Starting phenix.real_space_refine on Fri Dec 8 17:16:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j03_5138/12_2023/3j03_5138.pdb" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.043 sd= 0.182 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 384 5.16 5 C 36352 2.51 5 N 10160 2.21 5 O 11744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 2724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 3215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 3706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 4197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 5179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 5670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 6149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 6161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 6652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 7131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 7143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 7622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 7634": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 58640 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "B" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "C" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "D" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "E" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "F" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "G" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "H" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "I" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "J" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "K" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "L" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "M" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "N" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "O" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "P" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3665 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Time building chain proxies: 22.66, per 1000 atoms: 0.39 Number of scatterers: 58640 At special positions: 0 Unit cell: (174.23, 174.23, 160.93, 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 384 16.00 O 11744 8.00 N 10160 7.00 C 36352 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: 17.99 Conformation dependent library (CDL) restraints added in 8.4 seconds 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14528 Finding SS restraints... Secondary structure from input PDB file: 352 helices and 80 sheets defined 60.3% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 66 through 83 Processing helix chain 'A' and resid 86 through 107 removed outlier: 3.580A pdb=" N VAL A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 removed outlier: 3.566A pdb=" N GLU A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.819A pdb=" N LYS A 159 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 4.229A pdb=" N ASP A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.577A pdb=" N VAL A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 282 through 294 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 345 through 369 Processing helix chain 'A' and resid 377 through 395 removed outlier: 3.843A pdb=" N GLU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 removed outlier: 4.059A pdb=" N ALA A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 439 removed outlier: 3.688A pdb=" N ALA A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 483 Processing helix chain 'B' and resid 502 through 521 Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 557 through 574 Processing helix chain 'B' and resid 577 through 598 removed outlier: 3.579A pdb=" N VAL B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU B 594 " --> pdb=" O ARG B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 624 removed outlier: 3.566A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.819A pdb=" N LYS B 650 " --> pdb=" O GLY B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 668 removed outlier: 4.229A pdb=" N ASP B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 676 No H-bonds generated for 'chain 'B' and resid 674 through 676' Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 728 through 742 removed outlier: 3.578A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 764 Processing helix chain 'B' and resid 773 through 785 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 836 through 860 Processing helix chain 'B' and resid 868 through 886 removed outlier: 3.842A pdb=" N GLU B 883 " --> pdb=" O ARG B 879 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 900 removed outlier: 4.059A pdb=" N ALA B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 912 Processing helix chain 'B' and resid 914 through 930 removed outlier: 3.688A pdb=" N ALA B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 974 Processing helix chain 'C' and resid 993 through 1012 Processing helix chain 'C' and resid 1013 through 1015 No H-bonds generated for 'chain 'C' and resid 1013 through 1015' Processing helix chain 'C' and resid 1036 through 1044 Processing helix chain 'C' and resid 1048 through 1065 Processing helix chain 'C' and resid 1068 through 1089 removed outlier: 3.579A pdb=" N VAL C1075 " --> pdb=" O THR C1071 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU C1085 " --> pdb=" O ARG C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1115 removed outlier: 3.567A pdb=" N GLU C1109 " --> pdb=" O GLN C1105 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1135 Processing helix chain 'C' and resid 1137 through 1141 removed outlier: 3.821A pdb=" N LYS C1141 " --> pdb=" O GLY C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1159 removed outlier: 4.228A pdb=" N ASP C1159 " --> pdb=" O SER C1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1167 No H-bonds generated for 'chain 'C' and resid 1165 through 1167' Processing helix chain 'C' and resid 1178 through 1182 Processing helix chain 'C' and resid 1219 through 1233 removed outlier: 3.579A pdb=" N VAL C1227 " --> pdb=" O LEU C1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 1245 through 1255 Processing helix chain 'C' and resid 1264 through 1276 Processing helix chain 'C' and resid 1282 through 1286 Processing helix chain 'C' and resid 1287 through 1291 Processing helix chain 'C' and resid 1327 through 1351 Processing helix chain 'C' and resid 1359 through 1377 removed outlier: 3.842A pdb=" N GLU C1374 " --> pdb=" O ARG C1370 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C1375 " --> pdb=" O GLU C1371 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1391 removed outlier: 4.059A pdb=" N ALA C1383 " --> pdb=" O ARG C1379 " (cutoff:3.500A) Processing helix chain 'C' and resid 1392 through 1403 Processing helix chain 'C' and resid 1405 through 1421 removed outlier: 3.688A pdb=" N ALA C1415 " --> pdb=" O VAL C1411 " (cutoff:3.500A) Processing helix chain 'C' and resid 1446 through 1465 Processing helix chain 'D' and resid 1484 through 1503 Processing helix chain 'D' and resid 1504 through 1506 No H-bonds generated for 'chain 'D' and resid 1504 through 1506' Processing helix chain 'D' and resid 1527 through 1535 Processing helix chain 'D' and resid 1539 through 1556 Processing helix chain 'D' and resid 1559 through 1580 removed outlier: 3.580A pdb=" N VAL D1566 " --> pdb=" O THR D1562 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D1576 " --> pdb=" O ARG D1572 " (cutoff:3.500A) Processing helix chain 'D' and resid 1583 through 1606 removed outlier: 3.567A pdb=" N GLU D1600 " --> pdb=" O GLN D1596 " (cutoff:3.500A) Processing helix chain 'D' and resid 1613 through 1626 Processing helix chain 'D' and resid 1628 through 1632 removed outlier: 3.820A pdb=" N LYS D1632 " --> pdb=" O GLY D1629 " (cutoff:3.500A) Processing helix chain 'D' and resid 1633 through 1650 removed outlier: 4.230A pdb=" N ASP D1650 " --> pdb=" O SER D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1658 No H-bonds generated for 'chain 'D' and resid 1656 through 1658' Processing helix chain 'D' and resid 1669 through 1673 Processing helix chain 'D' and resid 1710 through 1724 removed outlier: 3.579A pdb=" N VAL D1718 " --> pdb=" O LEU D1714 " (cutoff:3.500A) Processing helix chain 'D' and resid 1736 through 1746 Processing helix chain 'D' and resid 1755 through 1767 Processing helix chain 'D' and resid 1773 through 1777 Processing helix chain 'D' and resid 1778 through 1782 Processing helix chain 'D' and resid 1818 through 1842 Processing helix chain 'D' and resid 1850 through 1868 removed outlier: 3.843A pdb=" N GLU D1865 " --> pdb=" O ARG D1861 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D1866 " --> pdb=" O GLU D1862 " (cutoff:3.500A) Processing helix chain 'D' and resid 1870 through 1882 removed outlier: 4.060A pdb=" N ALA D1874 " --> pdb=" O ARG D1870 " (cutoff:3.500A) Processing helix chain 'D' and resid 1883 through 1894 Processing helix chain 'D' and resid 1896 through 1912 removed outlier: 3.688A pdb=" N ALA D1906 " --> pdb=" O VAL D1902 " (cutoff:3.500A) Processing helix chain 'D' and resid 1937 through 1956 Processing helix chain 'E' and resid 1975 through 1994 Processing helix chain 'E' and resid 1995 through 1997 No H-bonds generated for 'chain 'E' and resid 1995 through 1997' Processing helix chain 'E' and resid 2018 through 2026 Processing helix chain 'E' and resid 2030 through 2047 Processing helix chain 'E' and resid 2050 through 2071 removed outlier: 3.579A pdb=" N VAL E2057 " --> pdb=" O THR E2053 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E2067 " --> pdb=" O ARG E2063 " (cutoff:3.500A) Processing helix chain 'E' and resid 2074 through 2097 removed outlier: 3.567A pdb=" N GLU E2091 " --> pdb=" O GLN E2087 " (cutoff:3.500A) Processing helix chain 'E' and resid 2104 through 2117 Processing helix chain 'E' and resid 2119 through 2123 removed outlier: 3.821A pdb=" N LYS E2123 " --> pdb=" O GLY E2120 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2141 removed outlier: 4.229A pdb=" N ASP E2141 " --> pdb=" O SER E2137 " (cutoff:3.500A) Processing helix chain 'E' and resid 2147 through 2149 No H-bonds generated for 'chain 'E' and resid 2147 through 2149' Processing helix chain 'E' and resid 2160 through 2164 Processing helix chain 'E' and resid 2201 through 2215 removed outlier: 3.578A pdb=" N VAL E2209 " --> pdb=" O LEU E2205 " (cutoff:3.500A) Processing helix chain 'E' and resid 2227 through 2237 Processing helix chain 'E' and resid 2246 through 2258 Processing helix chain 'E' and resid 2264 through 2268 Processing helix chain 'E' and resid 2269 through 2273 Processing helix chain 'E' and resid 2309 through 2333 Processing helix chain 'E' and resid 2341 through 2359 removed outlier: 3.842A pdb=" N GLU E2356 " --> pdb=" O ARG E2352 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E2357 " --> pdb=" O GLU E2353 " (cutoff:3.500A) Processing helix chain 'E' and resid 2361 through 2373 removed outlier: 4.059A pdb=" N ALA E2365 " --> pdb=" O ARG E2361 " (cutoff:3.500A) Processing helix chain 'E' and resid 2374 through 2385 Processing helix chain 'E' and resid 2387 through 2403 removed outlier: 3.688A pdb=" N ALA E2397 " --> pdb=" O VAL E2393 " (cutoff:3.500A) Processing helix chain 'E' and resid 2428 through 2447 Processing helix chain 'F' and resid 2466 through 2485 Processing helix chain 'F' and resid 2486 through 2488 No H-bonds generated for 'chain 'F' and resid 2486 through 2488' Processing helix chain 'F' and resid 2509 through 2517 Processing helix chain 'F' and resid 2521 through 2538 Processing helix chain 'F' and resid 2541 through 2562 removed outlier: 3.579A pdb=" N VAL F2548 " --> pdb=" O THR F2544 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU F2558 " --> pdb=" O ARG F2554 " (cutoff:3.500A) Processing helix chain 'F' and resid 2565 through 2588 removed outlier: 3.566A pdb=" N GLU F2582 " --> pdb=" O GLN F2578 " (cutoff:3.500A) Processing helix chain 'F' and resid 2595 through 2608 Processing helix chain 'F' and resid 2610 through 2614 removed outlier: 3.820A pdb=" N LYS F2614 " --> pdb=" O GLY F2611 " (cutoff:3.500A) Processing helix chain 'F' and resid 2615 through 2632 removed outlier: 4.229A pdb=" N ASP F2632 " --> pdb=" O SER F2628 " (cutoff:3.500A) Processing helix chain 'F' and resid 2638 through 2640 No H-bonds generated for 'chain 'F' and resid 2638 through 2640' Processing helix chain 'F' and resid 2651 through 2655 Processing helix chain 'F' and resid 2692 through 2706 removed outlier: 3.579A pdb=" N VAL F2700 " --> pdb=" O LEU F2696 " (cutoff:3.500A) Processing helix chain 'F' and resid 2718 through 2728 Processing helix chain 'F' and resid 2737 through 2749 Processing helix chain 'F' and resid 2755 through 2759 Processing helix chain 'F' and resid 2760 through 2764 Processing helix chain 'F' and resid 2800 through 2824 Processing helix chain 'F' and resid 2832 through 2850 removed outlier: 3.843A pdb=" N GLU F2847 " --> pdb=" O ARG F2843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY F2848 " --> pdb=" O GLU F2844 " (cutoff:3.500A) Processing helix chain 'F' and resid 2852 through 2864 removed outlier: 4.059A pdb=" N ALA F2856 " --> pdb=" O ARG F2852 " (cutoff:3.500A) Processing helix chain 'F' and resid 2865 through 2876 Processing helix chain 'F' and resid 2878 through 2894 removed outlier: 3.688A pdb=" N ALA F2888 " --> pdb=" O VAL F2884 " (cutoff:3.500A) Processing helix chain 'F' and resid 2919 through 2938 Processing helix chain 'G' and resid 2957 through 2976 Processing helix chain 'G' and resid 2977 through 2979 No H-bonds generated for 'chain 'G' and resid 2977 through 2979' Processing helix chain 'G' and resid 3000 through 3008 Processing helix chain 'G' and resid 3012 through 3029 Processing helix chain 'G' and resid 3032 through 3053 removed outlier: 3.579A pdb=" N VAL G3039 " --> pdb=" O THR G3035 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU G3049 " --> pdb=" O ARG G3045 " (cutoff:3.500A) Processing helix chain 'G' and resid 3056 through 3079 removed outlier: 3.566A pdb=" N GLU G3073 " --> pdb=" O GLN G3069 " (cutoff:3.500A) Processing helix chain 'G' and resid 3086 through 3099 Processing helix chain 'G' and resid 3101 through 3105 removed outlier: 3.820A pdb=" N LYS G3105 " --> pdb=" O GLY G3102 " (cutoff:3.500A) Processing helix chain 'G' and resid 3106 through 3123 removed outlier: 4.229A pdb=" N ASP G3123 " --> pdb=" O SER G3119 " (cutoff:3.500A) Processing helix chain 'G' and resid 3129 through 3131 No H-bonds generated for 'chain 'G' and resid 3129 through 3131' Processing helix chain 'G' and resid 3142 through 3146 Processing helix chain 'G' and resid 3183 through 3197 removed outlier: 3.577A pdb=" N VAL G3191 " --> pdb=" O LEU G3187 " (cutoff:3.500A) Processing helix chain 'G' and resid 3209 through 3219 Processing helix chain 'G' and resid 3228 through 3240 Processing helix chain 'G' and resid 3246 through 3250 Processing helix chain 'G' and resid 3251 through 3255 Processing helix chain 'G' and resid 3291 through 3315 Processing helix chain 'G' and resid 3323 through 3341 removed outlier: 3.843A pdb=" N GLU G3338 " --> pdb=" O ARG G3334 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY G3339 " --> pdb=" O GLU G3335 " (cutoff:3.500A) Processing helix chain 'G' and resid 3343 through 3355 removed outlier: 4.058A pdb=" N ALA G3347 " --> pdb=" O ARG G3343 " (cutoff:3.500A) Processing helix chain 'G' and resid 3356 through 3367 Processing helix chain 'G' and resid 3369 through 3385 removed outlier: 3.688A pdb=" N ALA G3379 " --> pdb=" O VAL G3375 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3429 Processing helix chain 'H' and resid 3448 through 3467 Processing helix chain 'H' and resid 3468 through 3470 No H-bonds generated for 'chain 'H' and resid 3468 through 3470' Processing helix chain 'H' and resid 3491 through 3499 Processing helix chain 'H' and resid 3503 through 3520 Processing helix chain 'H' and resid 3523 through 3544 removed outlier: 3.580A pdb=" N VAL H3530 " --> pdb=" O THR H3526 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU H3540 " --> pdb=" O ARG H3536 " (cutoff:3.500A) Processing helix chain 'H' and resid 3547 through 3570 removed outlier: 3.566A pdb=" N GLU H3564 " --> pdb=" O GLN H3560 " (cutoff:3.500A) Processing helix chain 'H' and resid 3577 through 3590 Processing helix chain 'H' and resid 3592 through 3596 removed outlier: 3.820A pdb=" N LYS H3596 " --> pdb=" O GLY H3593 " (cutoff:3.500A) Processing helix chain 'H' and resid 3597 through 3614 removed outlier: 4.229A pdb=" N ASP H3614 " --> pdb=" O SER H3610 " (cutoff:3.500A) Processing helix chain 'H' and resid 3620 through 3622 No H-bonds generated for 'chain 'H' and resid 3620 through 3622' Processing helix chain 'H' and resid 3633 through 3637 Processing helix chain 'H' and resid 3674 through 3688 removed outlier: 3.579A pdb=" N VAL H3682 " --> pdb=" O LEU H3678 " (cutoff:3.500A) Processing helix chain 'H' and resid 3700 through 3710 Processing helix chain 'H' and resid 3719 through 3731 Processing helix chain 'H' and resid 3737 through 3741 Processing helix chain 'H' and resid 3742 through 3746 Processing helix chain 'H' and resid 3782 through 3806 Processing helix chain 'H' and resid 3814 through 3832 removed outlier: 3.842A pdb=" N GLU H3829 " --> pdb=" O ARG H3825 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY H3830 " --> pdb=" O GLU H3826 " (cutoff:3.500A) Processing helix chain 'H' and resid 3834 through 3846 removed outlier: 4.059A pdb=" N ALA H3838 " --> pdb=" O ARG H3834 " (cutoff:3.500A) Processing helix chain 'H' and resid 3847 through 3858 Processing helix chain 'H' and resid 3860 through 3876 removed outlier: 3.688A pdb=" N ALA H3870 " --> pdb=" O VAL H3866 " (cutoff:3.500A) Processing helix chain 'H' and resid 3901 through 3920 Processing helix chain 'I' and resid 3939 through 3958 Processing helix chain 'I' and resid 3959 through 3961 No H-bonds generated for 'chain 'I' and resid 3959 through 3961' Processing helix chain 'I' and resid 3982 through 3990 Processing helix chain 'I' and resid 3994 through 4011 Processing helix chain 'I' and resid 4014 through 4035 removed outlier: 3.580A pdb=" N VAL I4021 " --> pdb=" O THR I4017 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU I4031 " --> pdb=" O ARG I4027 " (cutoff:3.500A) Processing helix chain 'I' and resid 4038 through 4061 removed outlier: 3.567A pdb=" N GLU I4055 " --> pdb=" O GLN I4051 " (cutoff:3.500A) Processing helix chain 'I' and resid 4068 through 4081 Processing helix chain 'I' and resid 4083 through 4087 removed outlier: 3.820A pdb=" N LYS I4087 " --> pdb=" O GLY I4084 " (cutoff:3.500A) Processing helix chain 'I' and resid 4088 through 4105 removed outlier: 4.229A pdb=" N ASP I4105 " --> pdb=" O SER I4101 " (cutoff:3.500A) Processing helix chain 'I' and resid 4111 through 4113 No H-bonds generated for 'chain 'I' and resid 4111 through 4113' Processing helix chain 'I' and resid 4124 through 4128 Processing helix chain 'I' and resid 4165 through 4179 removed outlier: 3.578A pdb=" N VAL I4173 " --> pdb=" O LEU I4169 " (cutoff:3.500A) Processing helix chain 'I' and resid 4191 through 4201 Processing helix chain 'I' and resid 4210 through 4222 Processing helix chain 'I' and resid 4228 through 4232 Processing helix chain 'I' and resid 4233 through 4237 Processing helix chain 'I' and resid 4273 through 4297 Processing helix chain 'I' and resid 4305 through 4323 removed outlier: 3.842A pdb=" N GLU I4320 " --> pdb=" O ARG I4316 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY I4321 " --> pdb=" O GLU I4317 " (cutoff:3.500A) Processing helix chain 'I' and resid 4325 through 4337 removed outlier: 4.059A pdb=" N ALA I4329 " --> pdb=" O ARG I4325 " (cutoff:3.500A) Processing helix chain 'I' and resid 4338 through 4349 Processing helix chain 'I' and resid 4351 through 4367 removed outlier: 3.689A pdb=" N ALA I4361 " --> pdb=" O VAL I4357 " (cutoff:3.500A) Processing helix chain 'I' and resid 4392 through 4411 Processing helix chain 'J' and resid 4430 through 4449 Processing helix chain 'J' and resid 4450 through 4452 No H-bonds generated for 'chain 'J' and resid 4450 through 4452' Processing helix chain 'J' and resid 4473 through 4481 Processing helix chain 'J' and resid 4485 through 4502 Processing helix chain 'J' and resid 4505 through 4526 removed outlier: 3.579A pdb=" N VAL J4512 " --> pdb=" O THR J4508 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU J4522 " --> pdb=" O ARG J4518 " (cutoff:3.500A) Processing helix chain 'J' and resid 4529 through 4552 removed outlier: 3.567A pdb=" N GLU J4546 " --> pdb=" O GLN J4542 " (cutoff:3.500A) Processing helix chain 'J' and resid 4559 through 4572 Processing helix chain 'J' and resid 4574 through 4578 removed outlier: 3.820A pdb=" N LYS J4578 " --> pdb=" O GLY J4575 " (cutoff:3.500A) Processing helix chain 'J' and resid 4579 through 4596 removed outlier: 4.229A pdb=" N ASP J4596 " --> pdb=" O SER J4592 " (cutoff:3.500A) Processing helix chain 'J' and resid 4602 through 4604 No H-bonds generated for 'chain 'J' and resid 4602 through 4604' Processing helix chain 'J' and resid 4615 through 4619 Processing helix chain 'J' and resid 4656 through 4670 removed outlier: 3.578A pdb=" N VAL J4664 " --> pdb=" O LEU J4660 " (cutoff:3.500A) Processing helix chain 'J' and resid 4682 through 4692 Processing helix chain 'J' and resid 4701 through 4713 Processing helix chain 'J' and resid 4719 through 4723 Processing helix chain 'J' and resid 4724 through 4728 Processing helix chain 'J' and resid 4764 through 4788 Processing helix chain 'J' and resid 4796 through 4814 removed outlier: 3.842A pdb=" N GLU J4811 " --> pdb=" O ARG J4807 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY J4812 " --> pdb=" O GLU J4808 " (cutoff:3.500A) Processing helix chain 'J' and resid 4816 through 4828 removed outlier: 4.059A pdb=" N ALA J4820 " --> pdb=" O ARG J4816 " (cutoff:3.500A) Processing helix chain 'J' and resid 4829 through 4840 Processing helix chain 'J' and resid 4842 through 4858 removed outlier: 3.688A pdb=" N ALA J4852 " --> pdb=" O VAL J4848 " (cutoff:3.500A) Processing helix chain 'J' and resid 4883 through 4902 Processing helix chain 'K' and resid 4921 through 4940 Processing helix chain 'K' and resid 4941 through 4943 No H-bonds generated for 'chain 'K' and resid 4941 through 4943' Processing helix chain 'K' and resid 4964 through 4972 Processing helix chain 'K' and resid 4976 through 4993 Processing helix chain 'K' and resid 4996 through 5017 removed outlier: 3.579A pdb=" N VAL K5003 " --> pdb=" O THR K4999 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU K5013 " --> pdb=" O ARG K5009 " (cutoff:3.500A) Processing helix chain 'K' and resid 5020 through 5043 removed outlier: 3.566A pdb=" N GLU K5037 " --> pdb=" O GLN K5033 " (cutoff:3.500A) Processing helix chain 'K' and resid 5050 through 5063 Processing helix chain 'K' and resid 5065 through 5069 removed outlier: 3.820A pdb=" N LYS K5069 " --> pdb=" O GLY K5066 " (cutoff:3.500A) Processing helix chain 'K' and resid 5070 through 5087 removed outlier: 4.229A pdb=" N ASP K5087 " --> pdb=" O SER K5083 " (cutoff:3.500A) Processing helix chain 'K' and resid 5093 through 5095 No H-bonds generated for 'chain 'K' and resid 5093 through 5095' Processing helix chain 'K' and resid 5106 through 5110 Processing helix chain 'K' and resid 5147 through 5161 removed outlier: 3.578A pdb=" N VAL K5155 " --> pdb=" O LEU K5151 " (cutoff:3.500A) Processing helix chain 'K' and resid 5173 through 5183 Processing helix chain 'K' and resid 5192 through 5204 Processing helix chain 'K' and resid 5210 through 5214 Processing helix chain 'K' and resid 5215 through 5219 Processing helix chain 'K' and resid 5255 through 5279 Processing helix chain 'K' and resid 5287 through 5305 removed outlier: 3.843A pdb=" N GLU K5302 " --> pdb=" O ARG K5298 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY K5303 " --> pdb=" O GLU K5299 " (cutoff:3.500A) Processing helix chain 'K' and resid 5307 through 5319 removed outlier: 4.059A pdb=" N ALA K5311 " --> pdb=" O ARG K5307 " (cutoff:3.500A) Processing helix chain 'K' and resid 5320 through 5331 Processing helix chain 'K' and resid 5333 through 5349 removed outlier: 3.688A pdb=" N ALA K5343 " --> pdb=" O VAL K5339 " (cutoff:3.500A) Processing helix chain 'K' and resid 5374 through 5393 Processing helix chain 'L' and resid 5412 through 5431 Processing helix chain 'L' and resid 5432 through 5434 No H-bonds generated for 'chain 'L' and resid 5432 through 5434' Processing helix chain 'L' and resid 5455 through 5463 Processing helix chain 'L' and resid 5467 through 5484 Processing helix chain 'L' and resid 5487 through 5508 removed outlier: 3.579A pdb=" N VAL L5494 " --> pdb=" O THR L5490 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU L5504 " --> pdb=" O ARG L5500 " (cutoff:3.500A) Processing helix chain 'L' and resid 5511 through 5534 removed outlier: 3.567A pdb=" N GLU L5528 " --> pdb=" O GLN L5524 " (cutoff:3.500A) Processing helix chain 'L' and resid 5541 through 5554 Processing helix chain 'L' and resid 5556 through 5560 removed outlier: 3.820A pdb=" N LYS L5560 " --> pdb=" O GLY L5557 " (cutoff:3.500A) Processing helix chain 'L' and resid 5561 through 5578 removed outlier: 4.229A pdb=" N ASP L5578 " --> pdb=" O SER L5574 " (cutoff:3.500A) Processing helix chain 'L' and resid 5584 through 5586 No H-bonds generated for 'chain 'L' and resid 5584 through 5586' Processing helix chain 'L' and resid 5597 through 5601 Processing helix chain 'L' and resid 5638 through 5652 removed outlier: 3.579A pdb=" N VAL L5646 " --> pdb=" O LEU L5642 " (cutoff:3.500A) Processing helix chain 'L' and resid 5664 through 5674 Processing helix chain 'L' and resid 5683 through 5695 Processing helix chain 'L' and resid 5701 through 5705 Processing helix chain 'L' and resid 5706 through 5710 Processing helix chain 'L' and resid 5746 through 5770 Processing helix chain 'L' and resid 5778 through 5796 removed outlier: 3.842A pdb=" N GLU L5793 " --> pdb=" O ARG L5789 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L5794 " --> pdb=" O GLU L5790 " (cutoff:3.500A) Processing helix chain 'L' and resid 5798 through 5810 removed outlier: 4.059A pdb=" N ALA L5802 " --> pdb=" O ARG L5798 " (cutoff:3.500A) Processing helix chain 'L' and resid 5811 through 5822 Processing helix chain 'L' and resid 5824 through 5840 removed outlier: 3.688A pdb=" N ALA L5834 " --> pdb=" O VAL L5830 " (cutoff:3.500A) Processing helix chain 'L' and resid 5865 through 5884 Processing helix chain 'M' and resid 5903 through 5922 Processing helix chain 'M' and resid 5923 through 5925 No H-bonds generated for 'chain 'M' and resid 5923 through 5925' Processing helix chain 'M' and resid 5946 through 5954 Processing helix chain 'M' and resid 5958 through 5975 Processing helix chain 'M' and resid 5978 through 5999 removed outlier: 3.579A pdb=" N VAL M5985 " --> pdb=" O THR M5981 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU M5995 " --> pdb=" O ARG M5991 " (cutoff:3.500A) Processing helix chain 'M' and resid 6002 through 6025 removed outlier: 3.567A pdb=" N GLU M6019 " --> pdb=" O GLN M6015 " (cutoff:3.500A) Processing helix chain 'M' and resid 6032 through 6045 Processing helix chain 'M' and resid 6047 through 6051 removed outlier: 3.820A pdb=" N LYS M6051 " --> pdb=" O GLY M6048 " (cutoff:3.500A) Processing helix chain 'M' and resid 6052 through 6069 removed outlier: 4.229A pdb=" N ASP M6069 " --> pdb=" O SER M6065 " (cutoff:3.500A) Processing helix chain 'M' and resid 6075 through 6077 No H-bonds generated for 'chain 'M' and resid 6075 through 6077' Processing helix chain 'M' and resid 6088 through 6092 Processing helix chain 'M' and resid 6129 through 6143 removed outlier: 3.578A pdb=" N VAL M6137 " --> pdb=" O LEU M6133 " (cutoff:3.500A) Processing helix chain 'M' and resid 6155 through 6165 Processing helix chain 'M' and resid 6174 through 6186 Processing helix chain 'M' and resid 6192 through 6196 Processing helix chain 'M' and resid 6197 through 6201 Processing helix chain 'M' and resid 6237 through 6261 Processing helix chain 'M' and resid 6269 through 6287 removed outlier: 3.843A pdb=" N GLU M6284 " --> pdb=" O ARG M6280 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY M6285 " --> pdb=" O GLU M6281 " (cutoff:3.500A) Processing helix chain 'M' and resid 6289 through 6301 removed outlier: 4.060A pdb=" N ALA M6293 " --> pdb=" O ARG M6289 " (cutoff:3.500A) Processing helix chain 'M' and resid 6302 through 6313 Processing helix chain 'M' and resid 6315 through 6331 removed outlier: 3.688A pdb=" N ALA M6325 " --> pdb=" O VAL M6321 " (cutoff:3.500A) Processing helix chain 'M' and resid 6356 through 6375 Processing helix chain 'N' and resid 6394 through 6413 Processing helix chain 'N' and resid 6414 through 6416 No H-bonds generated for 'chain 'N' and resid 6414 through 6416' Processing helix chain 'N' and resid 6437 through 6445 Processing helix chain 'N' and resid 6449 through 6466 Processing helix chain 'N' and resid 6469 through 6490 removed outlier: 3.580A pdb=" N VAL N6476 " --> pdb=" O THR N6472 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU N6486 " --> pdb=" O ARG N6482 " (cutoff:3.500A) Processing helix chain 'N' and resid 6493 through 6516 removed outlier: 3.566A pdb=" N GLU N6510 " --> pdb=" O GLN N6506 " (cutoff:3.500A) Processing helix chain 'N' and resid 6523 through 6536 Processing helix chain 'N' and resid 6538 through 6542 removed outlier: 3.820A pdb=" N LYS N6542 " --> pdb=" O GLY N6539 " (cutoff:3.500A) Processing helix chain 'N' and resid 6543 through 6560 removed outlier: 4.229A pdb=" N ASP N6560 " --> pdb=" O SER N6556 " (cutoff:3.500A) Processing helix chain 'N' and resid 6566 through 6568 No H-bonds generated for 'chain 'N' and resid 6566 through 6568' Processing helix chain 'N' and resid 6579 through 6583 Processing helix chain 'N' and resid 6620 through 6634 removed outlier: 3.579A pdb=" N VAL N6628 " --> pdb=" O LEU N6624 " (cutoff:3.500A) Processing helix chain 'N' and resid 6646 through 6656 Processing helix chain 'N' and resid 6665 through 6677 Processing helix chain 'N' and resid 6683 through 6687 Processing helix chain 'N' and resid 6688 through 6692 Processing helix chain 'N' and resid 6728 through 6752 Processing helix chain 'N' and resid 6760 through 6778 removed outlier: 3.843A pdb=" N GLU N6775 " --> pdb=" O ARG N6771 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY N6776 " --> pdb=" O GLU N6772 " (cutoff:3.500A) Processing helix chain 'N' and resid 6780 through 6792 removed outlier: 4.059A pdb=" N ALA N6784 " --> pdb=" O ARG N6780 " (cutoff:3.500A) Processing helix chain 'N' and resid 6793 through 6804 Processing helix chain 'N' and resid 6806 through 6822 removed outlier: 3.688A pdb=" N ALA N6816 " --> pdb=" O VAL N6812 " (cutoff:3.500A) Processing helix chain 'N' and resid 6847 through 6866 Processing helix chain 'O' and resid 6885 through 6904 Processing helix chain 'O' and resid 6905 through 6907 No H-bonds generated for 'chain 'O' and resid 6905 through 6907' Processing helix chain 'O' and resid 6928 through 6936 Processing helix chain 'O' and resid 6940 through 6957 Processing helix chain 'O' and resid 6960 through 6981 removed outlier: 3.579A pdb=" N VAL O6967 " --> pdb=" O THR O6963 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU O6977 " --> pdb=" O ARG O6973 " (cutoff:3.500A) Processing helix chain 'O' and resid 6984 through 7007 removed outlier: 3.567A pdb=" N GLU O7001 " --> pdb=" O GLN O6997 " (cutoff:3.500A) Processing helix chain 'O' and resid 7014 through 7027 Processing helix chain 'O' and resid 7029 through 7033 removed outlier: 3.820A pdb=" N LYS O7033 " --> pdb=" O GLY O7030 " (cutoff:3.500A) Processing helix chain 'O' and resid 7034 through 7051 removed outlier: 4.228A pdb=" N ASP O7051 " --> pdb=" O SER O7047 " (cutoff:3.500A) Processing helix chain 'O' and resid 7057 through 7059 No H-bonds generated for 'chain 'O' and resid 7057 through 7059' Processing helix chain 'O' and resid 7070 through 7074 Processing helix chain 'O' and resid 7111 through 7125 removed outlier: 3.579A pdb=" N VAL O7119 " --> pdb=" O LEU O7115 " (cutoff:3.500A) Processing helix chain 'O' and resid 7137 through 7147 Processing helix chain 'O' and resid 7156 through 7168 Processing helix chain 'O' and resid 7174 through 7178 Processing helix chain 'O' and resid 7179 through 7183 Processing helix chain 'O' and resid 7219 through 7243 Processing helix chain 'O' and resid 7251 through 7269 removed outlier: 3.842A pdb=" N GLU O7266 " --> pdb=" O ARG O7262 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY O7267 " --> pdb=" O GLU O7263 " (cutoff:3.500A) Processing helix chain 'O' and resid 7271 through 7283 removed outlier: 4.060A pdb=" N ALA O7275 " --> pdb=" O ARG O7271 " (cutoff:3.500A) Processing helix chain 'O' and resid 7284 through 7295 Processing helix chain 'O' and resid 7297 through 7313 removed outlier: 3.688A pdb=" N ALA O7307 " --> pdb=" O VAL O7303 " (cutoff:3.500A) Processing helix chain 'O' and resid 7338 through 7357 Processing helix chain 'P' and resid 7376 through 7395 Processing helix chain 'P' and resid 7396 through 7398 No H-bonds generated for 'chain 'P' and resid 7396 through 7398' Processing helix chain 'P' and resid 7419 through 7427 Processing helix chain 'P' and resid 7431 through 7448 Processing helix chain 'P' and resid 7451 through 7472 removed outlier: 3.579A pdb=" N VAL P7458 " --> pdb=" O THR P7454 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU P7468 " --> pdb=" O ARG P7464 " (cutoff:3.500A) Processing helix chain 'P' and resid 7475 through 7498 removed outlier: 3.566A pdb=" N GLU P7492 " --> pdb=" O GLN P7488 " (cutoff:3.500A) Processing helix chain 'P' and resid 7505 through 7518 Processing helix chain 'P' and resid 7520 through 7524 removed outlier: 3.819A pdb=" N LYS P7524 " --> pdb=" O GLY P7521 " (cutoff:3.500A) Processing helix chain 'P' and resid 7525 through 7542 removed outlier: 4.229A pdb=" N ASP P7542 " --> pdb=" O SER P7538 " (cutoff:3.500A) Processing helix chain 'P' and resid 7548 through 7550 No H-bonds generated for 'chain 'P' and resid 7548 through 7550' Processing helix chain 'P' and resid 7561 through 7565 Processing helix chain 'P' and resid 7602 through 7616 removed outlier: 3.579A pdb=" N VAL P7610 " --> pdb=" O LEU P7606 " (cutoff:3.500A) Processing helix chain 'P' and resid 7628 through 7638 Processing helix chain 'P' and resid 7647 through 7659 Processing helix chain 'P' and resid 7665 through 7669 Processing helix chain 'P' and resid 7670 through 7674 Processing helix chain 'P' and resid 7710 through 7734 Processing helix chain 'P' and resid 7742 through 7760 removed outlier: 3.842A pdb=" N GLU P7757 " --> pdb=" O ARG P7753 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY P7758 " --> pdb=" O GLU P7754 " (cutoff:3.500A) Processing helix chain 'P' and resid 7762 through 7774 removed outlier: 4.059A pdb=" N ALA P7766 " --> pdb=" O ARG P7762 " (cutoff:3.500A) Processing helix chain 'P' and resid 7775 through 7786 Processing helix chain 'P' and resid 7788 through 7804 removed outlier: 3.688A pdb=" N ALA P7798 " --> pdb=" O VAL P7794 " (cutoff:3.500A) Processing helix chain 'P' and resid 7829 through 7848 Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 4.225A pdb=" N ILE A 484 " --> pdb=" O ASP B 530 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET B 532 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP A 486 " --> pdb=" O MET B 532 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL B 534 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 488 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.321A pdb=" N ASP A 39 " --> pdb=" O ILE H3921 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP H3923 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 134 through 135 Processing sheet with id= D, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.206A pdb=" N LYS A 188 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 341 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 190 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 205 through 208 removed outlier: 7.055A pdb=" N ASP A 311 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS A 225 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY A 313 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 445 through 446 Processing sheet with id= G, first strand: chain 'B' and resid 498 through 501 removed outlier: 4.228A pdb=" N ILE B 975 " --> pdb=" O ASP C1021 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET C1023 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 977 " --> pdb=" O MET C1023 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL C1025 " --> pdb=" O ASP B 977 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 979 " --> pdb=" O VAL C1025 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 625 through 626 Processing sheet with id= I, first strand: chain 'B' and resid 678 through 682 removed outlier: 6.207A pdb=" N LYS B 679 " --> pdb=" O MET B 830 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 832 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 681 " --> pdb=" O ILE B 832 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 696 through 699 removed outlier: 7.055A pdb=" N ASP B 802 " --> pdb=" O LYS B 716 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS B 716 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY B 804 " --> pdb=" O ASP B 714 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 936 through 937 Processing sheet with id= L, first strand: chain 'C' and resid 989 through 992 removed outlier: 4.227A pdb=" N ILE C1466 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET D1514 " --> pdb=" O ILE C1466 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP C1468 " --> pdb=" O MET D1514 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL D1516 " --> pdb=" O ASP C1468 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C1470 " --> pdb=" O VAL D1516 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 1116 through 1117 Processing sheet with id= N, first strand: chain 'C' and resid 1169 through 1173 removed outlier: 6.206A pdb=" N LYS C1170 " --> pdb=" O MET C1321 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE C1323 " --> pdb=" O LYS C1170 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU C1172 " --> pdb=" O ILE C1323 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 1187 through 1190 removed outlier: 7.055A pdb=" N ASP C1293 " --> pdb=" O LYS C1207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS C1207 " --> pdb=" O ASP C1293 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C1295 " --> pdb=" O ASP C1205 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1427 through 1428 Processing sheet with id= Q, first strand: chain 'D' and resid 1480 through 1483 removed outlier: 4.228A pdb=" N ILE D1957 " --> pdb=" O ASP E2003 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET E2005 " --> pdb=" O ILE D1957 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP D1959 " --> pdb=" O MET E2005 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL E2007 " --> pdb=" O ASP D1959 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D1961 " --> pdb=" O VAL E2007 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 1607 through 1608 Processing sheet with id= S, first strand: chain 'D' and resid 1660 through 1664 removed outlier: 6.207A pdb=" N LYS D1661 " --> pdb=" O MET D1812 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE D1814 " --> pdb=" O LYS D1661 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU D1663 " --> pdb=" O ILE D1814 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 1678 through 1681 removed outlier: 7.056A pdb=" N ASP D1784 " --> pdb=" O LYS D1698 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS D1698 " --> pdb=" O ASP D1784 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY D1786 " --> pdb=" O ASP D1696 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 1918 through 1919 Processing sheet with id= V, first strand: chain 'E' and resid 1971 through 1974 removed outlier: 4.225A pdb=" N ILE E2448 " --> pdb=" O ASP F2494 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET F2496 " --> pdb=" O ILE E2448 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP E2450 " --> pdb=" O MET F2496 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL F2498 " --> pdb=" O ASP E2450 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE E2452 " --> pdb=" O VAL F2498 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 2098 through 2099 Processing sheet with id= X, first strand: chain 'E' and resid 2151 through 2155 removed outlier: 6.206A pdb=" N LYS E2152 " --> pdb=" O MET E2303 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE E2305 " --> pdb=" O LYS E2152 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU E2154 " --> pdb=" O ILE E2305 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 2169 through 2172 removed outlier: 7.055A pdb=" N ASP E2275 " --> pdb=" O LYS E2189 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS E2189 " --> pdb=" O ASP E2275 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY E2277 " --> pdb=" O ASP E2187 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 2409 through 2410 Processing sheet with id= AA, first strand: chain 'F' and resid 2462 through 2465 removed outlier: 4.229A pdb=" N ILE F2939 " --> pdb=" O ASP G2985 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET G2987 " --> pdb=" O ILE F2939 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP F2941 " --> pdb=" O MET G2987 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL G2989 " --> pdb=" O ASP F2941 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE F2943 " --> pdb=" O VAL G2989 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 2589 through 2590 Processing sheet with id= AC, first strand: chain 'F' and resid 2642 through 2646 removed outlier: 6.206A pdb=" N LYS F2643 " --> pdb=" O MET F2794 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE F2796 " --> pdb=" O LYS F2643 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU F2645 " --> pdb=" O ILE F2796 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 2660 through 2663 removed outlier: 7.055A pdb=" N ASP F2766 " --> pdb=" O LYS F2680 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS F2680 " --> pdb=" O ASP F2766 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F2768 " --> pdb=" O ASP F2678 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 2900 through 2901 Processing sheet with id= AF, first strand: chain 'G' and resid 2953 through 2956 removed outlier: 4.224A pdb=" N ILE G3430 " --> pdb=" O ASP H3476 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET H3478 " --> pdb=" O ILE G3430 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP G3432 " --> pdb=" O MET H3478 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL H3480 " --> pdb=" O ASP G3432 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE G3434 " --> pdb=" O VAL H3480 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 3080 through 3081 Processing sheet with id= AH, first strand: chain 'G' and resid 3133 through 3137 removed outlier: 6.207A pdb=" N LYS G3134 " --> pdb=" O MET G3285 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE G3287 " --> pdb=" O LYS G3134 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU G3136 " --> pdb=" O ILE G3287 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 3151 through 3154 removed outlier: 7.055A pdb=" N ASP G3257 " --> pdb=" O LYS G3171 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS G3171 " --> pdb=" O ASP G3257 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY G3259 " --> pdb=" O ASP G3169 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 3391 through 3392 Processing sheet with id= AK, first strand: chain 'H' and resid 3571 through 3572 Processing sheet with id= AL, first strand: chain 'H' and resid 3624 through 3628 removed outlier: 6.206A pdb=" N LYS H3625 " --> pdb=" O MET H3776 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE H3778 " --> pdb=" O LYS H3625 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU H3627 " --> pdb=" O ILE H3778 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 3642 through 3645 removed outlier: 7.055A pdb=" N ASP H3748 " --> pdb=" O LYS H3662 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS H3662 " --> pdb=" O ASP H3748 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY H3750 " --> pdb=" O ASP H3660 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 3882 through 3883 Processing sheet with id= AO, first strand: chain 'I' and resid 3935 through 3938 removed outlier: 4.230A pdb=" N ILE I4412 " --> pdb=" O ASP J4458 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET J4460 " --> pdb=" O ILE I4412 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP I4414 " --> pdb=" O MET J4460 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL J4462 " --> pdb=" O ASP I4414 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE I4416 " --> pdb=" O VAL J4462 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 3977 through 3980 removed outlier: 6.322A pdb=" N ASP I3967 " --> pdb=" O ILE P7849 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP P7851 " --> pdb=" O ASP I3967 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 4062 through 4063 Processing sheet with id= AR, first strand: chain 'I' and resid 4115 through 4119 removed outlier: 6.207A pdb=" N LYS I4116 " --> pdb=" O MET I4267 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE I4269 " --> pdb=" O LYS I4116 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU I4118 " --> pdb=" O ILE I4269 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 4133 through 4136 removed outlier: 7.055A pdb=" N ASP I4239 " --> pdb=" O LYS I4153 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS I4153 " --> pdb=" O ASP I4239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY I4241 " --> pdb=" O ASP I4151 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'I' and resid 4373 through 4374 Processing sheet with id= AU, first strand: chain 'J' and resid 4426 through 4429 removed outlier: 4.225A pdb=" N ILE J4903 " --> pdb=" O ASP K4949 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET K4951 " --> pdb=" O ILE J4903 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP J4905 " --> pdb=" O MET K4951 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL K4953 " --> pdb=" O ASP J4905 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE J4907 " --> pdb=" O VAL K4953 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 4553 through 4554 Processing sheet with id= AW, first strand: chain 'J' and resid 4606 through 4610 removed outlier: 6.206A pdb=" N LYS J4607 " --> pdb=" O MET J4758 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE J4760 " --> pdb=" O LYS J4607 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU J4609 " --> pdb=" O ILE J4760 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 4624 through 4627 removed outlier: 7.055A pdb=" N ASP J4730 " --> pdb=" O LYS J4644 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS J4644 " --> pdb=" O ASP J4730 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY J4732 " --> pdb=" O ASP J4642 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 4864 through 4865 Processing sheet with id= AZ, first strand: chain 'K' and resid 4917 through 4920 removed outlier: 4.228A pdb=" N ILE K5394 " --> pdb=" O ASP L5440 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N MET L5442 " --> pdb=" O ILE K5394 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP K5396 " --> pdb=" O MET L5442 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL L5444 " --> pdb=" O ASP K5396 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE K5398 " --> pdb=" O VAL L5444 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 5044 through 5045 Processing sheet with id= BB, first strand: chain 'K' and resid 5097 through 5101 removed outlier: 6.207A pdb=" N LYS K5098 " --> pdb=" O MET K5249 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE K5251 " --> pdb=" O LYS K5098 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU K5100 " --> pdb=" O ILE K5251 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 5115 through 5118 removed outlier: 7.055A pdb=" N ASP K5221 " --> pdb=" O LYS K5135 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS K5135 " --> pdb=" O ASP K5221 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY K5223 " --> pdb=" O ASP K5133 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'K' and resid 5355 through 5356 Processing sheet with id= BE, first strand: chain 'L' and resid 5408 through 5411 removed outlier: 4.226A pdb=" N ILE L5885 " --> pdb=" O ASP M5931 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET M5933 " --> pdb=" O ILE L5885 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP L5887 " --> pdb=" O MET M5933 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL M5935 " --> pdb=" O ASP L5887 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE L5889 " --> pdb=" O VAL M5935 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 5535 through 5536 Processing sheet with id= BG, first strand: chain 'L' and resid 5588 through 5592 removed outlier: 6.207A pdb=" N LYS L5589 " --> pdb=" O MET L5740 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE L5742 " --> pdb=" O LYS L5589 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU L5591 " --> pdb=" O ILE L5742 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 5606 through 5609 removed outlier: 7.056A pdb=" N ASP L5712 " --> pdb=" O LYS L5626 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS L5626 " --> pdb=" O ASP L5712 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY L5714 " --> pdb=" O ASP L5624 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'L' and resid 5846 through 5847 Processing sheet with id= BJ, first strand: chain 'M' and resid 5899 through 5902 removed outlier: 4.229A pdb=" N ILE M6376 " --> pdb=" O ASP N6422 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N MET N6424 " --> pdb=" O ILE M6376 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP M6378 " --> pdb=" O MET N6424 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL N6426 " --> pdb=" O ASP M6378 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE M6380 " --> pdb=" O VAL N6426 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'M' and resid 6026 through 6027 Processing sheet with id= BL, first strand: chain 'M' and resid 6079 through 6083 removed outlier: 6.207A pdb=" N LYS M6080 " --> pdb=" O MET M6231 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE M6233 " --> pdb=" O LYS M6080 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU M6082 " --> pdb=" O ILE M6233 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'M' and resid 6097 through 6100 removed outlier: 7.055A pdb=" N ASP M6203 " --> pdb=" O LYS M6117 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS M6117 " --> pdb=" O ASP M6203 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY M6205 " --> pdb=" O ASP M6115 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'M' and resid 6337 through 6338 Processing sheet with id= BO, first strand: chain 'N' and resid 6390 through 6393 removed outlier: 4.224A pdb=" N ILE N6867 " --> pdb=" O ASP O6913 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET O6915 " --> pdb=" O ILE N6867 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP N6869 " --> pdb=" O MET O6915 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL O6917 " --> pdb=" O ASP N6869 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE N6871 " --> pdb=" O VAL O6917 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'N' and resid 6517 through 6518 Processing sheet with id= BQ, first strand: chain 'N' and resid 6570 through 6574 removed outlier: 6.206A pdb=" N LYS N6571 " --> pdb=" O MET N6722 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE N6724 " --> pdb=" O LYS N6571 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU N6573 " --> pdb=" O ILE N6724 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'N' and resid 6588 through 6591 removed outlier: 7.055A pdb=" N ASP N6694 " --> pdb=" O LYS N6608 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS N6608 " --> pdb=" O ASP N6694 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY N6696 " --> pdb=" O ASP N6606 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'N' and resid 6828 through 6829 Processing sheet with id= BT, first strand: chain 'O' and resid 6881 through 6884 removed outlier: 4.230A pdb=" N ILE O7358 " --> pdb=" O ASP P7404 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET P7406 " --> pdb=" O ILE O7358 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP O7360 " --> pdb=" O MET P7406 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL P7408 " --> pdb=" O ASP O7360 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE O7362 " --> pdb=" O VAL P7408 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'O' and resid 7008 through 7009 Processing sheet with id= BV, first strand: chain 'O' and resid 7061 through 7065 removed outlier: 6.206A pdb=" N LYS O7062 " --> pdb=" O MET O7213 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE O7215 " --> pdb=" O LYS O7062 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU O7064 " --> pdb=" O ILE O7215 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'O' and resid 7079 through 7082 removed outlier: 7.055A pdb=" N ASP O7185 " --> pdb=" O LYS O7099 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS O7099 " --> pdb=" O ASP O7185 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY O7187 " --> pdb=" O ASP O7097 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'O' and resid 7319 through 7320 Processing sheet with id= BY, first strand: chain 'P' and resid 7499 through 7500 Processing sheet with id= BZ, first strand: chain 'P' and resid 7552 through 7556 removed outlier: 6.206A pdb=" N LYS P7553 " --> pdb=" O MET P7704 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE P7706 " --> pdb=" O LYS P7553 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU P7555 " --> pdb=" O ILE P7706 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'P' and resid 7570 through 7573 removed outlier: 7.055A pdb=" N ASP P7676 " --> pdb=" O LYS P7590 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LYS P7590 " --> pdb=" O ASP P7676 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY P7678 " --> pdb=" O ASP P7588 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'P' and resid 7810 through 7811 3910 hydrogen bonds defined for protein. 11106 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: 53.38 Time building geometry restraints manager: 19.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 13756 1.32 - 1.44: 8532 1.44 - 1.57: 36032 1.57 - 1.69: 0 1.69 - 1.81: 656 Bond restraints: 58976 Sorted by residual: bond pdb=" C ALA D1916 " pdb=" O ALA D1916 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C ALA O7317 " pdb=" O ALA O7317 " ideal model delta sigma weight residual 1.235 1.325 -0.090 1.26e-02 6.30e+03 5.11e+01 bond pdb=" C ALA M6335 " pdb=" O ALA M6335 " ideal model delta sigma weight residual 1.235 1.325 -0.090 1.26e-02 6.30e+03 5.11e+01 bond pdb=" C ALA H3880 " pdb=" O ALA H3880 " ideal model delta sigma weight residual 1.235 1.325 -0.090 1.26e-02 6.30e+03 5.11e+01 bond pdb=" C ALA B 934 " pdb=" O ALA B 934 " ideal model delta sigma weight residual 1.235 1.325 -0.090 1.26e-02 6.30e+03 5.11e+01 ... (remaining 58971 not shown) Histogram of bond angle deviations from ideal: 97.38 - 104.16: 656 104.16 - 110.93: 22121 110.93 - 117.71: 25493 117.71 - 124.49: 28898 124.49 - 131.27: 2240 Bond angle restraints: 79408 Sorted by residual: angle pdb=" CA GLU N6387 " pdb=" C GLU N6387 " pdb=" O GLU N6387 " ideal model delta sigma weight residual 120.92 106.19 14.73 1.14e+00 7.69e-01 1.67e+02 angle pdb=" CA GLU B 495 " pdb=" C GLU B 495 " pdb=" O GLU B 495 " ideal model delta sigma weight residual 120.92 106.19 14.73 1.14e+00 7.69e-01 1.67e+02 angle pdb=" CA GLU F2459 " pdb=" C GLU F2459 " pdb=" O GLU F2459 " ideal model delta sigma weight residual 120.92 106.19 14.73 1.14e+00 7.69e-01 1.67e+02 angle pdb=" CA GLU M5896 " pdb=" C GLU M5896 " pdb=" O GLU M5896 " ideal model delta sigma weight residual 120.92 106.21 14.71 1.14e+00 7.69e-01 1.67e+02 angle pdb=" CA GLU G2950 " pdb=" C GLU G2950 " pdb=" O GLU G2950 " ideal model delta sigma weight residual 120.92 106.21 14.71 1.14e+00 7.69e-01 1.66e+02 ... (remaining 79403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 34563 15.29 - 30.57: 1437 30.57 - 45.86: 575 45.86 - 61.15: 433 61.15 - 76.43: 80 Dihedral angle restraints: 37088 sinusoidal: 14656 harmonic: 22432 Sorted by residual: dihedral pdb=" C ALA D1916 " pdb=" N ALA D1916 " pdb=" CA ALA D1916 " pdb=" CB ALA D1916 " ideal model delta harmonic sigma weight residual -122.60 -133.71 11.11 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C ALA J4862 " pdb=" N ALA J4862 " pdb=" CA ALA J4862 " pdb=" CB ALA J4862 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C ALA F2898 " pdb=" N ALA F2898 " pdb=" CA ALA F2898 " pdb=" CB ALA F2898 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 37085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 7506 0.084 - 0.168: 1761 0.168 - 0.252: 393 0.252 - 0.336: 52 0.336 - 0.420: 32 Chirality restraints: 9744 Sorted by residual: chirality pdb=" CA ALA D1916 " pdb=" N ALA D1916 " pdb=" C ALA D1916 " pdb=" CB ALA D1916 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA ALA L5844 " pdb=" N ALA L5844 " pdb=" C ALA L5844 " pdb=" CB ALA L5844 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA ALA F2898 " pdb=" N ALA F2898 " pdb=" C ALA F2898 " pdb=" CB ALA F2898 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 9741 not shown) Planarity restraints: 10288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 119 " 0.042 2.00e-02 2.50e+03 8.50e-02 7.22e+01 pdb=" C GLN A 119 " -0.147 2.00e-02 2.50e+03 pdb=" O GLN A 119 " 0.052 2.00e-02 2.50e+03 pdb=" N ALA A 120 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L5520 " 0.042 2.00e-02 2.50e+03 8.50e-02 7.22e+01 pdb=" C GLN L5520 " -0.147 2.00e-02 2.50e+03 pdb=" O GLN L5520 " 0.052 2.00e-02 2.50e+03 pdb=" N ALA L5521 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN M6011 " 0.042 2.00e-02 2.50e+03 8.49e-02 7.20e+01 pdb=" C GLN M6011 " -0.147 2.00e-02 2.50e+03 pdb=" O GLN M6011 " 0.052 2.00e-02 2.50e+03 pdb=" N ALA M6012 " 0.053 2.00e-02 2.50e+03 ... (remaining 10285 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 29524 2.99 - 3.47: 66661 3.47 - 3.94: 99662 3.94 - 4.42: 113047 4.42 - 4.90: 186001 Nonbonded interactions: 494895 Sorted by model distance: nonbonded pdb=" O VAL C1033 " pdb=" OE1 GLU C1333 " model vdw 2.510 3.040 nonbonded pdb=" O VAL A 51 " pdb=" OE1 GLU A 351 " model vdw 2.510 3.040 nonbonded pdb=" O VAL E2015 " pdb=" OE1 GLU E2315 " model vdw 2.510 3.040 nonbonded pdb=" O VAL D1524 " pdb=" OE1 GLU D1824 " model vdw 2.510 3.040 nonbonded pdb=" O VAL I3979 " pdb=" OE1 GLU I4279 " model vdw 2.510 3.040 ... (remaining 494890 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 4.270 Check model and map are aligned: 0.670 Set scattering table: 0.430 Process input model: 151.280 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4637 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 : 0.014 0.091 58976 Z= 0.898 Angle : 1.506 14.733 79408 Z= 1.102 Chirality : 0.082 0.420 9744 Planarity : 0.019 0.085 10288 Dihedral : 13.066 76.432 22560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.48 % Favored : 96.32 % Rotamer: Outliers : 1.78 % Allowed : 6.62 % Favored : 91.60 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.08), residues: 7824 helix: -1.42 (0.06), residues: 4320 sheet: -1.01 (0.13), residues: 1136 loop : -0.52 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G3279 PHE 0.038 0.005 PHE B 939 TYR 0.037 0.004 TYR N6501 ARG 0.022 0.004 ARG E2306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15648 Ramachandran restraints generated. 7824 Oldfield, 0 Emsley, 7824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 155 average time/residue: 0.2176 time to fit residues: 38.6074 Evaluate side-chains 96 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 662 optimal weight: 2.9990 chunk 594 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 614 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 373 optimal weight: 0.7980 chunk 457 optimal weight: 8.9990 chunk 711 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 838 HIS B 937 ASN B 963 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58976 Z= 0.205 Angle : 0.628 6.990 79408 Z= 0.341 Chirality : 0.043 0.195 9744 Planarity : 0.004 0.039 10288 Dihedral : 4.974 57.270 8256 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.25 % Allowed : 4.07 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.09), residues: 7824 helix: 0.57 (0.07), residues: 4320 sheet: -0.22 (0.14), residues: 1408 loop : 0.32 (0.15), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H3784 PHE 0.008 0.002 PHE G3273 TYR 0.004 0.001 TYR H3446 ARG 0.005 0.001 ARG J4833 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14670 Ramachandran restraints generated. 7335 Oldfield, 0 Emsley, 7335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14670 Ramachandran restraints generated. 7335 Oldfield, 0 Emsley, 7335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1704 time to fit residues: 23.1794 Evaluate side-chains 78 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 395 optimal weight: 0.0970 chunk 220 optimal weight: 0.6980 chunk 592 optimal weight: 0.0040 chunk 484 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 713 optimal weight: 5.9990 chunk 770 optimal weight: 2.9990 chunk 635 optimal weight: 9.9990 chunk 707 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 572 optimal weight: 30.0000 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1919 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 58976 Z= 0.186 Angle : 0.630 7.165 79408 Z= 0.338 Chirality : 0.043 0.185 9744 Planarity : 0.004 0.033 10288 Dihedral : 4.952 47.900 8256 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 7824 helix: 0.60 (0.07), residues: 4352 sheet: -0.06 (0.13), residues: 1360 loop : -0.02 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N6730 PHE 0.009 0.002 PHE K5237 TYR 0.032 0.003 TYR G3336 ARG 0.005 0.001 ARG E2378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13692 Ramachandran restraints generated. 6846 Oldfield, 0 Emsley, 6846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13692 Ramachandran restraints generated. 6846 Oldfield, 0 Emsley, 6846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1909 time to fit residues: 22.1118 Evaluate side-chains 79 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 704 optimal weight: 8.9990 chunk 536 optimal weight: 7.9990 chunk 370 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 478 optimal weight: 30.0000 chunk 715 optimal weight: 20.0000 chunk 757 optimal weight: 0.8980 chunk 373 optimal weight: 7.9990 chunk 678 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 HIS B 937 ASN ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.7373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 58976 Z= 0.240 Angle : 0.656 5.424 79408 Z= 0.361 Chirality : 0.043 0.148 9744 Planarity : 0.004 0.040 10288 Dihedral : 5.121 36.589 8256 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.09), residues: 7824 helix: 0.91 (0.07), residues: 4288 sheet: -0.40 (0.14), residues: 1168 loop : -0.30 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS K5020 PHE 0.011 0.003 PHE D1921 TYR 0.004 0.001 TYR G3336 ARG 0.007 0.001 ARG F2938 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13692 Ramachandran restraints generated. 6846 Oldfield, 0 Emsley, 6846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13692 Ramachandran restraints generated. 6846 Oldfield, 0 Emsley, 6846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1727 time to fit residues: 20.0415 Evaluate side-chains 75 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 631 optimal weight: 9.9990 chunk 430 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 564 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 646 optimal weight: 7.9990 chunk 523 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 386 optimal weight: 7.9990 chunk 680 optimal weight: 10.0000 chunk 191 optimal weight: 0.0670 overall best weight: 3.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O6892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O7312 ASN O7320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5416 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 58976 Z= 0.183 Angle : 0.624 6.278 79408 Z= 0.339 Chirality : 0.042 0.167 9744 Planarity : 0.004 0.040 10288 Dihedral : 5.095 36.249 8256 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.45 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 7824 helix: 0.84 (0.08), residues: 4288 sheet: -0.44 (0.15), residues: 1120 loop : -0.36 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS K5020 PHE 0.016 0.003 PHE A 257 TYR 0.004 0.001 TYR B 881 ARG 0.004 0.001 ARG K5324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12714 Ramachandran restraints generated. 6357 Oldfield, 0 Emsley, 6357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12714 Ramachandran restraints generated. 6357 Oldfield, 0 Emsley, 6357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1939 time to fit residues: 22.0016 Evaluate side-chains 74 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 254 optimal weight: 10.0000 chunk 682 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 758 optimal weight: 7.9990 chunk 629 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 398 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K5020 HIS K5356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.8445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 58976 Z= 0.182 Angle : 0.597 7.044 79408 Z= 0.321 Chirality : 0.041 0.136 9744 Planarity : 0.003 0.034 10288 Dihedral : 5.106 40.564 8256 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 7824 helix: 0.64 (0.08), residues: 4320 sheet: -0.59 (0.15), residues: 992 loop : -0.44 (0.13), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L5511 PHE 0.017 0.003 PHE H3842 TYR 0.016 0.002 TYR F2845 ARG 0.006 0.001 ARG C1465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2014 time to fit residues: 22.0563 Evaluate side-chains 75 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 731 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 432 optimal weight: 0.2980 chunk 553 optimal weight: 0.0030 chunk 429 optimal weight: 0.0870 chunk 638 optimal weight: 0.8980 chunk 423 optimal weight: 0.0980 chunk 755 optimal weight: 2.9990 chunk 472 optimal weight: 0.8980 chunk 460 optimal weight: 0.8980 chunk 348 optimal weight: 0.0570 overall best weight: 0.1086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O6892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5294 moved from start: 0.8631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 58976 Z= 0.167 Angle : 0.612 9.308 79408 Z= 0.321 Chirality : 0.042 0.139 9744 Planarity : 0.003 0.030 10288 Dihedral : 4.815 36.843 8256 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.25 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.09), residues: 7824 helix: 0.44 (0.08), residues: 4384 sheet: -0.32 (0.14), residues: 1104 loop : -0.52 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E2311 PHE 0.012 0.002 PHE A 257 TYR 0.005 0.001 TYR G3215 ARG 0.006 0.001 ARG D1827 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11736 Ramachandran restraints generated. 5868 Oldfield, 0 Emsley, 5868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2195 time to fit residues: 23.8661 Evaluate side-chains 79 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 467 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 451 optimal weight: 7.9990 chunk 227 optimal weight: 0.0060 chunk 148 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 480 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 373 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 593 optimal weight: 0.2980 overall best weight: 0.8758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E2030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2194 ASN E2311 HIS E2410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.8929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 58976 Z= 0.169 Angle : 0.636 7.926 79408 Z= 0.332 Chirality : 0.042 0.176 9744 Planarity : 0.004 0.040 10288 Dihedral : 4.590 31.291 8256 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.45 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.11 (0.09), residues: 7824 helix: 0.40 (0.08), residues: 4416 sheet: -0.45 (0.14), residues: 1136 loop : -0.52 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K5257 PHE 0.009 0.001 PHE B 818 TYR 0.028 0.003 TYR N6773 ARG 0.007 0.001 ARG C1005 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1934 time to fit residues: 21.3824 Evaluate side-chains 79 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 687 optimal weight: 0.1980 chunk 723 optimal weight: 0.2980 chunk 660 optimal weight: 0.0020 chunk 704 optimal weight: 8.9990 chunk 423 optimal weight: 0.5980 chunk 306 optimal weight: 0.9990 chunk 552 optimal weight: 0.3980 chunk 216 optimal weight: 20.0000 chunk 636 optimal weight: 0.9980 chunk 665 optimal weight: 4.9990 chunk 701 optimal weight: 20.0000 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O6940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O7221 HIS O7312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 moved from start: 0.9152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 58976 Z= 0.194 Angle : 0.694 8.828 79408 Z= 0.360 Chirality : 0.044 0.259 9744 Planarity : 0.005 0.074 10288 Dihedral : 4.609 31.197 8256 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.39 (0.09), residues: 7824 helix: 0.13 (0.07), residues: 4384 sheet: -0.59 (0.13), residues: 1136 loop : -0.53 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O7221 PHE 0.007 0.001 PHE J4746 TYR 0.034 0.003 TYR P7483 ARG 0.015 0.001 ARG H3460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1967 time to fit residues: 21.0111 Evaluate side-chains 69 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 462 optimal weight: 0.7980 chunk 744 optimal weight: 2.9990 chunk 454 optimal weight: 0.0170 chunk 353 optimal weight: 0.2980 chunk 517 optimal weight: 0.8980 chunk 781 optimal weight: 0.0060 chunk 718 optimal weight: 0.7980 chunk 621 optimal weight: 0.0040 chunk 64 optimal weight: 20.0000 chunk 480 optimal weight: 8.9990 chunk 381 optimal weight: 9.9990 overall best weight: 0.2246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5268 moved from start: 0.9433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 58976 Z= 0.196 Angle : 0.690 8.082 79408 Z= 0.359 Chirality : 0.045 0.227 9744 Planarity : 0.005 0.078 10288 Dihedral : 4.617 29.318 8256 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.09), residues: 7824 helix: 0.11 (0.07), residues: 4384 sheet: -0.39 (0.14), residues: 1136 loop : -0.52 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K5257 PHE 0.028 0.002 PHE P7692 TYR 0.006 0.001 TYR O6992 ARG 0.018 0.001 ARG K4933 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10758 Ramachandran restraints generated. 5379 Oldfield, 0 Emsley, 5379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1928 time to fit residues: 20.4616 Evaluate side-chains 81 residues out of total 393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 784 random chunks: chunk 494 optimal weight: 0.5980 chunk 662 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 573 optimal weight: 0.0170 chunk 91 optimal weight: 0.0000 chunk 172 optimal weight: 0.0060 chunk 622 optimal weight: 0.7980 chunk 260 optimal weight: 20.0000 chunk 639 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 GLN C1329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.093985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074237 restraints weight = 22381.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076475 restraints weight = 16931.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.078339 restraints weight = 13467.250| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.9606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 58976 Z= 0.207 Angle : 0.751 12.617 79408 Z= 0.383 Chirality : 0.045 0.153 9744 Planarity : 0.005 0.088 10288 Dihedral : 4.877 29.684 8256 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 7824 helix: -0.06 (0.07), residues: 4384 sheet: -0.68 (0.16), residues: 864 loop : -0.77 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M6239 PHE 0.023 0.002 PHE J4746 TYR 0.022 0.002 TYR G3064 ARG 0.014 0.001 ARG E1987 =============================================================================== Job complete usr+sys time: 4926.43 seconds wall clock time: 92 minutes 2.42 seconds (5522.42 seconds total)