34e-02 1.83e+03 8.34e+00 bond pdb=" C THR C 198 " pdb=" N PRO C 199 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.20e+00 ... (remaining 99490 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.63: 1790 105.63 - 112.74: 51061 112.74 - 119.84: 34597 119.84 - 126.95: 46476 126.95 - 134.06: 1216 Bond angle restraints: 135140 Sorted by residual: angle pdb=" C THR A2381 " pdb=" N ASP A2382 " pdb=" CA ASP A2382 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C THR C2381 " pdb=" N ASP C2382 " pdb=" CA ASP C2382 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C THR D2381 " pdb=" N ASP D2382 " pdb=" CA ASP D2382 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C THR B2381 " pdb=" N ASP B2382 " pdb=" CA ASP B2382 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C THR E2381 " pdb=" N ASP E2382 " pdb=" CA ASP E2382 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 ... (remaining 135135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 58164 17.07 - 34.15: 1160 34.15 - 51.22: 261 51.22 - 68.30: 15 68.30 - 85.37: 45 Dihedral angle restraints: 59645 sinusoidal: 23510 harmonic: 36135 Sorted by residual: dihedral pdb=" CA THR A 521 " pdb=" C THR A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA THR C 521 " pdb=" C THR C 521 " pdb=" N PRO C 522 " pdb=" CA PRO C 522 " ideal model delta harmonic sigma weight residual 180.00 137.11 42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CA THR E 521 " pdb=" C THR E 521 " pdb=" N PRO E 522 " pdb=" CA PRO E 522 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.36e+01 ... (remaining 59642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 12819 0.065 - 0.131: 1922 0.131 - 0.196: 169 0.196 - 0.262: 42 0.262 - 0.327: 8 Chirality restraints: 14960 Sorted by residual: chirality pdb=" CB THR B 521 " pdb=" CA THR B 521 " pdb=" OG1 THR B 521 " pdb=" CG2 THR B 521 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB THR E 521 " pdb=" CA THR E 521 " pdb=" OG1 THR E 521 " pdb=" CG2 THR E 521 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB THR C 521 " pdb=" CA THR C 521 " pdb=" OG1 THR C 521 " pdb=" CG2 THR C 521 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 14957 not shown) Planarity restraints: 17580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 521 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO B 522 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 521 " -0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO D 522 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 522 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 521 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO C 522 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 522 " -0.049 5.00e-02 4.00e+02 ... (remaining 17577 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 11611 2.75 - 3.29: 89861 3.29 - 3.83: 159845 3.83 - 4.36: 199333 4.36 - 4.90: 340218 Nonbonded interactions: 800868 Sorted by model distance: nonbonded pdb=" O PRO B 194 " pdb=" OH TYR B 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO D 194 " pdb=" OH TYR D 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO A 194 " pdb=" OH TYR A 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO E 194 " pdb=" OH TYR E 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO C 194 " pdb=" OH TYR C 285 " model vdw 2.217 2.440 ... (remaining 800863 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.080 Extract box with map and model: 15.380 Check model and map are aligned: 1.160 Set scattering table: 0.690 Process input model: 233.120 Find NCS groups from input model: 4.770 Set up NCS constraints: 0.440 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 263.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.004 0.068 99495 Z= 0.253 Angle : 0.778 13.778 135140 Z= 0.432 Chirality : 0.048 0.327 14960 Planarity : 0.006 0.088 17580 Dihedral : 8.537 85.369 36385 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.86 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.06), residues: 12240 helix: -4.32 (0.03), residues: 5410 sheet: -1.24 (0.11), residues: 2005 loop : -2.20 (0.07), residues: 4825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B1827 HIS 0.012 0.002 HIS E1888 PHE 0.036 0.002 PHE D1532 TYR 0.043 0.003 TYR E1239 ARG 0.008 0.001 ARG A2189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2681 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2676 time to evaluate : 8.889 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 2681 average time/residue: 0.9763 time to fit residues: 4366.5724 Evaluate side-chains 1284 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1284 time to evaluate : 8.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.6376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1034 optimal weight: 0.5980 chunk 928 optimal weight: 3.9990 chunk 515 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 626 optimal weight: 0.8980 chunk 496 optimal weight: 4.9990 chunk 960 optimal weight: 0.8980 chunk 371 optimal weight: 0.1980 chunk 583 optimal weight: 0.2980 chunk 714 optimal weight: 3.9990 chunk 1112 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS A 340 GLN A 511 GLN A 587 ASN A 618 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A 858 HIS A 875 ASN A 914 GLN A1043 ASN A1189 GLN A1229 ASN A1240 GLN A1531 GLN A1543 ASN A1630 GLN A1674 HIS A1843 HIS ** A2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 ASN A2348 ASN A2452 HIS A2459 GLN B 56 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 102 GLN B 130 HIS B 587 ASN B 749 GLN B 875 ASN B1090 ASN B1180 GLN B1293 GLN B1304 ASN B1373 ASN B1531 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 GLN B1843 HIS B1919 HIS B2285 ASN B2348 ASN B2373 ASN B2459 GLN B2497 GLN C 94 ASN C 102 GLN C 130 HIS C 302 ASN C 556 ASN C 587 ASN ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 834 GLN C 848 GLN C 858 HIS C 875 ASN C1090 ASN C1180 GLN C1293 GLN C1304 ASN C1373 ASN C1413 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1531 GLN C1543 ASN C1630 GLN C1674 HIS C1764 ASN C1785 HIS C1812 GLN C1815 GLN C1843 HIS C2042 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2205 GLN C2242 GLN ** C2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2285 ASN C2348 ASN C2459 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2505 ASN D 130 HIS D 206 ASN D 373 ASN D 587 ASN D 618 ASN D 834 GLN D 848 GLN D 858 HIS D1103 ASN D1189 GLN D1293 GLN D1304 ASN D1373 ASN D1509 GLN D1531 GLN D1674 HIS D1701 GLN D1764 ASN D1972 HIS D2035 GLN D2348 ASN D2452 HIS D2459 GLN E 130 HIS E 514 GLN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 ASN E 618 ASN E 761 GLN E 772 ASN E 834 GLN E 848 GLN E 858 HIS E 875 ASN E1180 GLN E1293 GLN E1304 ASN E1373 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1418 ASN E1425 HIS E1531 GLN E1543 ASN E1589 ASN E1674 HIS E1787 GLN E1808 HIS E1810 GLN E1812 GLN E1843 HIS E1928 GLN E1951 GLN E2035 GLN ** E2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 99495 Z= 0.158 Angle : 0.518 8.653 135140 Z= 0.278 Chirality : 0.041 0.322 14960 Planarity : 0.005 0.075 17580 Dihedral : 4.648 38.721 13370 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.28 % Allowed : 6.57 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.06 (0.07), residues: 12240 helix: -1.27 (0.06), residues: 5530 sheet: -0.66 (0.11), residues: 1980 loop : -1.59 (0.08), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E1598 HIS 0.006 0.001 HIS A 767 PHE 0.017 0.001 PHE E 937 TYR 0.021 0.001 TYR E1239 ARG 0.006 0.000 ARG D1659 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1500 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1366 time to evaluate : 8.781 Fit side-chains revert: symmetry clash outliers start: 134 outliers final: 71 residues processed: 1455 average time/residue: 0.9219 time to fit residues: 2309.0374 Evaluate side-chains 1133 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1062 time to evaluate : 8.914 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.7497 time to fit residues: 112.6529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 618 optimal weight: 6.9990 chunk 345 optimal weight: 0.9980 chunk 925 optimal weight: 2.9990 chunk 757 optimal weight: 0.6980 chunk 306 optimal weight: 0.5980 chunk 1114 optimal weight: 3.9990 chunk 1203 optimal weight: 0.5980 chunk 992 optimal weight: 1.9990 chunk 1105 optimal weight: 3.9990 chunk 379 optimal weight: 4.9990 chunk 894 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1781 GLN A1916 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 212 GLN B 340 GLN B 520 ASN B 709 HIS B 749 GLN ** B1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 GLN B1781 GLN C 94 ASN C 302 ASN C 709 HIS C1016 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 ASN C1334 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1680 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 206 ASN D 709 HIS D 834 GLN D 969 GLN D1152 ASN D1367 GLN D1397 ASN D1701 GLN D1781 GLN D1785 HIS D1843 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN E 94 ASN E 222 ASN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 587 ASN E 761 GLN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1764 ASN E1810 GLN E2230 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 99495 Z= 0.200 Angle : 0.505 8.060 135140 Z= 0.265 Chirality : 0.041 0.313 14960 Planarity : 0.004 0.064 17580 Dihedral : 4.376 34.817 13370 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.96 % Allowed : 7.76 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.07), residues: 12240 helix: 0.52 (0.07), residues: 5535 sheet: -0.36 (0.11), residues: 2100 loop : -1.31 (0.08), residues: 4605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D1437 HIS 0.007 0.001 HIS A1888 PHE 0.019 0.001 PHE B 937 TYR 0.022 0.001 TYR E 103 ARG 0.006 0.001 ARG C 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1130 time to evaluate : 9.088 Fit side-chains outliers start: 101 outliers final: 57 residues processed: 1194 average time/residue: 0.9429 time to fit residues: 1943.3844 Evaluate side-chains 1063 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1006 time to evaluate : 8.822 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.7690 time to fit residues: 93.4160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1101 optimal weight: 0.6980 chunk 837 optimal weight: 0.4980 chunk 578 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 531 optimal weight: 0.7980 chunk 748 optimal weight: 0.2980 chunk 1118 optimal weight: 2.9990 chunk 1184 optimal weight: 1.9990 chunk 584 optimal weight: 4.9990 chunk 1060 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1068 GLN A1240 GLN A1808 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1812 GLN C 302 ASN C1016 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1152 ASN D1413 ASN D1588 HIS D2452 HIS ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN E2348 ASN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 99495 Z= 0.151 Angle : 0.460 9.962 135140 Z= 0.242 Chirality : 0.040 0.231 14960 Planarity : 0.003 0.063 17580 Dihedral : 4.154 31.665 13370 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.84 % Allowed : 8.34 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.08), residues: 12240 helix: 1.33 (0.07), residues: 5525 sheet: -0.34 (0.11), residues: 2180 loop : -1.04 (0.09), residues: 4535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1437 HIS 0.005 0.001 HIS D1888 PHE 0.018 0.001 PHE B 937 TYR 0.016 0.001 TYR D2262 ARG 0.008 0.000 ARG D 806 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1082 time to evaluate : 8.854 Fit side-chains outliers start: 88 outliers final: 42 residues processed: 1129 average time/residue: 0.9390 time to fit residues: 1833.7293 Evaluate side-chains 1049 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1007 time to evaluate : 8.824 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.7102 time to fit residues: 69.4198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 986 optimal weight: 0.4980 chunk 672 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 881 optimal weight: 0.0060 chunk 488 optimal weight: 2.9990 chunk 1010 optimal weight: 0.9990 chunk 818 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 604 optimal weight: 4.9990 chunk 1062 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A1007 ASN A1304 ASN A1674 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B1373 ASN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN C1293 GLN C1425 HIS ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1152 ASN D1701 GLN D1785 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1752 ASN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 99495 Z= 0.242 Angle : 0.506 9.862 135140 Z= 0.263 Chirality : 0.042 0.375 14960 Planarity : 0.003 0.063 17580 Dihedral : 4.271 33.187 13370 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.75 % Allowed : 8.68 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.08), residues: 12240 helix: 1.54 (0.07), residues: 5530 sheet: -0.11 (0.11), residues: 2135 loop : -0.96 (0.09), residues: 4575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1437 HIS 0.008 0.001 HIS A1888 PHE 0.027 0.001 PHE E 937 TYR 0.024 0.001 TYR B 968 ARG 0.009 0.000 ARG D1659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1059 time to evaluate : 8.969 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 38 residues processed: 1106 average time/residue: 0.9515 time to fit residues: 1820.4663 Evaluate side-chains 1018 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 980 time to evaluate : 8.860 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.7241 time to fit residues: 64.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 398 optimal weight: 3.9990 chunk 1066 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 695 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 1185 optimal weight: 0.5980 chunk 983 optimal weight: 3.9990 chunk 548 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 622 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1003 ASN A1007 ASN A1180 GLN ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2298 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN C1252 GLN C1334 ASN C1373 ASN C2427 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1007 ASN D1520 GLN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 904 GLN E1373 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2348 ASN E2497 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 99495 Z= 0.225 Angle : 0.492 10.018 135140 Z= 0.257 Chirality : 0.041 0.287 14960 Planarity : 0.003 0.065 17580 Dihedral : 4.248 33.379 13370 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.67 % Allowed : 9.21 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.08), residues: 12240 helix: 1.66 (0.07), residues: 5570 sheet: -0.04 (0.11), residues: 2135 loop : -0.86 (0.09), residues: 4535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1437 HIS 0.007 0.001 HIS A1888 PHE 0.021 0.001 PHE B 937 TYR 0.021 0.001 TYR B 968 ARG 0.008 0.000 ARG D1659 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1023 time to evaluate : 8.917 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 32 residues processed: 1060 average time/residue: 0.9812 time to fit residues: 1803.1663 Evaluate side-chains 993 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 961 time to evaluate : 9.765 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.7364 time to fit residues: 57.0708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1142 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 675 optimal weight: 2.9990 chunk 865 optimal weight: 3.9990 chunk 670 optimal weight: 0.6980 chunk 997 optimal weight: 0.8980 chunk 661 optimal weight: 1.9990 chunk 1180 optimal weight: 0.6980 chunk 738 optimal weight: 0.0040 chunk 719 optimal weight: 2.9990 chunk 545 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1007 ASN A1394 ASN ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN D 749 GLN D1007 ASN D1152 ASN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2041 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 99495 Z= 0.151 Angle : 0.457 9.992 135140 Z= 0.239 Chirality : 0.040 0.293 14960 Planarity : 0.003 0.062 17580 Dihedral : 4.073 32.541 13370 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.41 % Allowed : 9.73 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 12240 helix: 1.92 (0.07), residues: 5575 sheet: 0.03 (0.11), residues: 2165 loop : -0.76 (0.09), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1437 HIS 0.005 0.001 HIS E1888 PHE 0.028 0.001 PHE E 937 TYR 0.014 0.001 TYR C2262 ARG 0.007 0.000 ARG A2153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1029 time to evaluate : 9.028 Fit side-chains outliers start: 43 outliers final: 19 residues processed: 1054 average time/residue: 0.9450 time to fit residues: 1725.6687 Evaluate side-chains 989 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 970 time to evaluate : 8.805 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.8092 time to fit residues: 39.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 730 optimal weight: 2.9990 chunk 471 optimal weight: 7.9990 chunk 705 optimal weight: 0.6980 chunk 355 optimal weight: 0.6980 chunk 232 optimal weight: 6.9990 chunk 228 optimal weight: 0.6980 chunk 750 optimal weight: 2.9990 chunk 804 optimal weight: 0.8980 chunk 583 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 928 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: