Starting phenix.real_space_refine on Tue Feb 20 06:49:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdt_29012/02_2024/8fdt_29012_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians V 1 8.30 5 P 9 5.49 5 S 150 5.16 5 C 17195 2.51 5 N 4702 2.21 5 O 5039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A ASP 1380": "OD1" <-> "OD2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A PHE 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1459": "OE1" <-> "OE2" Residue "A ASP 1462": "OD1" <-> "OD2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A PHE 1732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1738": "OE1" <-> "OE2" Residue "A GLU 1755": "OE1" <-> "OE2" Residue "A PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1999": "OD1" <-> "OD2" Residue "A PHE 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2161": "OD1" <-> "OD2" Residue "A ARG 2183": "NH1" <-> "NH2" Residue "A GLU 2249": "OE1" <-> "OE2" Residue "A GLU 2254": "OE1" <-> "OE2" Residue "A GLU 2271": "OE1" <-> "OE2" Residue "A PHE 2291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2320": "OE1" <-> "OE2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A TYR 2527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2559": "OD1" <-> "OD2" Residue "A GLU 2607": "OE1" <-> "OE2" Residue "A GLU 2670": "OE1" <-> "OE2" Residue "A ASP 2689": "OD1" <-> "OD2" Residue "A PHE 2751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 388": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27096 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 21981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2736, 21981 Classifications: {'peptide': 2736} Link IDs: {'PTRANS': 127, 'TRANS': 2608} Chain breaks: 7 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "C" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'ATP': 1, 'VO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 13.91, per 1000 atoms: 0.51 Number of scatterers: 27096 At special positions: 0 Unit cell: (125.241, 167.754, 172.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 1 22.97 S 150 16.00 P 9 15.00 O 5039 8.00 N 4702 7.00 C 17195 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: 10.95 Conformation dependent library (CDL) restraints added in 4.8 seconds 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 31 sheets defined 44.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.35 Creating SS restraints... Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.555A pdb=" N MET A 202 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 273 removed outlier: 3.999A pdb=" N ILE A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 322 through 342 Processing helix chain 'A' and resid 347 through 373 removed outlier: 3.706A pdb=" N HIS A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.830A pdb=" N GLN A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 removed outlier: 3.751A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 624 Proline residue: A 616 - end of helix removed outlier: 3.645A pdb=" N GLU A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 699 through 709 Processing helix chain 'A' and resid 721 through 734 removed outlier: 4.099A pdb=" N GLU A 726 " --> pdb=" O ALA A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 761 Processing helix chain 'A' and resid 775 through 789 removed outlier: 3.781A pdb=" N ARG A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 810 Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 839 through 841 No H-bonds generated for 'chain 'A' and resid 839 through 841' Processing helix chain 'A' and resid 857 through 860 Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 916 through 927 Processing helix chain 'A' and resid 956 through 972 Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 977 through 987 Processing helix chain 'A' and resid 996 through 1020 Processing helix chain 'A' and resid 1028 through 1047 removed outlier: 3.997A pdb=" N VAL A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1066 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1117 through 1131 Processing helix chain 'A' and resid 1146 through 1156 removed outlier: 3.669A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1183 Processing helix chain 'A' and resid 1223 through 1233 Processing helix chain 'A' and resid 1270 through 1275 removed outlier: 3.571A pdb=" N ARG A1274 " --> pdb=" O HIS A1270 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N HIS A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1270 through 1275' Processing helix chain 'A' and resid 1286 through 1303 removed outlier: 3.621A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU A1303 " --> pdb=" O ALA A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1328 removed outlier: 4.328A pdb=" N GLU A1312 " --> pdb=" O THR A1309 " (cutoff:3.500A) Proline residue: A1313 - end of helix removed outlier: 3.990A pdb=" N ARG A1328 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1355 Processing helix chain 'A' and resid 1363 through 1378 Processing helix chain 'A' and resid 1385 through 1402 Processing helix chain 'A' and resid 1408 through 1411 No H-bonds generated for 'chain 'A' and resid 1408 through 1411' Processing helix chain 'A' and resid 1431 through 1448 removed outlier: 3.613A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1472 Processing helix chain 'A' and resid 1488 through 1498 Processing helix chain 'A' and resid 1514 through 1528 Processing helix chain 'A' and resid 1547 through 1559 Processing helix chain 'A' and resid 1569 through 1585 Processing helix chain 'A' and resid 1592 through 1605 Processing helix chain 'A' and resid 1619 through 1626 Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1644 through 1656 Processing helix chain 'A' and resid 1684 through 1708 removed outlier: 3.685A pdb=" N ASN A1690 " --> pdb=" O GLU A1686 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1718 through 1764 Processing helix chain 'A' and resid 1951 through 1994 removed outlier: 3.840A pdb=" N GLU A1963 " --> pdb=" O SER A1959 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG A1966 " --> pdb=" O ALA A1962 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A1975 " --> pdb=" O SER A1971 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A1982 " --> pdb=" O MET A1978 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2016 Processing helix chain 'A' and resid 2027 through 2031 Processing helix chain 'A' and resid 2034 through 2042 removed outlier: 3.563A pdb=" N ARG A2039 " --> pdb=" O ASP A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2059 Processing helix chain 'A' and resid 2073 through 2081 Processing helix chain 'A' and resid 2083 through 2085 No H-bonds generated for 'chain 'A' and resid 2083 through 2085' Processing helix chain 'A' and resid 2095 through 2107 removed outlier: 4.094A pdb=" N ARG A2098 " --> pdb=" O ASP A2095 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A2100 " --> pdb=" O PHE A2097 " (cutoff:3.500A) Processing helix chain 'A' and resid 2121 through 2128 Proline residue: A2125 - end of helix Processing helix chain 'A' and resid 2168 through 2171 No H-bonds generated for 'chain 'A' and resid 2168 through 2171' Processing helix chain 'A' and resid 2183 through 2198 Processing helix chain 'A' and resid 2200 through 2233 Processing helix chain 'A' and resid 2241 through 2267 removed outlier: 3.761A pdb=" N ILE A2245 " --> pdb=" O ASP A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2269 through 2298 removed outlier: 3.819A pdb=" N TYR A2279 " --> pdb=" O VAL A2275 " (cutoff:3.500A) Proline residue: A2281 - end of helix removed outlier: 4.346A pdb=" N LYS A2297 " --> pdb=" O MET A2293 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLN A2298 " --> pdb=" O GLU A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2318 Processing helix chain 'A' and resid 2330 through 2352 removed outlier: 4.090A pdb=" N GLY A2352 " --> pdb=" O ARG A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2358 through 2371 Processing helix chain 'A' and resid 2380 through 2387 Processing helix chain 'A' and resid 2407 through 2418 removed outlier: 4.107A pdb=" N CYS A2418 " --> pdb=" O VAL A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2420 through 2422 No H-bonds generated for 'chain 'A' and resid 2420 through 2422' Processing helix chain 'A' and resid 2425 through 2430 removed outlier: 3.580A pdb=" N GLN A2430 " --> pdb=" O ILE A2426 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2439 Processing helix chain 'A' and resid 2460 through 2474 Processing helix chain 'A' and resid 2476 through 2491 removed outlier: 4.127A pdb=" N LEU A2480 " --> pdb=" O ASP A2477 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A2491 " --> pdb=" O SER A2488 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2500 No H-bonds generated for 'chain 'A' and resid 2498 through 2500' Processing helix chain 'A' and resid 2505 through 2511 Processing helix chain 'A' and resid 2530 through 2539 Processing helix chain 'A' and resid 2554 through 2567 removed outlier: 4.280A pdb=" N LYS A2567 " --> pdb=" O ASN A2563 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2591 Processing helix chain 'A' and resid 2614 through 2619 Processing helix chain 'A' and resid 2630 through 2641 Processing helix chain 'A' and resid 2652 through 2674 removed outlier: 3.544A pdb=" N ALA A2655 " --> pdb=" O ASN A2652 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A2668 " --> pdb=" O HIS A2665 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A2670 " --> pdb=" O ILE A2667 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A2671 " --> pdb=" O ILE A2668 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG A2673 " --> pdb=" O GLU A2670 " (cutoff:3.500A) Processing helix chain 'A' and resid 2687 through 2704 Processing helix chain 'A' and resid 2713 through 2715 No H-bonds generated for 'chain 'A' and resid 2713 through 2715' Processing helix chain 'A' and resid 2718 through 2727 Processing helix chain 'A' and resid 2731 through 2733 No H-bonds generated for 'chain 'A' and resid 2731 through 2733' Processing helix chain 'A' and resid 2737 through 2750 Processing helix chain 'A' and resid 2753 through 2756 Processing helix chain 'A' and resid 2780 through 2788 Processing helix chain 'A' and resid 2796 through 2799 Processing helix chain 'A' and resid 2807 through 2824 Processing helix chain 'A' and resid 2854 through 2868 Processing helix chain 'A' and resid 2886 through 2916 Processing helix chain 'A' and resid 2924 through 2934 Processing helix chain 'A' and resid 2953 through 2976 Processing helix chain 'A' and resid 2995 through 3009 Processing helix chain 'A' and resid 3110 through 3115 Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.234A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 298 removed outlier: 4.853A pdb=" N SER C 292 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 228 through 230 Processing sheet with id= B, first strand: chain 'A' and resid 446 through 450 removed outlier: 3.649A pdb=" N LEU A 584 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 472 through 476 removed outlier: 6.554A pdb=" N TRP A 499 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N PHE A 475 " --> pdb=" O TRP A 499 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N CYS A 501 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 558 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 502 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 560 " --> pdb=" O PHE A 502 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 542 through 545 removed outlier: 4.332A pdb=" N ILE A 542 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 544 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 551 " --> pdb=" O CYS A 544 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 905 through 908 removed outlier: 7.974A pdb=" N LEU A 765 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 886 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N MET A 767 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE A 888 " --> pdb=" O MET A 767 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLN A 844 " --> pdb=" O ARG A 885 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET A 887 " --> pdb=" O GLN A 844 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 846 " --> pdb=" O MET A 887 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU A 889 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 848 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 811 through 813 Processing sheet with id= G, first strand: chain 'A' and resid 869 through 871 Processing sheet with id= H, first strand: chain 'A' and resid 1277 through 1280 removed outlier: 3.651A pdb=" N VAL A1254 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A1161 " --> pdb=" O TRP A1203 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1193 through 1195 removed outlier: 3.933A pdb=" N VAL A1193 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1536 through 1540 removed outlier: 6.334A pdb=" N HIS A1608 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET A1539 " --> pdb=" O HIS A1608 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A1610 " --> pdb=" O MET A1539 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A1478 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET A1613 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1480 " --> pdb=" O MET A1613 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A1635 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A1481 " --> pdb=" O VAL A1635 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN A1637 " --> pdb=" O ILE A1481 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 2175 through 2178 removed outlier: 7.800A pdb=" N ILE A2155 " --> pdb=" O PRO A2065 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N ILE A2067 " --> pdb=" O ILE A2155 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A2157 " --> pdb=" O ILE A2067 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A2111 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N SER A2158 " --> pdb=" O LEU A2111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A2113 " --> pdb=" O SER A2158 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A2088 " --> pdb=" O LEU A2112 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A2114 " --> pdb=" O THR A2088 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A2090 " --> pdb=" O GLN A2114 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2138 through 2142 removed outlier: 4.466A pdb=" N VAL A2138 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 2621 through 2625 removed outlier: 3.567A pdb=" N MET A2606 " --> pdb=" O MET A2521 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A2572 " --> pdb=" O PHE A2603 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR A2605 " --> pdb=" O VAL A2572 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A2574 " --> pdb=" O THR A2605 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLU A2607 " --> pdb=" O LEU A2574 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 2986 through 2988 removed outlier: 7.032A pdb=" N GLY A3037 " --> pdb=" O VAL A2987 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A3036 " --> pdb=" O LEU A3068 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 3041 through 3043 removed outlier: 3.900A pdb=" N LEU A3041 " --> pdb=" O LEU A3063 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 3046 through 3048 Processing sheet with id= Q, first strand: chain 'A' and resid 3082 through 3088 removed outlier: 3.887A pdb=" N PHE A3098 " --> pdb=" O VAL A3087 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 112 through 117 removed outlier: 6.681A pdb=" N ALA B 127 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL B 115 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 125 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP B 137 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 143 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 154 through 159 removed outlier: 6.907A pdb=" N CYS B 169 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 157 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 167 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE B 159 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 165 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 170 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 187 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 179 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 185 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 196 through 201 removed outlier: 6.591A pdb=" N ALA B 211 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 199 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 209 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE B 201 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS B 207 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 212 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 229 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU B 221 " --> pdb=" O CYS B 227 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS B 227 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 238 through 243 removed outlier: 6.722A pdb=" N CYS B 253 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 241 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 251 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 249 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 263 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS B 269 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 280 through 285 removed outlier: 6.814A pdb=" N GLY B 315 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 283 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 313 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP B 285 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE B 311 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 316 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 325 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 331 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 374 through 377 Processing sheet with id= X, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.859A pdb=" N VAL B 407 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 104 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 405 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 386 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.815A pdb=" N ALA C 127 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL C 115 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 125 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP C 137 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 143 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 154 through 159 removed outlier: 6.933A pdb=" N CYS C 169 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 157 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 167 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 159 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C 165 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 187 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP C 179 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N CYS C 185 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 196 through 201 removed outlier: 6.295A pdb=" N ALA C 211 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 199 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 209 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE C 201 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS C 207 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 212 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR C 216 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 229 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU C 221 " --> pdb=" O CYS C 227 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 227 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 238 through 243 removed outlier: 6.846A pdb=" N CYS C 253 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 241 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 251 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU C 249 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL C 263 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS C 269 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 280 through 285 removed outlier: 6.889A pdb=" N GLY C 315 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 283 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C 313 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP C 285 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE C 311 " --> pdb=" O TRP C 285 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 316 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 325 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS C 331 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.408A pdb=" N THR C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 358 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 387 through 389 removed outlier: 6.347A pdb=" N GLU C 409 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU C 101 " --> pdb=" O GLU C 409 " (cutoff:3.500A) 1193 hydrogen bonds defined for protein. 3282 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: 14.43 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 8895 1.35 - 1.49: 6941 1.49 - 1.63: 11619 1.63 - 1.77: 0 1.77 - 1.91: 248 Bond restraints: 27703 Sorted by residual: bond pdb=" C4 ADP A3204 " pdb=" C5 ADP A3204 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP A3202 " pdb=" C5 ADP A3202 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP A3203 " pdb=" C5 ADP A3203 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta sigma weight residual 1.455 1.490 -0.035 7.00e-03 2.04e+04 2.56e+01 bond pdb=" C5 ADP A3202 " pdb=" C6 ADP A3202 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 27698 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.12: 427 104.12 - 111.74: 13226 111.74 - 119.35: 10348 119.35 - 126.96: 13163 126.96 - 134.57: 404 Bond angle restraints: 37568 Sorted by residual: angle pdb=" PB ATP A3201 " pdb=" O3B ATP A3201 " pdb=" PG ATP A3201 " ideal model delta sigma weight residual 139.87 129.63 10.24 1.00e+00 1.00e+00 1.05e+02 angle pdb=" PA ATP A3201 " pdb=" O3A ATP A3201 " pdb=" PB ATP A3201 " ideal model delta sigma weight residual 136.83 129.26 7.57 1.00e+00 1.00e+00 5.74e+01 angle pdb=" N PRO C 99 " pdb=" CA PRO C 99 " pdb=" C PRO C 99 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 angle pdb=" N PRO B 99 " pdb=" CA PRO B 99 " pdb=" C PRO B 99 " ideal model delta sigma weight residual 110.70 117.56 -6.86 1.22e+00 6.72e-01 3.16e+01 angle pdb=" N VAL A1674 " pdb=" CA VAL A1674 " pdb=" C VAL A1674 " ideal model delta sigma weight residual 111.56 106.75 4.81 8.60e-01 1.35e+00 3.13e+01 ... (remaining 37563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 16185 30.36 - 60.72: 468 60.72 - 91.08: 44 91.08 - 121.43: 1 121.43 - 151.79: 2 Dihedral angle restraints: 16700 sinusoidal: 6874 harmonic: 9826 Sorted by residual: dihedral pdb=" O1B ADP A3204 " pdb=" O3A ADP A3204 " pdb=" PB ADP A3204 " pdb=" PA ADP A3204 " ideal model delta sinusoidal sigma weight residual 300.00 148.20 151.79 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP A3202 " pdb=" O5' ADP A3202 " pdb=" PA ADP A3202 " pdb=" O2A ADP A3202 " ideal model delta sinusoidal sigma weight residual 300.00 169.69 130.31 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" O2A ADP A3204 " pdb=" O3A ADP A3204 " pdb=" PA ADP A3204 " pdb=" PB ADP A3204 " ideal model delta sinusoidal sigma weight residual -60.00 51.45 -111.45 1 2.00e+01 2.50e-03 3.28e+01 ... (remaining 16697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2924 0.043 - 0.085: 861 0.085 - 0.128: 322 0.128 - 0.171: 84 0.171 - 0.214: 18 Chirality restraints: 4209 Sorted by residual: chirality pdb=" C3' ADP A3203 " pdb=" C2' ADP A3203 " pdb=" C4' ADP A3203 " pdb=" O3' ADP A3203 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' ADP A3204 " pdb=" C2' ADP A3204 " pdb=" C4' ADP A3204 " pdb=" O3' ADP A3204 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL A 857 " pdb=" CA VAL A 857 " pdb=" CG1 VAL A 857 " pdb=" CG2 VAL A 857 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4206 not shown) Planarity restraints: 4790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2650 " -0.058 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A2651 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A2651 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A2651 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1089 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C GLU A1089 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A1089 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP A1090 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2456 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A2457 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2457 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2457 " -0.027 5.00e-02 4.00e+02 ... (remaining 4787 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 15 2.25 - 2.92: 11191 2.92 - 3.58: 41112 3.58 - 4.24: 65048 4.24 - 4.90: 109925 Nonbonded interactions: 227291 Sorted by model distance: nonbonded pdb=" N GLN A 426 " pdb=" OE1 GLN A 426 " model vdw 1.592 2.520 nonbonded pdb=" OE2 GLU A 787 " pdb=" NH1 ARG A 788 " model vdw 2.146 2.520 nonbonded pdb=" OE1 GLU A 354 " pdb=" OG SER A 601 " model vdw 2.200 2.440 nonbonded pdb=" OG SER A 380 " pdb=" OE1 GLU A 382 " model vdw 2.200 2.440 nonbonded pdb=" O LEU A 599 " pdb=" N GLN A 602 " model vdw 2.207 2.520 ... (remaining 227286 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 11.490 Check model and map are aligned: 0.410 Set scattering table: 0.280 Process input model: 75.140 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.005 0.110 27703 Z= 0.366 Angle : 0.797 12.955 37568 Z= 0.497 Chirality : 0.050 0.214 4209 Planarity : 0.004 0.086 4790 Dihedral : 13.940 151.793 10320 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.88 % Rotamer: Outliers : 0.27 % Allowed : 0.94 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3348 helix: 1.30 (0.13), residues: 1537 sheet: -0.85 (0.23), residues: 511 loop : -0.77 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1093 HIS 0.008 0.001 HIS B 382 PHE 0.018 0.001 PHE B 347 TYR 0.019 0.002 TYR A 283 ARG 0.010 0.000 ARG A2260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 625 time to evaluate : 3.009 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: A 160 LEU cc_start: 0.6716 (tt) cc_final: 0.6497 (tp) REVERT: A 165 GLU cc_start: 0.6249 (mm-30) cc_final: 0.5777 (tm-30) REVERT: A 361 VAL cc_start: 0.7386 (p) cc_final: 0.6706 (m) REVERT: A 557 MET cc_start: 0.6886 (tpp) cc_final: 0.6614 (mmm) REVERT: A 678 GLU cc_start: 0.6867 (pm20) cc_final: 0.6640 (mm-30) REVERT: A 1026 MET cc_start: 0.7677 (tmm) cc_final: 0.7047 (ttt) REVERT: A 1169 SER cc_start: 0.8427 (p) cc_final: 0.7602 (t) REVERT: A 1507 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6898 (mtmm) REVERT: A 1658 MET cc_start: 0.7923 (mtp) cc_final: 0.7552 (mtp) REVERT: A 1677 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7749 (tmtt) REVERT: A 1762 GLU cc_start: 0.6183 (pp20) cc_final: 0.5726 (tt0) REVERT: A 1981 ILE cc_start: 0.8266 (tt) cc_final: 0.7972 (tt) REVERT: A 2189 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7117 (mt0) REVERT: A 2204 GLU cc_start: 0.7715 (tp30) cc_final: 0.7241 (tp30) REVERT: A 2219 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6434 (tpt90) REVERT: A 2252 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7184 (pttp) REVERT: A 2601 ARG cc_start: 0.8722 (mmt-90) cc_final: 0.8465 (mpt180) REVERT: A 2606 MET cc_start: 0.8069 (ptm) cc_final: 0.7602 (ptt) REVERT: A 2679 TRP cc_start: 0.7511 (m100) cc_final: 0.6978 (m100) REVERT: A 2706 LYS cc_start: 0.6506 (tptp) cc_final: 0.6113 (mptt) REVERT: A 2725 MET cc_start: 0.6825 (mmt) cc_final: 0.6525 (mmt) REVERT: A 2863 SER cc_start: 0.7538 (t) cc_final: 0.6918 (p) REVERT: A 2911 ASP cc_start: 0.6332 (t0) cc_final: 0.5914 (m-30) REVERT: B 114 ARG cc_start: 0.6062 (mtt90) cc_final: 0.5235 (ttt180) REVERT: B 156 ASP cc_start: 0.5948 (t0) cc_final: 0.5523 (m-30) REVERT: B 204 ASN cc_start: 0.7028 (p0) cc_final: 0.6713 (p0) REVERT: B 206 ASP cc_start: 0.7765 (m-30) cc_final: 0.6992 (p0) REVERT: B 219 MET cc_start: 0.5919 (tmm) cc_final: 0.5533 (tmm) REVERT: B 229 LYS cc_start: 0.5708 (ptpt) cc_final: 0.5434 (pptt) REVERT: B 390 HIS cc_start: 0.3893 (t-90) cc_final: 0.3368 (t-170) REVERT: C 189 MET cc_start: 0.6354 (mtt) cc_final: 0.5769 (mmt) REVERT: C 201 ILE cc_start: 0.7445 (mp) cc_final: 0.7186 (mt) REVERT: C 204 ASN cc_start: 0.6584 (t0) cc_final: 0.6260 (p0) REVERT: C 334 THR cc_start: 0.8205 (t) cc_final: 0.7770 (m) outliers start: 8 outliers final: 2 residues processed: 631 average time/residue: 0.4471 time to fit residues: 431.9256 Evaluate side-chains 352 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 350 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 86 optimal weight: 0.0070 chunk 171 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 198 HIS A 716 HIS A 922 ASN A1166 ASN A1577 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2000 GLN A2013 HIS A2114 GLN A2217 GLN A2270 GLN A2315 HIS ** A2434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2501 GLN A2532 HIS A2586 GLN A2875 HIS A3022 ASN A3051 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27703 Z= 0.192 Angle : 0.587 10.685 37568 Z= 0.295 Chirality : 0.042 0.167 4209 Planarity : 0.005 0.083 4790 Dihedral : 6.322 136.302 3717 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 1.40 % Allowed : 9.03 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3348 helix: 1.57 (0.13), residues: 1521 sheet: -0.67 (0.23), residues: 488 loop : -0.65 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 136 HIS 0.005 0.001 HIS C 390 PHE 0.024 0.001 PHE B 183 TYR 0.025 0.001 TYR A1293 ARG 0.009 0.000 ARG A2415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 383 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6759 (tt) cc_final: 0.6509 (tp) REVERT: A 165 GLU cc_start: 0.6140 (mm-30) cc_final: 0.5759 (tm-30) REVERT: A 251 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6528 (pm20) REVERT: A 361 VAL cc_start: 0.7285 (p) cc_final: 0.6546 (m) REVERT: A 557 MET cc_start: 0.6939 (tpp) cc_final: 0.6598 (ttt) REVERT: A 563 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8310 (mtm) REVERT: A 678 GLU cc_start: 0.7093 (pm20) cc_final: 0.6773 (mm-30) REVERT: A 1026 MET cc_start: 0.7769 (tmm) cc_final: 0.7220 (ttt) REVERT: A 1373 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 1412 MET cc_start: 0.6228 (mmt) cc_final: 0.5978 (mmm) REVERT: A 1427 ILE cc_start: 0.8248 (tt) cc_final: 0.8018 (mt) REVERT: A 1507 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6681 (mtmm) REVERT: A 1541 GLU cc_start: 0.6724 (pt0) cc_final: 0.6508 (pt0) REVERT: A 1658 MET cc_start: 0.8235 (mtp) cc_final: 0.7994 (mtt) REVERT: A 1677 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7728 (tmtt) REVERT: A 1762 GLU cc_start: 0.5925 (pp20) cc_final: 0.5590 (tt0) REVERT: A 2107 PHE cc_start: 0.7298 (m-80) cc_final: 0.7084 (m-10) REVERT: A 2204 GLU cc_start: 0.7543 (tp30) cc_final: 0.7278 (tp30) REVERT: A 2219 ARG cc_start: 0.7641 (tpt170) cc_final: 0.7393 (ttm170) REVERT: A 2252 LYS cc_start: 0.7598 (mtmm) cc_final: 0.7350 (mtmm) REVERT: A 2279 TYR cc_start: 0.5526 (m-10) cc_final: 0.4956 (m-10) REVERT: A 2601 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8464 (mpt180) REVERT: A 2606 MET cc_start: 0.7954 (ptm) cc_final: 0.7752 (ptt) REVERT: A 2679 TRP cc_start: 0.7519 (m100) cc_final: 0.6976 (m100) REVERT: A 2706 LYS cc_start: 0.6485 (tptp) cc_final: 0.6110 (mptt) REVERT: A 2725 MET cc_start: 0.6803 (mmt) cc_final: 0.6592 (mmt) REVERT: A 2863 SER cc_start: 0.7511 (t) cc_final: 0.6887 (p) REVERT: A 2911 ASP cc_start: 0.6348 (t0) cc_final: 0.5943 (m-30) REVERT: B 114 ARG cc_start: 0.6049 (mtt90) cc_final: 0.5066 (ttt180) REVERT: B 183 PHE cc_start: 0.8264 (m-10) cc_final: 0.7996 (m-10) REVERT: B 204 ASN cc_start: 0.7076 (p0) cc_final: 0.6732 (p0) REVERT: B 206 ASP cc_start: 0.7824 (m-30) cc_final: 0.6986 (p0) REVERT: B 219 MET cc_start: 0.5772 (tmm) cc_final: 0.5272 (tmm) REVERT: B 323 MET cc_start: 0.4379 (OUTLIER) cc_final: 0.3931 (mpp) REVERT: B 333 MET cc_start: 0.3668 (ttm) cc_final: 0.3297 (tpt) REVERT: B 390 HIS cc_start: 0.4086 (t-90) cc_final: 0.3586 (t-170) REVERT: C 109 ARG cc_start: 0.7519 (tpt90) cc_final: 0.7154 (mtp-110) REVERT: C 189 MET cc_start: 0.6522 (mtt) cc_final: 0.5462 (mmt) REVERT: C 204 ASN cc_start: 0.6719 (t0) cc_final: 0.6402 (p0) REVERT: C 272 GLU cc_start: 0.7585 (tt0) cc_final: 0.7075 (tm-30) REVERT: C 353 PHE cc_start: 0.6958 (m-80) cc_final: 0.6723 (m-80) REVERT: C 374 MET cc_start: 0.7484 (tmm) cc_final: 0.6884 (tmm) outliers start: 42 outliers final: 26 residues processed: 409 average time/residue: 0.4437 time to fit residues: 291.9385 Evaluate side-chains 356 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1530 CYS Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 124 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 0.0980 chunk 253 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 304 optimal weight: 0.3980 chunk 329 optimal weight: 0.2980 chunk 271 optimal weight: 3.9990 chunk 302 optimal weight: 0.0980 chunk 103 optimal weight: 0.1980 chunk 244 optimal weight: 0.9980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2004 GLN A2532 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27703 Z= 0.142 Angle : 0.543 12.670 37568 Z= 0.270 Chirality : 0.040 0.151 4209 Planarity : 0.004 0.080 4790 Dihedral : 5.775 115.875 3717 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 1.67 % Allowed : 11.17 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3348 helix: 1.72 (0.13), residues: 1519 sheet: -0.68 (0.23), residues: 499 loop : -0.55 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 262 HIS 0.008 0.001 HIS A2532 PHE 0.028 0.001 PHE C 183 TYR 0.014 0.001 TYR A2030 ARG 0.006 0.000 ARG A1302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 359 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.6778 (tt) cc_final: 0.6535 (tp) REVERT: A 165 GLU cc_start: 0.6435 (mm-30) cc_final: 0.5980 (tm-30) REVERT: A 175 TYR cc_start: 0.6491 (m-80) cc_final: 0.6268 (m-80) REVERT: A 215 ASN cc_start: 0.7818 (t0) cc_final: 0.7596 (t0) REVERT: A 361 VAL cc_start: 0.7280 (p) cc_final: 0.6582 (m) REVERT: A 557 MET cc_start: 0.6830 (tpp) cc_final: 0.6595 (ttt) REVERT: A 678 GLU cc_start: 0.7031 (pm20) cc_final: 0.6735 (mm-30) REVERT: A 1026 MET cc_start: 0.7853 (tmm) cc_final: 0.7429 (ttt) REVERT: A 1373 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 1424 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8156 (ptpp) REVERT: A 1507 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6671 (mtmm) REVERT: A 1677 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7475 (tmtt) REVERT: A 1686 GLU cc_start: 0.7015 (mp0) cc_final: 0.6693 (mp0) REVERT: A 1991 PHE cc_start: 0.8345 (t80) cc_final: 0.7996 (t80) REVERT: A 2204 GLU cc_start: 0.7389 (tp30) cc_final: 0.7098 (tp30) REVERT: A 2219 ARG cc_start: 0.7690 (tpt170) cc_final: 0.7156 (ttm170) REVERT: A 2279 TYR cc_start: 0.5506 (m-10) cc_final: 0.4993 (m-10) REVERT: A 2601 ARG cc_start: 0.8684 (mmt-90) cc_final: 0.8434 (mpt180) REVERT: A 2679 TRP cc_start: 0.7361 (m100) cc_final: 0.6881 (m100) REVERT: A 2706 LYS cc_start: 0.6397 (tptp) cc_final: 0.6061 (mptt) REVERT: A 2774 MET cc_start: 0.8090 (tpp) cc_final: 0.7272 (tpt) REVERT: A 2863 SER cc_start: 0.7489 (t) cc_final: 0.6887 (p) REVERT: A 2911 ASP cc_start: 0.6358 (t0) cc_final: 0.5953 (m-30) REVERT: B 114 ARG cc_start: 0.5674 (mtt90) cc_final: 0.4603 (ttt180) REVERT: B 192 HIS cc_start: 0.5485 (t-90) cc_final: 0.5120 (t-90) REVERT: B 204 ASN cc_start: 0.7290 (p0) cc_final: 0.6913 (p0) REVERT: B 323 MET cc_start: 0.4383 (OUTLIER) cc_final: 0.3989 (mpp) REVERT: B 333 MET cc_start: 0.3550 (ttm) cc_final: 0.3229 (tpt) REVERT: B 390 HIS cc_start: 0.3625 (t-90) cc_final: 0.3061 (t-170) REVERT: C 183 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5250 (m-10) REVERT: C 189 MET cc_start: 0.6458 (mtt) cc_final: 0.5392 (mmt) REVERT: C 204 ASN cc_start: 0.6604 (t0) cc_final: 0.6365 (p0) REVERT: C 272 GLU cc_start: 0.7565 (tt0) cc_final: 0.7086 (tm-30) REVERT: C 324 TRP cc_start: 0.7187 (OUTLIER) cc_final: 0.6440 (m100) REVERT: C 374 MET cc_start: 0.7187 (tmm) cc_final: 0.6539 (tmm) outliers start: 50 outliers final: 31 residues processed: 386 average time/residue: 0.4025 time to fit residues: 249.5945 Evaluate side-chains 364 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 330 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2189 GLN Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain A residue 3048 CYS Chi-restraints excluded: chain A residue 3101 ASP Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 183 PHE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 30.0000 chunk 229 optimal weight: 0.0010 chunk 158 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 305 optimal weight: 0.7980 chunk 323 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 GLN A2004 GLN A2013 HIS A2114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 27703 Z= 0.297 Angle : 0.606 11.224 37568 Z= 0.303 Chirality : 0.043 0.196 4209 Planarity : 0.004 0.081 4790 Dihedral : 5.916 118.045 3716 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.64 % Allowed : 12.70 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3348 helix: 1.46 (0.13), residues: 1522 sheet: -0.57 (0.23), residues: 472 loop : -0.58 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 136 HIS 0.014 0.001 HIS A2532 PHE 0.022 0.002 PHE C 183 TYR 0.022 0.002 TYR B 138 ARG 0.006 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 327 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5806 (tm-30) REVERT: A 175 TYR cc_start: 0.6575 (m-80) cc_final: 0.6280 (m-80) REVERT: A 201 LYS cc_start: 0.8218 (pptt) cc_final: 0.7895 (pptt) REVERT: A 361 VAL cc_start: 0.7242 (p) cc_final: 0.6406 (m) REVERT: A 479 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: A 678 GLU cc_start: 0.7102 (pm20) cc_final: 0.6802 (mm-30) REVERT: A 767 MET cc_start: 0.7977 (mtm) cc_final: 0.7622 (mtt) REVERT: A 1026 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7670 (ttt) REVERT: A 1373 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 1541 GLU cc_start: 0.6979 (pt0) cc_final: 0.6749 (pt0) REVERT: A 1677 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7690 (tmtt) REVERT: A 2076 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: A 2084 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5900 (p0) REVERT: A 2219 ARG cc_start: 0.7581 (tpt170) cc_final: 0.7223 (tpt170) REVERT: A 2279 TYR cc_start: 0.5908 (m-10) cc_final: 0.5432 (m-10) REVERT: A 2607 GLU cc_start: 0.7377 (tt0) cc_final: 0.7036 (mt-10) REVERT: A 2679 TRP cc_start: 0.7669 (m100) cc_final: 0.7038 (m100) REVERT: A 2706 LYS cc_start: 0.6528 (tptp) cc_final: 0.6074 (mptt) REVERT: A 2774 MET cc_start: 0.8440 (tpp) cc_final: 0.7441 (tpt) REVERT: A 2863 SER cc_start: 0.7402 (t) cc_final: 0.6762 (p) REVERT: A 2911 ASP cc_start: 0.6413 (t0) cc_final: 0.5942 (m-30) REVERT: B 114 ARG cc_start: 0.5987 (mtt90) cc_final: 0.4785 (ttt180) REVERT: B 192 HIS cc_start: 0.5125 (t-90) cc_final: 0.4578 (t-170) REVERT: B 204 ASN cc_start: 0.7239 (p0) cc_final: 0.7010 (p0) REVERT: B 206 ASP cc_start: 0.7867 (m-30) cc_final: 0.6879 (p0) REVERT: B 323 MET cc_start: 0.4439 (OUTLIER) cc_final: 0.4076 (mpp) REVERT: B 333 MET cc_start: 0.3515 (ttm) cc_final: 0.3220 (tpt) REVERT: C 189 MET cc_start: 0.6402 (mtt) cc_final: 0.5286 (mmt) REVERT: C 202 MET cc_start: 0.7777 (mmp) cc_final: 0.7533 (mmp) REVERT: C 204 ASN cc_start: 0.6773 (t0) cc_final: 0.6438 (p0) REVERT: C 374 MET cc_start: 0.7041 (tmm) cc_final: 0.6619 (tmm) outliers start: 79 outliers final: 49 residues processed: 377 average time/residue: 0.4024 time to fit residues: 243.9264 Evaluate side-chains 360 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 306 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1622 ASP Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2356 GLN Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2437 ILE Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2624 VAL Chi-restraints excluded: chain A residue 2736 ASN Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1372 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS A2532 HIS A2669 GLN B 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27703 Z= 0.307 Angle : 0.606 10.432 37568 Z= 0.305 Chirality : 0.043 0.215 4209 Planarity : 0.004 0.081 4790 Dihedral : 5.997 117.656 3716 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 2.77 % Allowed : 13.61 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3348 helix: 1.32 (0.13), residues: 1521 sheet: -0.60 (0.23), residues: 482 loop : -0.63 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 246 HIS 0.006 0.001 HIS A 466 PHE 0.021 0.002 PHE A 560 TYR 0.023 0.002 TYR B 138 ARG 0.006 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 325 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5733 (tm-30) REVERT: A 201 LYS cc_start: 0.8347 (pttt) cc_final: 0.7841 (pptt) REVERT: A 479 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: A 525 GLU cc_start: 0.6376 (tt0) cc_final: 0.5829 (mm-30) REVERT: A 678 GLU cc_start: 0.7125 (pm20) cc_final: 0.6747 (mm-30) REVERT: A 767 MET cc_start: 0.8083 (mtm) cc_final: 0.7802 (mtt) REVERT: A 787 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7301 (tt0) REVERT: A 1026 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7724 (ttt) REVERT: A 1373 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7905 (mm-30) REVERT: A 1541 GLU cc_start: 0.7065 (pt0) cc_final: 0.6788 (pt0) REVERT: A 1677 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7682 (tmtt) REVERT: A 1977 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6124 (mp10) REVERT: A 2076 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7034 (pm20) REVERT: A 2219 ARG cc_start: 0.7741 (tpt170) cc_final: 0.7338 (tpt170) REVERT: A 2260 ARG cc_start: 0.8801 (mtp180) cc_final: 0.8323 (ptp-170) REVERT: A 2279 TYR cc_start: 0.6120 (m-10) cc_final: 0.5754 (m-10) REVERT: A 2679 TRP cc_start: 0.7637 (m100) cc_final: 0.7069 (m100) REVERT: A 2706 LYS cc_start: 0.6545 (tptp) cc_final: 0.6086 (mptt) REVERT: A 2863 SER cc_start: 0.7544 (t) cc_final: 0.6910 (p) REVERT: A 2911 ASP cc_start: 0.6288 (t0) cc_final: 0.5925 (m-30) REVERT: A 3076 THR cc_start: 0.6456 (m) cc_final: 0.6250 (p) REVERT: B 114 ARG cc_start: 0.6042 (mtt90) cc_final: 0.4721 (ttt180) REVERT: B 192 HIS cc_start: 0.5290 (t-90) cc_final: 0.5001 (t-170) REVERT: B 204 ASN cc_start: 0.7239 (p0) cc_final: 0.7027 (p0) REVERT: B 206 ASP cc_start: 0.7841 (m-30) cc_final: 0.6809 (p0) REVERT: B 323 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.4326 (mpp) REVERT: B 324 TRP cc_start: 0.6297 (m-10) cc_final: 0.5680 (m-10) REVERT: B 333 MET cc_start: 0.3494 (ttm) cc_final: 0.3208 (tpt) REVERT: C 109 ARG cc_start: 0.7665 (tpt90) cc_final: 0.7322 (mmm160) REVERT: C 189 MET cc_start: 0.6477 (mtt) cc_final: 0.5386 (mmt) REVERT: C 204 ASN cc_start: 0.7160 (t0) cc_final: 0.6660 (p0) REVERT: C 374 MET cc_start: 0.7029 (tmm) cc_final: 0.6653 (tmm) outliers start: 83 outliers final: 53 residues processed: 381 average time/residue: 0.3763 time to fit residues: 233.5639 Evaluate side-chains 357 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 299 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1622 ASP Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2437 ILE Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2624 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 324 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS A2532 HIS B 161 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 27703 Z= 0.155 Angle : 0.537 11.382 37568 Z= 0.268 Chirality : 0.040 0.170 4209 Planarity : 0.004 0.080 4790 Dihedral : 5.626 105.564 3716 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 2.17 % Allowed : 15.08 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3348 helix: 1.60 (0.13), residues: 1519 sheet: -0.51 (0.24), residues: 488 loop : -0.51 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A2532 PHE 0.018 0.001 PHE A1024 TYR 0.024 0.001 TYR B 138 ARG 0.004 0.000 ARG A1302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 334 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6404 (mm-30) cc_final: 0.5899 (tm-30) REVERT: A 175 TYR cc_start: 0.6622 (m-80) cc_final: 0.6394 (m-80) REVERT: A 252 LYS cc_start: 0.7801 (tppt) cc_final: 0.7383 (ptmm) REVERT: A 479 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: A 525 GLU cc_start: 0.6364 (tt0) cc_final: 0.5826 (mm-30) REVERT: A 678 GLU cc_start: 0.7205 (pm20) cc_final: 0.6877 (mm-30) REVERT: A 787 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7347 (tt0) REVERT: A 971 TYR cc_start: 0.6810 (m-80) cc_final: 0.6565 (m-80) REVERT: A 1000 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8257 (mt) REVERT: A 1026 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7629 (ttt) REVERT: A 1373 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 1541 GLU cc_start: 0.6973 (pt0) cc_final: 0.6711 (pt0) REVERT: A 1677 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7574 (tmtt) REVERT: A 1977 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6117 (mp10) REVERT: A 2013 HIS cc_start: 0.7492 (t-90) cc_final: 0.7266 (t70) REVERT: A 2076 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: A 2204 GLU cc_start: 0.7065 (tp30) cc_final: 0.6771 (tp30) REVERT: A 2219 ARG cc_start: 0.7536 (tpt170) cc_final: 0.7212 (tpt170) REVERT: A 2279 TYR cc_start: 0.6103 (m-10) cc_final: 0.5794 (m-10) REVERT: A 2679 TRP cc_start: 0.7513 (m100) cc_final: 0.7014 (m100) REVERT: A 2706 LYS cc_start: 0.6391 (tptp) cc_final: 0.5936 (mptt) REVERT: A 2863 SER cc_start: 0.7472 (t) cc_final: 0.6866 (p) REVERT: A 2911 ASP cc_start: 0.6421 (t0) cc_final: 0.6034 (m-30) REVERT: A 3065 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5746 (tt) REVERT: B 114 ARG cc_start: 0.5792 (mtt90) cc_final: 0.4525 (ttt180) REVERT: B 192 HIS cc_start: 0.5240 (t-90) cc_final: 0.4905 (t-170) REVERT: B 204 ASN cc_start: 0.7188 (p0) cc_final: 0.6815 (p0) REVERT: B 285 TRP cc_start: 0.3496 (m100) cc_final: 0.3200 (m100) REVERT: B 323 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.4272 (mpp) REVERT: B 324 TRP cc_start: 0.6270 (m-10) cc_final: 0.5701 (m-10) REVERT: B 330 MET cc_start: 0.5120 (ppp) cc_final: 0.4731 (ppp) REVERT: C 189 MET cc_start: 0.6505 (mtt) cc_final: 0.5369 (mmt) REVERT: C 204 ASN cc_start: 0.7176 (t0) cc_final: 0.6643 (p0) REVERT: C 374 MET cc_start: 0.6957 (tmm) cc_final: 0.6585 (tmm) outliers start: 65 outliers final: 44 residues processed: 376 average time/residue: 0.3847 time to fit residues: 236.2560 Evaluate side-chains 361 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 310 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2268 VAL Chi-restraints excluded: chain A residue 2356 GLN Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2506 THR Chi-restraints excluded: chain A residue 2532 HIS Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2736 ASN Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain A residue 3065 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS A2343 GLN ** A2434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3090 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27703 Z= 0.297 Angle : 0.602 10.358 37568 Z= 0.301 Chirality : 0.042 0.190 4209 Planarity : 0.004 0.082 4790 Dihedral : 5.773 102.410 3716 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 2.88 % Allowed : 14.88 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3348 helix: 1.39 (0.13), residues: 1516 sheet: -0.62 (0.24), residues: 494 loop : -0.61 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 324 HIS 0.020 0.001 HIS A2532 PHE 0.019 0.002 PHE A 560 TYR 0.024 0.002 TYR B 138 ARG 0.008 0.001 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 314 time to evaluate : 3.087 Fit side-chains REVERT: A 165 GLU cc_start: 0.6088 (mm-30) cc_final: 0.5662 (tm-30) REVERT: A 175 TYR cc_start: 0.6690 (m-80) cc_final: 0.6341 (m-80) REVERT: A 177 VAL cc_start: 0.5892 (OUTLIER) cc_final: 0.5451 (t) REVERT: A 201 LYS cc_start: 0.8165 (pptt) cc_final: 0.7754 (pptt) REVERT: A 254 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6923 (ttp) REVERT: A 479 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: A 525 GLU cc_start: 0.6312 (tt0) cc_final: 0.5736 (mm-30) REVERT: A 678 GLU cc_start: 0.7138 (pm20) cc_final: 0.6688 (mm-30) REVERT: A 1000 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 1026 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7643 (ttt) REVERT: A 1373 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 1541 GLU cc_start: 0.7045 (pt0) cc_final: 0.6797 (pt0) REVERT: A 1677 LYS cc_start: 0.8269 (mmtp) cc_final: 0.7627 (tmtt) REVERT: A 1977 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: A 2076 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: A 2219 ARG cc_start: 0.7636 (tpt170) cc_final: 0.7316 (tpt170) REVERT: A 2260 ARG cc_start: 0.8837 (mtp180) cc_final: 0.8383 (ptp-170) REVERT: A 2679 TRP cc_start: 0.7571 (m100) cc_final: 0.7055 (m100) REVERT: A 2706 LYS cc_start: 0.6503 (tptp) cc_final: 0.6051 (mptt) REVERT: A 2863 SER cc_start: 0.7686 (t) cc_final: 0.7141 (p) REVERT: A 2911 ASP cc_start: 0.6321 (t0) cc_final: 0.6016 (m-30) REVERT: B 114 ARG cc_start: 0.5980 (mtt90) cc_final: 0.4729 (ttt90) REVERT: B 192 HIS cc_start: 0.5238 (t-90) cc_final: 0.4886 (t-170) REVERT: B 204 ASN cc_start: 0.7212 (p0) cc_final: 0.6726 (p0) REVERT: B 296 GLU cc_start: 0.3871 (OUTLIER) cc_final: 0.3033 (pm20) REVERT: B 324 TRP cc_start: 0.6252 (m-10) cc_final: 0.5822 (m-10) REVERT: B 330 MET cc_start: 0.5107 (ppp) cc_final: 0.4715 (ppp) REVERT: B 333 MET cc_start: 0.4969 (tpt) cc_final: 0.4693 (ttp) REVERT: C 189 MET cc_start: 0.6748 (mtt) cc_final: 0.5541 (mmt) REVERT: C 374 MET cc_start: 0.7066 (tmm) cc_final: 0.6744 (tmm) outliers start: 86 outliers final: 59 residues processed: 373 average time/residue: 0.3817 time to fit residues: 232.1061 Evaluate side-chains 361 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 294 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain A residue 1622 ASP Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2259 THR Chi-restraints excluded: chain A residue 2268 VAL Chi-restraints excluded: chain A residue 2269 MET Chi-restraints excluded: chain A residue 2356 GLN Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2437 ILE Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2520 LEU Chi-restraints excluded: chain A residue 2542 THR Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 97 optimal weight: 0.0170 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS A2532 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27703 Z= 0.169 Angle : 0.554 10.684 37568 Z= 0.275 Chirality : 0.040 0.146 4209 Planarity : 0.004 0.080 4790 Dihedral : 5.559 93.471 3716 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 2.31 % Allowed : 15.85 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3348 helix: 1.58 (0.13), residues: 1521 sheet: -0.60 (0.24), residues: 484 loop : -0.50 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.004 0.001 HIS A2532 PHE 0.019 0.001 PHE A1024 TYR 0.023 0.001 TYR B 138 ARG 0.005 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 315 time to evaluate : 3.309 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6361 (mm-30) cc_final: 0.5867 (tm-30) REVERT: A 175 TYR cc_start: 0.6614 (m-80) cc_final: 0.6269 (m-80) REVERT: A 254 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6894 (ttp) REVERT: A 479 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: A 525 GLU cc_start: 0.6303 (tt0) cc_final: 0.5734 (mm-30) REVERT: A 678 GLU cc_start: 0.7000 (pm20) cc_final: 0.6514 (mm-30) REVERT: A 1000 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 1026 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: A 1111 ASP cc_start: 0.7043 (p0) cc_final: 0.6709 (p0) REVERT: A 1541 GLU cc_start: 0.6996 (pt0) cc_final: 0.6727 (pt0) REVERT: A 1677 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7615 (tmtt) REVERT: A 1977 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6134 (mp10) REVERT: A 2076 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: A 2573 MET cc_start: 0.8933 (ttp) cc_final: 0.8718 (ttm) REVERT: A 2679 TRP cc_start: 0.7490 (m100) cc_final: 0.7019 (m100) REVERT: A 2706 LYS cc_start: 0.6494 (tptp) cc_final: 0.5994 (mptt) REVERT: A 2863 SER cc_start: 0.7630 (t) cc_final: 0.7113 (p) REVERT: A 2911 ASP cc_start: 0.6281 (t0) cc_final: 0.6023 (m-30) REVERT: B 114 ARG cc_start: 0.5945 (mtt90) cc_final: 0.4574 (ttt180) REVERT: B 192 HIS cc_start: 0.5103 (t-90) cc_final: 0.4827 (t-170) REVERT: B 296 GLU cc_start: 0.3848 (OUTLIER) cc_final: 0.3035 (pm20) REVERT: B 324 TRP cc_start: 0.6141 (m-10) cc_final: 0.5659 (m-10) REVERT: B 330 MET cc_start: 0.5118 (ppp) cc_final: 0.4786 (ppp) REVERT: C 189 MET cc_start: 0.6724 (mtt) cc_final: 0.5532 (mmt) REVERT: C 204 ASN cc_start: 0.7024 (t0) cc_final: 0.6737 (t0) REVERT: C 374 MET cc_start: 0.7032 (tmm) cc_final: 0.6603 (tmm) outliers start: 69 outliers final: 52 residues processed: 360 average time/residue: 0.3904 time to fit residues: 232.3496 Evaluate side-chains 358 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 299 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2152 SER Chi-restraints excluded: chain A residue 2268 VAL Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2520 LEU Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 407 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 282 optimal weight: 0.2980 chunk 300 optimal weight: 7.9990 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 299 optimal weight: 0.0040 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2315 HIS ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 27703 Z= 0.154 Angle : 0.541 10.664 37568 Z= 0.268 Chirality : 0.040 0.158 4209 Planarity : 0.004 0.080 4790 Dihedral : 5.377 86.748 3716 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.24 % Allowed : 16.18 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3348 helix: 1.70 (0.13), residues: 1519 sheet: -0.49 (0.24), residues: 482 loop : -0.45 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 246 HIS 0.006 0.001 HIS A2358 PHE 0.016 0.001 PHE A1457 TYR 0.023 0.001 TYR B 138 ARG 0.004 0.000 ARG A1302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 3.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5868 (tm-30) REVERT: A 175 TYR cc_start: 0.6697 (m-80) cc_final: 0.6400 (m-80) REVERT: A 201 LYS cc_start: 0.8164 (pptt) cc_final: 0.7349 (ptpt) REVERT: A 254 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6881 (ttp) REVERT: A 479 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: A 525 GLU cc_start: 0.6320 (tt0) cc_final: 0.5747 (mm-30) REVERT: A 678 GLU cc_start: 0.6971 (pm20) cc_final: 0.6502 (mm-30) REVERT: A 1000 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8237 (mt) REVERT: A 1006 MET cc_start: 0.6812 (mtm) cc_final: 0.6499 (mtm) REVERT: A 1026 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: A 1111 ASP cc_start: 0.7053 (p0) cc_final: 0.6776 (p0) REVERT: A 1541 GLU cc_start: 0.6926 (pt0) cc_final: 0.6654 (pt0) REVERT: A 1588 MET cc_start: 0.4980 (tmm) cc_final: 0.4770 (tmm) REVERT: A 1677 LYS cc_start: 0.8170 (mmtp) cc_final: 0.7617 (tmtt) REVERT: A 1977 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6119 (mp10) REVERT: A 2254 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7887 (mt-10) REVERT: A 2679 TRP cc_start: 0.7438 (m100) cc_final: 0.6971 (m100) REVERT: A 2706 LYS cc_start: 0.6421 (tptp) cc_final: 0.5895 (mptt) REVERT: A 2863 SER cc_start: 0.7557 (t) cc_final: 0.6961 (p) REVERT: A 2911 ASP cc_start: 0.6247 (t0) cc_final: 0.6027 (m-30) REVERT: B 114 ARG cc_start: 0.6040 (mtt90) cc_final: 0.4678 (ttt-90) REVERT: B 192 HIS cc_start: 0.5083 (t-90) cc_final: 0.4787 (t-170) REVERT: B 285 TRP cc_start: 0.3493 (m100) cc_final: 0.3159 (m100) REVERT: B 296 GLU cc_start: 0.3857 (OUTLIER) cc_final: 0.3051 (pm20) REVERT: B 324 TRP cc_start: 0.6127 (m-10) cc_final: 0.5463 (m-10) REVERT: B 330 MET cc_start: 0.5113 (ppp) cc_final: 0.4781 (ppp) REVERT: C 189 MET cc_start: 0.6706 (mtt) cc_final: 0.5502 (mmt) REVERT: C 374 MET cc_start: 0.6988 (tmm) cc_final: 0.6551 (tmm) outliers start: 67 outliers final: 54 residues processed: 355 average time/residue: 0.3843 time to fit residues: 223.0851 Evaluate side-chains 363 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 303 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2152 SER Chi-restraints excluded: chain A residue 2268 VAL Chi-restraints excluded: chain A residue 2287 SER Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2520 LEU Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain A residue 3089 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 10.0000 chunk 318 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 150 optimal weight: 0.1980 chunk 221 optimal weight: 3.9990 chunk 333 optimal weight: 0.8980 chunk 307 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 205 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27703 Z= 0.155 Angle : 0.543 10.651 37568 Z= 0.269 Chirality : 0.040 0.154 4209 Planarity : 0.004 0.078 4790 Dihedral : 5.287 81.018 3716 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 1.91 % Allowed : 16.55 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3348 helix: 1.74 (0.13), residues: 1517 sheet: -0.44 (0.24), residues: 480 loop : -0.43 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 262 HIS 0.003 0.001 HIS A 530 PHE 0.039 0.001 PHE A2077 TYR 0.025 0.001 TYR B 138 ARG 0.010 0.000 ARG C 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6696 Ramachandran restraints generated. 3348 Oldfield, 0 Emsley, 3348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 309 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8324 (pptt) cc_final: 0.7441 (ptpt) REVERT: A 254 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6869 (ttp) REVERT: A 525 GLU cc_start: 0.6333 (tt0) cc_final: 0.5762 (mm-30) REVERT: A 678 GLU cc_start: 0.6968 (pm20) cc_final: 0.6470 (mm-30) REVERT: A 1000 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8201 (mt) REVERT: A 1006 MET cc_start: 0.6774 (mtm) cc_final: 0.6475 (mtm) REVERT: A 1026 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7674 (ttt) REVERT: A 1111 ASP cc_start: 0.7068 (p0) cc_final: 0.6778 (p0) REVERT: A 1373 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 1541 GLU cc_start: 0.6798 (pt0) cc_final: 0.6510 (pt0) REVERT: A 1677 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7602 (tmtt) REVERT: A 1977 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6112 (mp10) REVERT: A 2254 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 2679 TRP cc_start: 0.7451 (m100) cc_final: 0.6987 (m100) REVERT: A 2706 LYS cc_start: 0.6384 (tptp) cc_final: 0.5977 (mptt) REVERT: A 2863 SER cc_start: 0.7505 (t) cc_final: 0.6915 (p) REVERT: A 2911 ASP cc_start: 0.6308 (t0) cc_final: 0.5982 (m-30) REVERT: A 3082 VAL cc_start: 0.8638 (t) cc_final: 0.8397 (m) REVERT: B 114 ARG cc_start: 0.6221 (mtt90) cc_final: 0.4782 (ttt-90) REVERT: B 192 HIS cc_start: 0.5066 (t-90) cc_final: 0.4740 (t-170) REVERT: B 231 PHE cc_start: 0.2870 (t80) cc_final: 0.1594 (t80) REVERT: B 285 TRP cc_start: 0.3442 (m100) cc_final: 0.3115 (m100) REVERT: B 296 GLU cc_start: 0.3869 (OUTLIER) cc_final: 0.3065 (pm20) REVERT: B 330 MET cc_start: 0.5098 (ppp) cc_final: 0.4884 (ppp) REVERT: C 189 MET cc_start: 0.6721 (mtt) cc_final: 0.5515 (mmt) REVERT: C 202 MET cc_start: 0.7590 (mmp) cc_final: 0.7335 (mmp) REVERT: C 204 ASN cc_start: 0.7042 (t0) cc_final: 0.6700 (p0) REVERT: C 333 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6659 (ttp) REVERT: C 374 MET cc_start: 0.6959 (tmm) cc_final: 0.6527 (tmm) outliers start: 57 outliers final: 48 residues processed: 345 average time/residue: 0.3949 time to fit residues: 222.4658 Evaluate side-chains 352 residues out of total 2991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 298 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 807 ASP Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1333 THR Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1637 ASN Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1977 GLN Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2152 SER Chi-restraints excluded: chain A residue 2268 VAL Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain A residue 2505 LEU Chi-restraints excluded: chain A residue 2520 LEU Chi-restraints excluded: chain A residue 2612 VAL Chi-restraints excluded: chain A residue 2766 VAL Chi-restraints excluded: chain A residue 2785 GLN Chi-restraints excluded: chain A residue 2803 ASN Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 354 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 0.9980 chunk 283 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 245 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.148259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117909 restraints weight = 49681.371| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.64 r_work: 0.3512 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27703 Z= 0.161 Angle : 0.549 13.056 37568 Z= 0.270 Chirality : 0.040 0.151 4209 Planarity : 0.004 0.078 4790 Dihedral : 5.244 76.356 3716 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 2.14 % Allowed : 16.52 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 3348 helix: 1.73 (0.13), residues: 1516 sheet: -0.39 (0.24), residues: 482 loop : -0.45 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 262 HIS 0.003 0.001 HIS A 530 PHE 0.037 0.001 PHE A2077 TYR 0.025 0.001 TYR B 138 ARG 0.003 0.000 ARG A2098 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6549.15 seconds wall clock time: 119 minutes 42.88 seconds (7182.88 seconds total)