Starting phenix.real_space_refine on Fri Dec 8 16:47:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3izk_5247/12_2023/3izk_5247.pdb" } resolution = 4.9 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= 0.022 sd= 0.108 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 36256 2.51 5 N 10128 2.21 5 O 11680 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 "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 3694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 6149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 6640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 7131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 7622": "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: 58448 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "E" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "F" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "G" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "H" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "I" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "J" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "K" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "L" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "M" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "N" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "O" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Chain: "P" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3653 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 481} Time building chain proxies: 22.30, per 1000 atoms: 0.38 Number of scatterers: 58448 At special positions: 0 Unit cell: (171.57, 171.57, 166.25, 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 11680 8.00 N 10128 7.00 C 36256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.05 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: 336 helices and 96 sheets defined 59.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 removed outlier: 3.554A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 140 through 153 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.702A pdb=" N LYS A 159 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 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 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 removed outlier: 3.520A pdb=" N GLU A 351 " --> pdb=" O HIS A 347 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 395 removed outlier: 3.566A pdb=" N GLU A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 removed outlier: 3.710A pdb=" N ALA A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 439 removed outlier: 3.615A pdb=" N LEU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 483 Processing helix chain 'B' and resid 502 through 522 removed outlier: 3.553A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL B 582 " --> pdb=" O THR B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 624 Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 646 through 650 removed outlier: 3.702A pdb=" N LYS B 650 " --> pdb=" O GLY B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 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 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 removed outlier: 3.520A pdb=" N GLU B 842 " --> pdb=" O HIS B 838 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 886 removed outlier: 3.566A pdb=" N GLU B 880 " --> pdb=" O MET B 876 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 883 " --> pdb=" O ARG B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 900 removed outlier: 3.710A pdb=" N ALA B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 900 " --> pdb=" O PHE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 912 Processing helix chain 'B' and resid 914 through 930 removed outlier: 3.614A pdb=" N LEU B 919 " --> pdb=" O ALA B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 974 Processing helix chain 'C' and resid 993 through 1013 removed outlier: 3.553A pdb=" N ILE C1007 " --> pdb=" O ALA C1003 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C1013 " --> pdb=" O GLU C1009 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL C1073 " --> pdb=" O THR C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1115 Processing helix chain 'C' and resid 1122 through 1135 Processing helix chain 'C' and resid 1137 through 1141 removed outlier: 3.702A pdb=" N LYS C1141 " --> pdb=" O GLY C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1158 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 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 removed outlier: 3.520A pdb=" N GLU C1333 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C1343 " --> pdb=" O ASP C1339 " (cutoff:3.500A) Processing helix chain 'C' and resid 1359 through 1377 removed outlier: 3.566A pdb=" N GLU C1371 " --> pdb=" O MET C1367 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C1374 " --> pdb=" O ARG C1370 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1391 removed outlier: 3.710A pdb=" N ALA C1383 " --> pdb=" O ARG C1379 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1391 " --> pdb=" O PHE C1387 " (cutoff:3.500A) Processing helix chain 'C' and resid 1392 through 1403 Processing helix chain 'C' and resid 1405 through 1421 removed outlier: 3.615A pdb=" N LEU C1410 " --> pdb=" O ALA C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1446 through 1465 Processing helix chain 'D' and resid 1484 through 1504 removed outlier: 3.553A pdb=" N ILE D1498 " --> pdb=" O ALA D1494 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D1504 " --> pdb=" O GLU D1500 " (cutoff:3.500A) 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: 3.692A pdb=" N VAL D1564 " --> pdb=" O THR D1560 " (cutoff:3.500A) Processing helix chain 'D' and resid 1583 through 1606 Processing helix chain 'D' and resid 1613 through 1626 Processing helix chain 'D' and resid 1628 through 1632 removed outlier: 3.701A pdb=" N LYS D1632 " --> pdb=" O GLY D1629 " (cutoff:3.500A) Processing helix chain 'D' and resid 1633 through 1649 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 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 removed outlier: 3.520A pdb=" N GLU D1824 " --> pdb=" O HIS D1820 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D1834 " --> pdb=" O ASP D1830 " (cutoff:3.500A) Processing helix chain 'D' and resid 1850 through 1868 removed outlier: 3.566A pdb=" N GLU D1862 " --> pdb=" O MET D1858 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D1865 " --> pdb=" O ARG D1861 " (cutoff:3.500A) Processing helix chain 'D' and resid 1870 through 1882 removed outlier: 3.710A pdb=" N ALA D1874 " --> pdb=" O ARG D1870 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D1882 " --> pdb=" O PHE D1878 " (cutoff:3.500A) Processing helix chain 'D' and resid 1883 through 1894 Processing helix chain 'D' and resid 1896 through 1912 removed outlier: 3.614A pdb=" N LEU D1901 " --> pdb=" O ALA D1897 " (cutoff:3.500A) Processing helix chain 'D' and resid 1937 through 1956 Processing helix chain 'E' and resid 1975 through 1995 removed outlier: 3.554A pdb=" N ILE E1989 " --> pdb=" O ALA E1985 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER E1995 " --> pdb=" O GLU E1991 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL E2055 " --> pdb=" O THR E2051 " (cutoff:3.500A) Processing helix chain 'E' and resid 2074 through 2097 Processing helix chain 'E' and resid 2104 through 2117 Processing helix chain 'E' and resid 2119 through 2123 removed outlier: 3.701A pdb=" N LYS E2123 " --> pdb=" O GLY E2120 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2140 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 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 removed outlier: 3.520A pdb=" N GLU E2315 " --> pdb=" O HIS E2311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E2325 " --> pdb=" O ASP E2321 " (cutoff:3.500A) Processing helix chain 'E' and resid 2341 through 2359 removed outlier: 3.566A pdb=" N GLU E2353 " --> pdb=" O MET E2349 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E2356 " --> pdb=" O ARG E2352 " (cutoff:3.500A) Processing helix chain 'E' and resid 2361 through 2373 removed outlier: 3.709A pdb=" N ALA E2365 " --> pdb=" O ARG E2361 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E2373 " --> pdb=" O PHE E2369 " (cutoff:3.500A) Processing helix chain 'E' and resid 2374 through 2385 Processing helix chain 'E' and resid 2387 through 2403 removed outlier: 3.614A pdb=" N LEU E2392 " --> pdb=" O ALA E2388 " (cutoff:3.500A) Processing helix chain 'E' and resid 2428 through 2447 Processing helix chain 'F' and resid 2466 through 2486 removed outlier: 3.553A pdb=" N ILE F2480 " --> pdb=" O ALA F2476 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER F2486 " --> pdb=" O GLU F2482 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL F2546 " --> pdb=" O THR F2542 " (cutoff:3.500A) Processing helix chain 'F' and resid 2565 through 2588 Processing helix chain 'F' and resid 2595 through 2608 Processing helix chain 'F' and resid 2610 through 2614 removed outlier: 3.702A pdb=" N LYS F2614 " --> pdb=" O GLY F2611 " (cutoff:3.500A) Processing helix chain 'F' and resid 2615 through 2631 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 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 removed outlier: 3.520A pdb=" N GLU F2806 " --> pdb=" O HIS F2802 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F2816 " --> pdb=" O ASP F2812 " (cutoff:3.500A) Processing helix chain 'F' and resid 2832 through 2850 removed outlier: 3.566A pdb=" N GLU F2844 " --> pdb=" O MET F2840 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU F2847 " --> pdb=" O ARG F2843 " (cutoff:3.500A) Processing helix chain 'F' and resid 2852 through 2864 removed outlier: 3.710A pdb=" N ALA F2856 " --> pdb=" O ARG F2852 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU F2864 " --> pdb=" O PHE F2860 " (cutoff:3.500A) Processing helix chain 'F' and resid 2865 through 2876 Processing helix chain 'F' and resid 2878 through 2894 removed outlier: 3.615A pdb=" N LEU F2883 " --> pdb=" O ALA F2879 " (cutoff:3.500A) Processing helix chain 'F' and resid 2919 through 2938 Processing helix chain 'G' and resid 2957 through 2977 removed outlier: 3.553A pdb=" N ILE G2971 " --> pdb=" O ALA G2967 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER G2977 " --> pdb=" O GLU G2973 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL G3037 " --> pdb=" O THR G3033 " (cutoff:3.500A) Processing helix chain 'G' and resid 3056 through 3079 Processing helix chain 'G' and resid 3086 through 3099 Processing helix chain 'G' and resid 3101 through 3105 removed outlier: 3.702A pdb=" N LYS G3105 " --> pdb=" O GLY G3102 " (cutoff:3.500A) Processing helix chain 'G' and resid 3106 through 3122 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 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 removed outlier: 3.520A pdb=" N GLU G3297 " --> pdb=" O HIS G3293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY G3307 " --> pdb=" O ASP G3303 " (cutoff:3.500A) Processing helix chain 'G' and resid 3323 through 3341 removed outlier: 3.566A pdb=" N GLU G3335 " --> pdb=" O MET G3331 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G3338 " --> pdb=" O ARG G3334 " (cutoff:3.500A) Processing helix chain 'G' and resid 3343 through 3355 removed outlier: 3.709A pdb=" N ALA G3347 " --> pdb=" O ARG G3343 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU G3355 " --> pdb=" O PHE G3351 " (cutoff:3.500A) Processing helix chain 'G' and resid 3356 through 3367 Processing helix chain 'G' and resid 3369 through 3385 removed outlier: 3.614A pdb=" N LEU G3374 " --> pdb=" O ALA G3370 " (cutoff:3.500A) Processing helix chain 'G' and resid 3410 through 3429 Processing helix chain 'H' and resid 3448 through 3468 removed outlier: 3.553A pdb=" N ILE H3462 " --> pdb=" O ALA H3458 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER H3468 " --> pdb=" O GLU H3464 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL H3528 " --> pdb=" O THR H3524 " (cutoff:3.500A) Processing helix chain 'H' and resid 3547 through 3570 Processing helix chain 'H' and resid 3577 through 3590 Processing helix chain 'H' and resid 3592 through 3596 removed outlier: 3.702A pdb=" N LYS H3596 " --> pdb=" O GLY H3593 " (cutoff:3.500A) Processing helix chain 'H' and resid 3597 through 3613 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 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 removed outlier: 3.521A pdb=" N GLU H3788 " --> pdb=" O HIS H3784 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY H3798 " --> pdb=" O ASP H3794 " (cutoff:3.500A) Processing helix chain 'H' and resid 3814 through 3832 removed outlier: 3.566A pdb=" N GLU H3826 " --> pdb=" O MET H3822 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU H3829 " --> pdb=" O ARG H3825 " (cutoff:3.500A) Processing helix chain 'H' and resid 3834 through 3846 removed outlier: 3.710A pdb=" N ALA H3838 " --> pdb=" O ARG H3834 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU H3846 " --> pdb=" O PHE H3842 " (cutoff:3.500A) Processing helix chain 'H' and resid 3847 through 3858 Processing helix chain 'H' and resid 3860 through 3876 removed outlier: 3.615A pdb=" N LEU H3865 " --> pdb=" O ALA H3861 " (cutoff:3.500A) Processing helix chain 'H' and resid 3901 through 3920 Processing helix chain 'I' and resid 3939 through 3959 removed outlier: 3.552A pdb=" N ILE I3953 " --> pdb=" O ALA I3949 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER I3959 " --> pdb=" O GLU I3955 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL I4019 " --> pdb=" O THR I4015 " (cutoff:3.500A) Processing helix chain 'I' and resid 4038 through 4061 Processing helix chain 'I' and resid 4068 through 4081 Processing helix chain 'I' and resid 4083 through 4087 removed outlier: 3.701A pdb=" N LYS I4087 " --> pdb=" O GLY I4084 " (cutoff:3.500A) Processing helix chain 'I' and resid 4088 through 4104 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 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 removed outlier: 3.520A pdb=" N GLU I4279 " --> pdb=" O HIS I4275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY I4289 " --> pdb=" O ASP I4285 " (cutoff:3.500A) Processing helix chain 'I' and resid 4305 through 4323 removed outlier: 3.566A pdb=" N GLU I4317 " --> pdb=" O MET I4313 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU I4320 " --> pdb=" O ARG I4316 " (cutoff:3.500A) Processing helix chain 'I' and resid 4325 through 4337 removed outlier: 3.710A pdb=" N ALA I4329 " --> pdb=" O ARG I4325 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU I4337 " --> pdb=" O PHE I4333 " (cutoff:3.500A) Processing helix chain 'I' and resid 4338 through 4349 Processing helix chain 'I' and resid 4351 through 4367 removed outlier: 3.615A pdb=" N LEU I4356 " --> pdb=" O ALA I4352 " (cutoff:3.500A) Processing helix chain 'I' and resid 4392 through 4411 Processing helix chain 'J' and resid 4430 through 4450 removed outlier: 3.553A pdb=" N ILE J4444 " --> pdb=" O ALA J4440 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER J4450 " --> pdb=" O GLU J4446 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL J4510 " --> pdb=" O THR J4506 " (cutoff:3.500A) Processing helix chain 'J' and resid 4529 through 4552 Processing helix chain 'J' and resid 4559 through 4572 Processing helix chain 'J' and resid 4574 through 4578 removed outlier: 3.702A pdb=" N LYS J4578 " --> pdb=" O GLY J4575 " (cutoff:3.500A) Processing helix chain 'J' and resid 4579 through 4595 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 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 removed outlier: 3.520A pdb=" N GLU J4770 " --> pdb=" O HIS J4766 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY J4780 " --> pdb=" O ASP J4776 " (cutoff:3.500A) Processing helix chain 'J' and resid 4796 through 4814 removed outlier: 3.566A pdb=" N GLU J4808 " --> pdb=" O MET J4804 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU J4811 " --> pdb=" O ARG J4807 " (cutoff:3.500A) Processing helix chain 'J' and resid 4816 through 4828 removed outlier: 3.710A pdb=" N ALA J4820 " --> pdb=" O ARG J4816 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU J4828 " --> pdb=" O PHE J4824 " (cutoff:3.500A) Processing helix chain 'J' and resid 4829 through 4840 Processing helix chain 'J' and resid 4842 through 4858 removed outlier: 3.614A pdb=" N LEU J4847 " --> pdb=" O ALA J4843 " (cutoff:3.500A) Processing helix chain 'J' and resid 4883 through 4902 Processing helix chain 'K' and resid 4921 through 4941 removed outlier: 3.553A pdb=" N ILE K4935 " --> pdb=" O ALA K4931 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER K4941 " --> pdb=" O GLU K4937 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL K5001 " --> pdb=" O THR K4997 " (cutoff:3.500A) Processing helix chain 'K' and resid 5020 through 5043 Processing helix chain 'K' and resid 5050 through 5063 Processing helix chain 'K' and resid 5065 through 5069 removed outlier: 3.701A pdb=" N LYS K5069 " --> pdb=" O GLY K5066 " (cutoff:3.500A) Processing helix chain 'K' and resid 5070 through 5086 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 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 removed outlier: 3.521A pdb=" N GLU K5261 " --> pdb=" O HIS K5257 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY K5271 " --> pdb=" O ASP K5267 " (cutoff:3.500A) Processing helix chain 'K' and resid 5287 through 5305 removed outlier: 3.566A pdb=" N GLU K5299 " --> pdb=" O MET K5295 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU K5302 " --> pdb=" O ARG K5298 " (cutoff:3.500A) Processing helix chain 'K' and resid 5307 through 5319 removed outlier: 3.710A pdb=" N ALA K5311 " --> pdb=" O ARG K5307 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU K5319 " --> pdb=" O PHE K5315 " (cutoff:3.500A) Processing helix chain 'K' and resid 5320 through 5331 Processing helix chain 'K' and resid 5333 through 5349 removed outlier: 3.615A pdb=" N LEU K5338 " --> pdb=" O ALA K5334 " (cutoff:3.500A) Processing helix chain 'K' and resid 5374 through 5393 Processing helix chain 'L' and resid 5412 through 5432 removed outlier: 3.553A pdb=" N ILE L5426 " --> pdb=" O ALA L5422 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER L5432 " --> pdb=" O GLU L5428 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL L5492 " --> pdb=" O THR L5488 " (cutoff:3.500A) Processing helix chain 'L' and resid 5511 through 5534 Processing helix chain 'L' and resid 5541 through 5554 Processing helix chain 'L' and resid 5556 through 5560 removed outlier: 3.702A pdb=" N LYS L5560 " --> pdb=" O GLY L5557 " (cutoff:3.500A) Processing helix chain 'L' and resid 5561 through 5577 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 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 removed outlier: 3.520A pdb=" N GLU L5752 " --> pdb=" O HIS L5748 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY L5762 " --> pdb=" O ASP L5758 " (cutoff:3.500A) Processing helix chain 'L' and resid 5778 through 5796 removed outlier: 3.566A pdb=" N GLU L5790 " --> pdb=" O MET L5786 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU L5793 " --> pdb=" O ARG L5789 " (cutoff:3.500A) Processing helix chain 'L' and resid 5798 through 5810 removed outlier: 3.710A pdb=" N ALA L5802 " --> pdb=" O ARG L5798 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU L5810 " --> pdb=" O PHE L5806 " (cutoff:3.500A) Processing helix chain 'L' and resid 5811 through 5822 Processing helix chain 'L' and resid 5824 through 5840 removed outlier: 3.615A pdb=" N LEU L5829 " --> pdb=" O ALA L5825 " (cutoff:3.500A) Processing helix chain 'L' and resid 5865 through 5884 Processing helix chain 'M' and resid 5903 through 5923 removed outlier: 3.553A pdb=" N ILE M5917 " --> pdb=" O ALA M5913 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER M5923 " --> pdb=" O GLU M5919 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL M5983 " --> pdb=" O THR M5979 " (cutoff:3.500A) Processing helix chain 'M' and resid 6002 through 6025 Processing helix chain 'M' and resid 6032 through 6045 Processing helix chain 'M' and resid 6047 through 6051 removed outlier: 3.701A pdb=" N LYS M6051 " --> pdb=" O GLY M6048 " (cutoff:3.500A) Processing helix chain 'M' and resid 6052 through 6068 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 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 removed outlier: 3.521A pdb=" N GLU M6243 " --> pdb=" O HIS M6239 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY M6253 " --> pdb=" O ASP M6249 " (cutoff:3.500A) Processing helix chain 'M' and resid 6269 through 6287 removed outlier: 3.566A pdb=" N GLU M6281 " --> pdb=" O MET M6277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU M6284 " --> pdb=" O ARG M6280 " (cutoff:3.500A) Processing helix chain 'M' and resid 6289 through 6301 removed outlier: 3.710A pdb=" N ALA M6293 " --> pdb=" O ARG M6289 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU M6301 " --> pdb=" O PHE M6297 " (cutoff:3.500A) Processing helix chain 'M' and resid 6302 through 6313 Processing helix chain 'M' and resid 6315 through 6331 removed outlier: 3.615A pdb=" N LEU M6320 " --> pdb=" O ALA M6316 " (cutoff:3.500A) Processing helix chain 'M' and resid 6356 through 6375 Processing helix chain 'N' and resid 6394 through 6414 removed outlier: 3.553A pdb=" N ILE N6408 " --> pdb=" O ALA N6404 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER N6414 " --> pdb=" O GLU N6410 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL N6474 " --> pdb=" O THR N6470 " (cutoff:3.500A) Processing helix chain 'N' and resid 6493 through 6516 Processing helix chain 'N' and resid 6523 through 6536 Processing helix chain 'N' and resid 6538 through 6542 removed outlier: 3.702A pdb=" N LYS N6542 " --> pdb=" O GLY N6539 " (cutoff:3.500A) Processing helix chain 'N' and resid 6543 through 6559 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 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 removed outlier: 3.520A pdb=" N GLU N6734 " --> pdb=" O HIS N6730 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY N6744 " --> pdb=" O ASP N6740 " (cutoff:3.500A) Processing helix chain 'N' and resid 6760 through 6778 removed outlier: 3.566A pdb=" N GLU N6772 " --> pdb=" O MET N6768 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU N6775 " --> pdb=" O ARG N6771 " (cutoff:3.500A) Processing helix chain 'N' and resid 6780 through 6792 removed outlier: 3.711A pdb=" N ALA N6784 " --> pdb=" O ARG N6780 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU N6792 " --> pdb=" O PHE N6788 " (cutoff:3.500A) Processing helix chain 'N' and resid 6793 through 6804 Processing helix chain 'N' and resid 6806 through 6822 removed outlier: 3.615A pdb=" N LEU N6811 " --> pdb=" O ALA N6807 " (cutoff:3.500A) Processing helix chain 'N' and resid 6847 through 6866 Processing helix chain 'O' and resid 6885 through 6905 removed outlier: 3.553A pdb=" N ILE O6899 " --> pdb=" O ALA O6895 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER O6905 " --> pdb=" O GLU O6901 " (cutoff:3.500A) 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: 3.694A pdb=" N VAL O6965 " --> pdb=" O THR O6961 " (cutoff:3.500A) Processing helix chain 'O' and resid 6984 through 7007 Processing helix chain 'O' and resid 7014 through 7027 Processing helix chain 'O' and resid 7029 through 7033 removed outlier: 3.702A pdb=" N LYS O7033 " --> pdb=" O GLY O7030 " (cutoff:3.500A) Processing helix chain 'O' and resid 7034 through 7050 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 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 removed outlier: 3.520A pdb=" N GLU O7225 " --> pdb=" O HIS O7221 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY O7235 " --> pdb=" O ASP O7231 " (cutoff:3.500A) Processing helix chain 'O' and resid 7251 through 7269 removed outlier: 3.566A pdb=" N GLU O7263 " --> pdb=" O MET O7259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU O7266 " --> pdb=" O ARG O7262 " (cutoff:3.500A) Processing helix chain 'O' and resid 7271 through 7283 removed outlier: 3.710A pdb=" N ALA O7275 " --> pdb=" O ARG O7271 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU O7283 " --> pdb=" O PHE O7279 " (cutoff:3.500A) Processing helix chain 'O' and resid 7284 through 7295 Processing helix chain 'O' and resid 7297 through 7313 removed outlier: 3.615A pdb=" N LEU O7302 " --> pdb=" O ALA O7298 " (cutoff:3.500A) Processing helix chain 'O' and resid 7338 through 7357 Processing helix chain 'P' and resid 7376 through 7396 removed outlier: 3.553A pdb=" N ILE P7390 " --> pdb=" O ALA P7386 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER P7396 " --> pdb=" O GLU P7392 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL P7456 " --> pdb=" O THR P7452 " (cutoff:3.500A) Processing helix chain 'P' and resid 7475 through 7498 Processing helix chain 'P' and resid 7505 through 7518 Processing helix chain 'P' and resid 7520 through 7524 removed outlier: 3.702A pdb=" N LYS P7524 " --> pdb=" O GLY P7521 " (cutoff:3.500A) Processing helix chain 'P' and resid 7525 through 7541 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 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 removed outlier: 3.520A pdb=" N GLU P7716 " --> pdb=" O HIS P7712 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY P7726 " --> pdb=" O ASP P7722 " (cutoff:3.500A) Processing helix chain 'P' and resid 7742 through 7760 removed outlier: 3.566A pdb=" N GLU P7754 " --> pdb=" O MET P7750 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU P7757 " --> pdb=" O ARG P7753 " (cutoff:3.500A) Processing helix chain 'P' and resid 7762 through 7774 removed outlier: 3.709A pdb=" N ALA P7766 " --> pdb=" O ARG P7762 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU P7774 " --> pdb=" O PHE P7770 " (cutoff:3.500A) Processing helix chain 'P' and resid 7775 through 7786 Processing helix chain 'P' and resid 7788 through 7804 removed outlier: 3.614A pdb=" N LEU P7793 " --> pdb=" O ALA P7789 " (cutoff:3.500A) Processing helix chain 'P' and resid 7829 through 7848 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 52 removed outlier: 7.345A pdb=" N ASP A 39 " --> pdb=" O ASP H3923 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE H3925 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET A 41 " --> pdb=" O ILE H3925 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 134 through 135 Processing sheet with id= C, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.450A pdb=" N LYS A 188 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 341 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU A 190 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.913A pdb=" N ASP A 311 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 225 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 313 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.913A pdb=" N ASP A 311 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 225 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 313 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE A 298 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 228 " --> pdb=" O ILE A 298 " (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 'A' and resid 484 through 489 removed outlier: 6.911A pdb=" N ASP B 530 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP A 486 " --> pdb=" O ASP B 530 " (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: 6.449A pdb=" N LYS B 679 " --> pdb=" O MET B 830 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE B 832 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU B 681 " --> pdb=" O ILE B 832 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 697 through 699 removed outlier: 6.914A pdb=" N ASP B 802 " --> pdb=" O LYS B 716 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS B 716 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY B 804 " --> pdb=" O ASP B 714 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 697 through 699 removed outlier: 6.914A pdb=" N ASP B 802 " --> pdb=" O LYS B 716 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS B 716 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY B 804 " --> pdb=" O ASP B 714 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE B 789 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 719 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 936 through 937 Processing sheet with id= M, first strand: chain 'B' and resid 975 through 980 removed outlier: 6.910A pdb=" N ASP C1021 " --> pdb=" O ILE B 975 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP B 977 " --> pdb=" O ASP C1021 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1116 through 1117 Processing sheet with id= O, first strand: chain 'C' and resid 1169 through 1173 removed outlier: 6.450A pdb=" N LYS C1170 " --> pdb=" O MET C1321 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE C1323 " --> pdb=" O LYS C1170 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU C1172 " --> pdb=" O ILE C1323 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 6.913A pdb=" N ASP C1293 " --> pdb=" O LYS C1207 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS C1207 " --> pdb=" O ASP C1293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY C1295 " --> pdb=" O ASP C1205 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 6.913A pdb=" N ASP C1293 " --> pdb=" O LYS C1207 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS C1207 " --> pdb=" O ASP C1293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY C1295 " --> pdb=" O ASP C1205 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE C1280 " --> pdb=" O ILE C1208 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C1210 " --> pdb=" O ILE C1280 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1427 through 1428 Processing sheet with id= S, first strand: chain 'C' and resid 1466 through 1471 removed outlier: 6.907A pdb=" N ASP D1512 " --> pdb=" O ILE C1466 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP C1468 " --> pdb=" O ASP D1512 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 1607 through 1608 Processing sheet with id= U, first strand: chain 'D' and resid 1660 through 1664 removed outlier: 6.450A pdb=" N LYS D1661 " --> pdb=" O MET D1812 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE D1814 " --> pdb=" O LYS D1661 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D1663 " --> pdb=" O ILE D1814 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 1679 through 1681 removed outlier: 6.914A pdb=" N ASP D1784 " --> pdb=" O LYS D1698 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS D1698 " --> pdb=" O ASP D1784 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY D1786 " --> pdb=" O ASP D1696 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1679 through 1681 removed outlier: 6.914A pdb=" N ASP D1784 " --> pdb=" O LYS D1698 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS D1698 " --> pdb=" O ASP D1784 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY D1786 " --> pdb=" O ASP D1696 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE D1771 " --> pdb=" O ILE D1699 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU D1701 " --> pdb=" O ILE D1771 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1918 through 1919 Processing sheet with id= Y, first strand: chain 'D' and resid 1957 through 1962 removed outlier: 6.911A pdb=" N ASP E2003 " --> pdb=" O ILE D1957 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP D1959 " --> pdb=" O ASP E2003 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 2098 through 2099 Processing sheet with id= AA, first strand: chain 'E' and resid 2151 through 2155 removed outlier: 6.449A pdb=" N LYS E2152 " --> pdb=" O MET E2303 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE E2305 " --> pdb=" O LYS E2152 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU E2154 " --> pdb=" O ILE E2305 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 2170 through 2172 removed outlier: 6.913A pdb=" N ASP E2275 " --> pdb=" O LYS E2189 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E2189 " --> pdb=" O ASP E2275 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E2277 " --> pdb=" O ASP E2187 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 2170 through 2172 removed outlier: 6.913A pdb=" N ASP E2275 " --> pdb=" O LYS E2189 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E2189 " --> pdb=" O ASP E2275 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E2277 " --> pdb=" O ASP E2187 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE E2262 " --> pdb=" O ILE E2190 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU E2192 " --> pdb=" O ILE E2262 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 2409 through 2410 Processing sheet with id= AE, first strand: chain 'E' and resid 2448 through 2453 removed outlier: 6.906A pdb=" N ASP F2494 " --> pdb=" O ILE E2448 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP E2450 " --> pdb=" O ASP F2494 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 2589 through 2590 Processing sheet with id= AG, first strand: chain 'F' and resid 2642 through 2646 removed outlier: 6.449A pdb=" N LYS F2643 " --> pdb=" O MET F2794 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE F2796 " --> pdb=" O LYS F2643 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU F2645 " --> pdb=" O ILE F2796 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 2661 through 2663 removed outlier: 6.914A pdb=" N ASP F2766 " --> pdb=" O LYS F2680 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS F2680 " --> pdb=" O ASP F2766 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY F2768 " --> pdb=" O ASP F2678 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 2661 through 2663 removed outlier: 6.914A pdb=" N ASP F2766 " --> pdb=" O LYS F2680 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS F2680 " --> pdb=" O ASP F2766 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY F2768 " --> pdb=" O ASP F2678 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE F2753 " --> pdb=" O ILE F2681 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU F2683 " --> pdb=" O ILE F2753 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 2900 through 2901 Processing sheet with id= AK, first strand: chain 'F' and resid 2939 through 2944 removed outlier: 6.910A pdb=" N ASP G2985 " --> pdb=" O ILE F2939 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP F2941 " --> pdb=" O ASP G2985 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 3080 through 3081 Processing sheet with id= AM, first strand: chain 'G' and resid 3133 through 3137 removed outlier: 6.450A pdb=" N LYS G3134 " --> pdb=" O MET G3285 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE G3287 " --> pdb=" O LYS G3134 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU G3136 " --> pdb=" O ILE G3287 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 3152 through 3154 removed outlier: 6.913A pdb=" N ASP G3257 " --> pdb=" O LYS G3171 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS G3171 " --> pdb=" O ASP G3257 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY G3259 " --> pdb=" O ASP G3169 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 3152 through 3154 removed outlier: 6.913A pdb=" N ASP G3257 " --> pdb=" O LYS G3171 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS G3171 " --> pdb=" O ASP G3257 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY G3259 " --> pdb=" O ASP G3169 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE G3244 " --> pdb=" O ILE G3172 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU G3174 " --> pdb=" O ILE G3244 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 3391 through 3392 Processing sheet with id= AQ, first strand: chain 'G' and resid 3430 through 3435 removed outlier: 6.908A pdb=" N ASP H3476 " --> pdb=" O ILE G3430 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G3432 " --> pdb=" O ASP H3476 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 3571 through 3572 Processing sheet with id= AS, first strand: chain 'H' and resid 3624 through 3628 removed outlier: 6.450A pdb=" N LYS H3625 " --> pdb=" O MET H3776 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE H3778 " --> pdb=" O LYS H3625 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU H3627 " --> pdb=" O ILE H3778 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 3643 through 3645 removed outlier: 6.914A pdb=" N ASP H3748 " --> pdb=" O LYS H3662 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS H3662 " --> pdb=" O ASP H3748 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY H3750 " --> pdb=" O ASP H3660 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 3643 through 3645 removed outlier: 6.914A pdb=" N ASP H3748 " --> pdb=" O LYS H3662 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS H3662 " --> pdb=" O ASP H3748 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY H3750 " --> pdb=" O ASP H3660 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE H3735 " --> pdb=" O ILE H3663 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU H3665 " --> pdb=" O ILE H3735 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 3882 through 3883 Processing sheet with id= AW, first strand: chain 'I' and resid 3977 through 3980 removed outlier: 7.347A pdb=" N ASP I3967 " --> pdb=" O ASP P7851 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE P7853 " --> pdb=" O ASP I3967 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET I3969 " --> pdb=" O ILE P7853 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 4062 through 4063 Processing sheet with id= AY, first strand: chain 'I' and resid 4115 through 4119 removed outlier: 6.450A pdb=" N LYS I4116 " --> pdb=" O MET I4267 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE I4269 " --> pdb=" O LYS I4116 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU I4118 " --> pdb=" O ILE I4269 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'I' and resid 4134 through 4136 removed outlier: 6.914A pdb=" N ASP I4239 " --> pdb=" O LYS I4153 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS I4153 " --> pdb=" O ASP I4239 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY I4241 " --> pdb=" O ASP I4151 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'I' and resid 4134 through 4136 removed outlier: 6.914A pdb=" N ASP I4239 " --> pdb=" O LYS I4153 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS I4153 " --> pdb=" O ASP I4239 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY I4241 " --> pdb=" O ASP I4151 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE I4226 " --> pdb=" O ILE I4154 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU I4156 " --> pdb=" O ILE I4226 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 4373 through 4374 Processing sheet with id= BC, first strand: chain 'I' and resid 4412 through 4417 removed outlier: 6.911A pdb=" N ASP J4458 " --> pdb=" O ILE I4412 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP I4414 " --> pdb=" O ASP J4458 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 4553 through 4554 Processing sheet with id= BE, first strand: chain 'J' and resid 4606 through 4610 removed outlier: 6.450A pdb=" N LYS J4607 " --> pdb=" O MET J4758 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE J4760 " --> pdb=" O LYS J4607 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU J4609 " --> pdb=" O ILE J4760 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 4625 through 4627 removed outlier: 6.913A pdb=" N ASP J4730 " --> pdb=" O LYS J4644 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS J4644 " --> pdb=" O ASP J4730 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY J4732 " --> pdb=" O ASP J4642 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'J' and resid 4625 through 4627 removed outlier: 6.913A pdb=" N ASP J4730 " --> pdb=" O LYS J4644 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS J4644 " --> pdb=" O ASP J4730 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY J4732 " --> pdb=" O ASP J4642 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE J4717 " --> pdb=" O ILE J4645 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU J4647 " --> pdb=" O ILE J4717 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 4864 through 4865 Processing sheet with id= BI, first strand: chain 'J' and resid 4903 through 4908 removed outlier: 6.906A pdb=" N ASP K4949 " --> pdb=" O ILE J4903 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP J4905 " --> pdb=" O ASP K4949 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'K' and resid 5044 through 5045 Processing sheet with id= BK, first strand: chain 'K' and resid 5097 through 5101 removed outlier: 6.450A pdb=" N LYS K5098 " --> pdb=" O MET K5249 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE K5251 " --> pdb=" O LYS K5098 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU K5100 " --> pdb=" O ILE K5251 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'K' and resid 5116 through 5118 removed outlier: 6.912A pdb=" N ASP K5221 " --> pdb=" O LYS K5135 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS K5135 " --> pdb=" O ASP K5221 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY K5223 " --> pdb=" O ASP K5133 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'K' and resid 5116 through 5118 removed outlier: 6.912A pdb=" N ASP K5221 " --> pdb=" O LYS K5135 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS K5135 " --> pdb=" O ASP K5221 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY K5223 " --> pdb=" O ASP K5133 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE K5208 " --> pdb=" O ILE K5136 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU K5138 " --> pdb=" O ILE K5208 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'K' and resid 5355 through 5356 Processing sheet with id= BO, first strand: chain 'K' and resid 5394 through 5399 removed outlier: 6.912A pdb=" N ASP L5440 " --> pdb=" O ILE K5394 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASP K5396 " --> pdb=" O ASP L5440 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'L' and resid 5535 through 5536 Processing sheet with id= BQ, first strand: chain 'L' and resid 5588 through 5592 removed outlier: 6.450A pdb=" N LYS L5589 " --> pdb=" O MET L5740 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE L5742 " --> pdb=" O LYS L5589 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU L5591 " --> pdb=" O ILE L5742 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'L' and resid 5607 through 5609 removed outlier: 6.913A pdb=" N ASP L5712 " --> pdb=" O LYS L5626 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS L5626 " --> pdb=" O ASP L5712 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY L5714 " --> pdb=" O ASP L5624 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'L' and resid 5607 through 5609 removed outlier: 6.913A pdb=" N ASP L5712 " --> pdb=" O LYS L5626 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS L5626 " --> pdb=" O ASP L5712 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY L5714 " --> pdb=" O ASP L5624 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ILE L5699 " --> pdb=" O ILE L5627 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU L5629 " --> pdb=" O ILE L5699 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'L' and resid 5846 through 5847 Processing sheet with id= BU, first strand: chain 'L' and resid 5885 through 5890 removed outlier: 6.906A pdb=" N ASP M5931 " --> pdb=" O ILE L5885 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP L5887 " --> pdb=" O ASP M5931 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'M' and resid 6026 through 6027 Processing sheet with id= BW, first strand: chain 'M' and resid 6079 through 6083 removed outlier: 6.449A pdb=" N LYS M6080 " --> pdb=" O MET M6231 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE M6233 " --> pdb=" O LYS M6080 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU M6082 " --> pdb=" O ILE M6233 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'M' and resid 6098 through 6100 removed outlier: 6.914A pdb=" N ASP M6203 " --> pdb=" O LYS M6117 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS M6117 " --> pdb=" O ASP M6203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY M6205 " --> pdb=" O ASP M6115 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'M' and resid 6098 through 6100 removed outlier: 6.914A pdb=" N ASP M6203 " --> pdb=" O LYS M6117 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS M6117 " --> pdb=" O ASP M6203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY M6205 " --> pdb=" O ASP M6115 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE M6190 " --> pdb=" O ILE M6118 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU M6120 " --> pdb=" O ILE M6190 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'M' and resid 6337 through 6338 Processing sheet with id= CA, first strand: chain 'M' and resid 6376 through 6381 removed outlier: 6.912A pdb=" N ASP N6422 " --> pdb=" O ILE M6376 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP M6378 " --> pdb=" O ASP N6422 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'N' and resid 6517 through 6518 Processing sheet with id= CC, first strand: chain 'N' and resid 6570 through 6574 removed outlier: 6.450A pdb=" N LYS N6571 " --> pdb=" O MET N6722 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE N6724 " --> pdb=" O LYS N6571 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU N6573 " --> pdb=" O ILE N6724 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'N' and resid 6589 through 6591 removed outlier: 6.913A pdb=" N ASP N6694 " --> pdb=" O LYS N6608 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS N6608 " --> pdb=" O ASP N6694 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY N6696 " --> pdb=" O ASP N6606 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'N' and resid 6589 through 6591 removed outlier: 6.913A pdb=" N ASP N6694 " --> pdb=" O LYS N6608 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS N6608 " --> pdb=" O ASP N6694 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY N6696 " --> pdb=" O ASP N6606 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE N6681 " --> pdb=" O ILE N6609 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU N6611 " --> pdb=" O ILE N6681 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'N' and resid 6828 through 6829 Processing sheet with id= CG, first strand: chain 'N' and resid 6867 through 6872 removed outlier: 6.908A pdb=" N ASP O6913 " --> pdb=" O ILE N6867 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP N6869 " --> pdb=" O ASP O6913 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'O' and resid 7008 through 7009 Processing sheet with id= CI, first strand: chain 'O' and resid 7061 through 7065 removed outlier: 6.450A pdb=" N LYS O7062 " --> pdb=" O MET O7213 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE O7215 " --> pdb=" O LYS O7062 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU O7064 " --> pdb=" O ILE O7215 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'O' and resid 7080 through 7082 removed outlier: 6.913A pdb=" N ASP O7185 " --> pdb=" O LYS O7099 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS O7099 " --> pdb=" O ASP O7185 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY O7187 " --> pdb=" O ASP O7097 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'O' and resid 7080 through 7082 removed outlier: 6.913A pdb=" N ASP O7185 " --> pdb=" O LYS O7099 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS O7099 " --> pdb=" O ASP O7185 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY O7187 " --> pdb=" O ASP O7097 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N ILE O7172 " --> pdb=" O ILE O7100 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU O7102 " --> pdb=" O ILE O7172 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'O' and resid 7319 through 7320 Processing sheet with id= CM, first strand: chain 'O' and resid 7358 through 7363 removed outlier: 6.909A pdb=" N ASP P7404 " --> pdb=" O ILE O7358 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP O7360 " --> pdb=" O ASP P7404 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'P' and resid 7499 through 7500 Processing sheet with id= CO, first strand: chain 'P' and resid 7552 through 7556 removed outlier: 6.449A pdb=" N LYS P7553 " --> pdb=" O MET P7704 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE P7706 " --> pdb=" O LYS P7553 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU P7555 " --> pdb=" O ILE P7706 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'P' and resid 7571 through 7573 removed outlier: 6.914A pdb=" N ASP P7676 " --> pdb=" O LYS P7590 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS P7590 " --> pdb=" O ASP P7676 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY P7678 " --> pdb=" O ASP P7588 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'P' and resid 7571 through 7573 removed outlier: 6.914A pdb=" N ASP P7676 " --> pdb=" O LYS P7590 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS P7590 " --> pdb=" O ASP P7676 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY P7678 " --> pdb=" O ASP P7588 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N ILE P7663 " --> pdb=" O ILE P7591 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU P7593 " --> pdb=" O ILE P7663 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'P' and resid 7810 through 7811 4106 hydrogen bonds defined for protein. 11598 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: 63.17 Time building geometry restraints manager: 19.92 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: 12836 1.32 - 1.44: 9356 1.44 - 1.56: 35936 1.56 - 1.69: 0 1.69 - 1.81: 656 Bond restraints: 58784 Sorted by residual: bond pdb=" C ALA O7317 " pdb=" O ALA O7317 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.08e-02 8.57e+03 7.12e+01 bond pdb=" C ALA H3880 " pdb=" O ALA H3880 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.08e-02 8.57e+03 7.12e+01 bond pdb=" C ALA K5353 " pdb=" O ALA K5353 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.08e-02 8.57e+03 7.12e+01 bond pdb=" C ALA P7808 " pdb=" O ALA P7808 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.08e-02 8.57e+03 7.10e+01 bond pdb=" C ALA G3389 " pdb=" O ALA G3389 " ideal model delta sigma weight residual 1.235 1.326 -0.091 1.08e-02 8.57e+03 7.10e+01 ... (remaining 58779 not shown) Histogram of bond angle deviations from ideal: 100.83 - 106.91: 1307 106.91 - 112.99: 32157 112.99 - 119.08: 18091 119.08 - 125.16: 26855 125.16 - 131.24: 758 Bond angle restraints: 79168 Sorted by residual: angle pdb=" CA GLU A 4 " pdb=" C GLU A 4 " pdb=" O GLU A 4 " ideal model delta sigma weight residual 120.92 106.14 14.78 1.14e+00 7.69e-01 1.68e+02 angle pdb=" CA GLU G2950 " pdb=" C GLU G2950 " pdb=" O GLU G2950 " ideal model delta sigma weight residual 120.92 106.14 14.78 1.14e+00 7.69e-01 1.68e+02 angle pdb=" CA GLU N6387 " pdb=" C GLU N6387 " pdb=" O GLU N6387 " ideal model delta sigma weight residual 120.92 106.14 14.78 1.14e+00 7.69e-01 1.68e+02 angle pdb=" CA GLU B 495 " pdb=" C GLU B 495 " pdb=" O GLU B 495 " ideal model delta sigma weight residual 120.92 106.15 14.77 1.14e+00 7.69e-01 1.68e+02 angle pdb=" CA GLU D1477 " pdb=" C GLU D1477 " pdb=" O GLU D1477 " ideal model delta sigma weight residual 120.92 106.15 14.77 1.14e+00 7.69e-01 1.68e+02 ... (remaining 79163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 34460 15.12 - 30.25: 1573 30.25 - 45.37: 431 45.37 - 60.49: 416 60.49 - 75.62: 64 Dihedral angle restraints: 36944 sinusoidal: 14512 harmonic: 22432 Sorted by residual: dihedral pdb=" C ALA P7808 " pdb=" N ALA P7808 " pdb=" CA ALA P7808 " pdb=" CB ALA P7808 " 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 D1916 " pdb=" N ALA D1916 " pdb=" CA ALA D1916 " pdb=" CB ALA D1916 " ideal model delta harmonic sigma weight residual -122.60 -133.69 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C ALA I4371 " pdb=" N ALA I4371 " pdb=" CA ALA I4371 " pdb=" CB ALA I4371 " ideal model delta harmonic sigma weight residual -122.60 -133.68 11.08 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 36941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 7401 0.084 - 0.167: 1803 0.167 - 0.251: 447 0.251 - 0.334: 61 0.334 - 0.418: 16 Chirality restraints: 9728 Sorted by residual: chirality pdb=" CA ALA P7808 " pdb=" N ALA P7808 " pdb=" C ALA P7808 " pdb=" CB ALA P7808 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.37e+00 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 2.07 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ALA E2407 " pdb=" N ALA E2407 " pdb=" C ALA E2407 " pdb=" CB ALA E2407 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 9725 not shown) Planarity restraints: 10256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M6011 " 0.042 2.00e-02 2.50e+03 8.50e-02 7.23e+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 delta sigma weight rms_deltas residual plane pdb=" CA GLN N6502 " 0.042 2.00e-02 2.50e+03 8.49e-02 7.21e+01 pdb=" C GLN N6502 " -0.147 2.00e-02 2.50e+03 pdb=" O GLN N6502 " 0.052 2.00e-02 2.50e+03 pdb=" N ALA N6503 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN P7484 " -0.042 2.00e-02 2.50e+03 8.49e-02 7.21e+01 pdb=" C GLN P7484 " 0.147 2.00e-02 2.50e+03 pdb=" O GLN P7484 " -0.052 2.00e-02 2.50e+03 pdb=" N ALA P7485 " -0.053 2.00e-02 2.50e+03 ... (remaining 10253 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 24980 2.95 - 3.44: 65191 3.44 - 3.92: 97891 3.92 - 4.41: 107270 4.41 - 4.90: 181299 Nonbonded interactions: 476631 Sorted by model distance: nonbonded pdb=" O VAL M5921 " pdb=" OG1 THR M5924 " model vdw 2.461 2.440 nonbonded pdb=" O VAL J4448 " pdb=" OG1 THR J4451 " model vdw 2.461 2.440 nonbonded pdb=" O VAL N6412 " pdb=" OG1 THR N6415 " model vdw 2.461 2.440 nonbonded pdb=" O VAL P7394 " pdb=" OG1 THR P7397 " model vdw 2.461 2.440 nonbonded pdb=" O VAL A 29 " pdb=" OG1 THR A 32 " model vdw 2.462 2.440 ... (remaining 476626 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: 0.040 Extract box with map and model: 4.440 Check model and map are aligned: 0.660 Set scattering table: 0.400 Process input model: 161.460 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5021 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 58784 Z= 0.915 Angle : 1.478 14.780 79168 Z= 1.097 Chirality : 0.082 0.418 9728 Planarity : 0.019 0.085 10256 Dihedral : 12.446 75.615 22416 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.04 % Favored : 97.55 % Rotamer: Outliers : 0.77 % Allowed : 4.63 % Favored : 94.60 % 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: -1.62 (0.08), residues: 7824 helix: -1.29 (0.06), residues: 4304 sheet: -0.90 (0.14), residues: 1120 loop : -0.21 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J4529 PHE 0.038 0.005 PHE F2903 TYR 0.054 0.006 TYR C 991 ARG 0.011 0.003 ARG N6701 *********************** 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 142 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 142 average time/residue: 0.1800 time to fit residues: 29.7757 Evaluate side-chains 84 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4504 ------------------------------------------------------------------------------- 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: 6.9990 chunk 594 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 400 optimal weight: 0.0470 chunk 317 optimal weight: 0.3980 chunk 614 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 457 optimal weight: 20.0000 chunk 711 optimal weight: 7.9990 overall best weight: 4.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1780 GLN D1919 ASN D1942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 58784 Z= 0.222 Angle : 0.633 6.215 79168 Z= 0.354 Chirality : 0.042 0.153 9728 Planarity : 0.005 0.058 10256 Dihedral : 4.494 16.101 8256 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.25 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 0.54 (0.09), residues: 7824 helix: 0.58 (0.07), residues: 4288 sheet: 0.55 (0.18), residues: 928 loop : 0.16 (0.11), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K4976 PHE 0.009 0.002 PHE P7692 TYR 0.007 0.002 TYR B 881 ARG 0.012 0.001 ARG F2938 *********************** 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 99 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.330 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: 99 average time/residue: 0.1567 time to fit residues: 18.6392 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4465 ------------------------------------------------------------------------------- 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: 9.9990 chunk 220 optimal weight: 6.9990 chunk 592 optimal weight: 1.9990 chunk 484 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 713 optimal weight: 0.0670 chunk 770 optimal weight: 10.0000 chunk 635 optimal weight: 8.9990 chunk 707 optimal weight: 0.0670 chunk 243 optimal weight: 10.0000 chunk 572 optimal weight: 9.9990 overall best weight: 3.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H3544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H3563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H3733 ASN ** H3872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H3883 ASN H3906 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58784 Z= 0.179 Angle : 0.611 8.166 79168 Z= 0.323 Chirality : 0.042 0.230 9728 Planarity : 0.004 0.036 10256 Dihedral : 4.395 15.840 8256 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: 0.90 (0.09), residues: 7824 helix: 1.03 (0.08), residues: 4368 sheet: 0.41 (0.17), residues: 928 loop : 0.12 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1417 PHE 0.007 0.002 PHE A 327 TYR 0.005 0.001 TYR D1863 ARG 0.004 0.001 ARG G3429 *********************** 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 76 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.342 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: 76 average time/residue: 0.1501 time to fit residues: 14.2678 Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4585 ------------------------------------------------------------------------------- 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: 1.9990 chunk 536 optimal weight: 9.9990 chunk 370 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 340 optimal weight: 5.9990 chunk 478 optimal weight: 0.1980 chunk 715 optimal weight: 0.7980 chunk 757 optimal weight: 5.9990 chunk 373 optimal weight: 20.0000 chunk 678 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N6490 GLN ** N6509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5594 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 58784 Z= 0.184 Angle : 0.603 7.472 79168 Z= 0.319 Chirality : 0.044 0.187 9728 Planarity : 0.004 0.043 10256 Dihedral : 4.424 20.007 8256 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.43 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.88 (0.09), residues: 7824 helix: 1.20 (0.08), residues: 4336 sheet: 0.66 (0.18), residues: 800 loop : -0.33 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C1417 PHE 0.007 0.001 PHE I4255 TYR 0.002 0.001 TYR K4919 ARG 0.008 0.001 ARG D1503 *********************** REFINEMENT MACRO_CYCLE 4 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 76 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.346 Fit side-chains revert: symmetry clash 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: 76 average time/residue: 0.1586 time to fit residues: 15.0523 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4631 ------------------------------------------------------------------------------- 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: 7.9990 chunk 430 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 564 optimal weight: 8.9990 chunk 312 optimal weight: 20.0000 chunk 646 optimal weight: 7.9990 chunk 523 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 386 optimal weight: 8.9990 chunk 680 optimal weight: 8.9990 chunk 191 optimal weight: 0.0030 overall best weight: 6.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M6018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M6332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M6338 ASN M6350 ASN ** M6361 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: 0.5923 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 58784 Z= 0.237 Angle : 0.686 6.814 79168 Z= 0.368 Chirality : 0.044 0.193 9728 Planarity : 0.005 0.035 10256 Dihedral : 4.768 21.029 8256 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.86 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.32 (0.09), residues: 7824 helix: 0.73 (0.08), residues: 4352 sheet: 0.36 (0.17), residues: 960 loop : -0.60 (0.11), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H3872 PHE 0.013 0.003 PHE A 448 TYR 0.008 0.001 TYR H3706 ARG 0.006 0.001 ARG C1465 *********************** REFINEMENT MACRO_CYCLE 5 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 78 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 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: 78 average time/residue: 0.1391 time to fit residues: 13.5763 Evaluate side-chains 58 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4479 ------------------------------------------------------------------------------- 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: 2.9990 chunk 682 optimal weight: 0.0270 chunk 149 optimal weight: 9.9990 chunk 444 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 758 optimal weight: 1.9990 chunk 629 optimal weight: 0.9990 chunk 351 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 250 optimal weight: 0.0770 chunk 398 optimal weight: 0.0170 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H3906 GLN ** 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: 0.5715 moved from start: 0.8055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 58784 Z= 0.186 Angle : 0.663 8.635 79168 Z= 0.348 Chirality : 0.045 0.205 9728 Planarity : 0.003 0.033 10256 Dihedral : 4.462 26.234 8256 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.64 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 0.30 (0.09), residues: 7824 helix: 0.71 (0.08), residues: 4352 sheet: 0.70 (0.18), residues: 800 loop : -0.67 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P7431 PHE 0.004 0.001 PHE E2291 TYR 0.010 0.002 TYR J4537 ARG 0.002 0.000 ARG G3429 *********************** 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 79 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.415 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: 79 average time/residue: 0.1516 time to fit residues: 14.9670 Evaluate side-chains 65 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4617 ------------------------------------------------------------------------------- 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: 0.6980 chunk 85 optimal weight: 10.0000 chunk 432 optimal weight: 0.9980 chunk 553 optimal weight: 0.0470 chunk 429 optimal weight: 20.0000 chunk 638 optimal weight: 5.9990 chunk 423 optimal weight: 9.9990 chunk 755 optimal weight: 0.3980 chunk 472 optimal weight: 6.9990 chunk 460 optimal weight: 0.4980 chunk 348 optimal weight: 0.0970 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1451 GLN ** 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: 0.5698 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58784 Z= 0.183 Angle : 0.632 7.556 79168 Z= 0.344 Chirality : 0.046 0.208 9728 Planarity : 0.004 0.039 10256 Dihedral : 4.318 25.326 8256 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: 0.49 (0.08), residues: 4320 sheet: 0.59 (0.18), residues: 800 loop : -0.92 (0.11), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O6940 PHE 0.003 0.001 PHE A 405 TYR 0.006 0.001 TYR A 269 ARG 0.005 0.000 ARG J4761 *********************** REFINEMENT MACRO_CYCLE 7 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 74 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1388 time to fit residues: 12.9092 Evaluate side-chains 58 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4509 ------------------------------------------------------------------------------- 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: 20.0000 chunk 301 optimal weight: 6.9990 chunk 451 optimal weight: 9.9990 chunk 227 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 480 optimal weight: 9.9990 chunk 514 optimal weight: 7.9990 chunk 373 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 593 optimal weight: 0.0980 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5527 GLN ** L5870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 moved from start: 0.8843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 58784 Z= 0.182 Angle : 0.657 8.741 79168 Z= 0.347 Chirality : 0.043 0.140 9728 Planarity : 0.004 0.038 10256 Dihedral : 4.386 18.281 8256 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.25 % Favored : 97.55 % 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 : 0.00 % 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: -0.02 (0.09), residues: 7824 helix: 0.46 (0.08), residues: 4336 sheet: 0.80 (0.18), residues: 800 loop : -0.91 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O6940 PHE 0.005 0.001 PHE G3394 TYR 0.006 0.001 TYR D1742 ARG 0.011 0.001 ARG E2063 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1503 time to fit residues: 14.1908 Evaluate side-chains 52 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5149 ------------------------------------------------------------------------------- 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: 6.9990 chunk 723 optimal weight: 20.0000 chunk 660 optimal weight: 0.0970 chunk 704 optimal weight: 20.0000 chunk 423 optimal weight: 0.2980 chunk 306 optimal weight: 20.0000 chunk 552 optimal weight: 0.0010 chunk 216 optimal weight: 0.0470 chunk 636 optimal weight: 7.9990 chunk 665 optimal weight: 8.9990 chunk 701 optimal weight: 3.9990 overall best weight: 0.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N6852 GLN ** 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: 0.5739 moved from start: 0.8993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58784 Z= 0.175 Angle : 0.664 9.346 79168 Z= 0.350 Chirality : 0.044 0.152 9728 Planarity : 0.003 0.032 10256 Dihedral : 4.328 22.123 8256 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.25 % Favored : 97.55 % 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: -0.29 (0.09), residues: 7824 helix: 0.19 (0.07), residues: 4240 sheet: 0.65 (0.17), residues: 800 loop : -0.88 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K4976 PHE 0.007 0.001 PHE G3273 TYR 0.006 0.001 TYR A 269 ARG 0.010 0.001 ARG D1887 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1376 time to fit residues: 12.5312 Evaluate side-chains 59 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4554 ------------------------------------------------------------------------------- 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: 3.9990 chunk 744 optimal weight: 6.9990 chunk 454 optimal weight: 0.0060 chunk 353 optimal weight: 10.0000 chunk 517 optimal weight: 0.0980 chunk 781 optimal weight: 0.0040 chunk 718 optimal weight: 0.9980 chunk 621 optimal weight: 0.0970 chunk 64 optimal weight: 20.0000 chunk 480 optimal weight: 9.9990 chunk 381 optimal weight: 0.0070 overall best weight: 0.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1451 GLN ** 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: 0.5696 moved from start: 0.9198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 58784 Z= 0.169 Angle : 0.656 9.578 79168 Z= 0.342 Chirality : 0.043 0.143 9728 Planarity : 0.003 0.033 10256 Dihedral : 4.143 15.581 8256 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % 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 : 0.00 % 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: 0.18 (0.07), residues: 4240 sheet: 0.68 (0.17), residues: 800 loop : -0.98 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 557 PHE 0.006 0.001 PHE H3764 TYR 0.006 0.001 TYR I4197 ARG 0.008 0.001 ARG H3851 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1617 time to fit residues: 15.0843 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4809 ------------------------------------------------------------------------------- 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: 0.0070 chunk 662 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 573 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 172 optimal weight: 2.9990 chunk 622 optimal weight: 5.9990 chunk 260 optimal weight: 0.2980 chunk 639 optimal weight: 8.9990 chunk 78 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P7834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.083193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063357 restraints weight = 22458.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.064998 restraints weight = 16684.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066356 restraints weight = 13304.508| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.9352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 58784 Z= 0.164 Angle : 0.662 9.291 79168 Z= 0.349 Chirality : 0.044 0.146 9728 Planarity : 0.003 0.032 10256 Dihedral : 4.243 22.373 8256 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -0.41 (0.09), residues: 7824 helix: 0.17 (0.07), residues: 4336 sheet: 0.56 (0.17), residues: 800 loop : -1.12 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS L5467 PHE 0.005 0.001 PHE J4746 TYR 0.005 0.001 TYR A 269 ARG 0.005 0.000 ARG B 833 =============================================================================== Job complete usr+sys time: 4669.91 seconds wall clock time: 87 minutes 21.35 seconds (5241.35 seconds total)