Starting phenix.real_space_refine on Fri Jun 20 12:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcy_28999/06_2025/8fcy_28999.cif" } resolution = 3.4 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= 0.044 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 116 5.16 5 C 14723 2.51 5 N 3996 2.21 5 O 4298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23142 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 23030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2864, 23030 Classifications: {'peptide': 2864} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 129, 'TRANS': 2734} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'ADP': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.53, per 1000 atoms: 0.58 Number of scatterers: 23142 At special positions: 0 Unit cell: (128.688, 170.052, 151.668, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 9 15.00 O 4298 8.00 N 3996 7.00 C 14723 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 - 3.00 Amino acid : True - 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: 5.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5450 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 19 sheets defined 60.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.768A pdb=" N ARG A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 55 Processing helix chain 'A' and resid 65 through 97 removed outlier: 4.028A pdb=" N ASP A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.573A pdb=" N SER A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 170 removed outlier: 3.595A pdb=" N SER A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.692A pdb=" N LYS A 197 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 199 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS A 200 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 274 removed outlier: 4.214A pdb=" N ILE A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 272 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.540A pdb=" N TYR A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 346 through 370 removed outlier: 3.579A pdb=" N HIS A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 427 through 443 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.906A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 509 through 528 Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 606 through 622 Proline residue: A 616 - end of helix removed outlier: 3.887A pdb=" N ASP A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 658 Processing helix chain 'A' and resid 677 through 691 Processing helix chain 'A' and resid 698 through 710 Processing helix chain 'A' and resid 720 through 734 removed outlier: 3.583A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 775 through 791 Processing helix chain 'A' and resid 806 through 810 Processing helix chain 'A' and resid 823 through 834 Processing helix chain 'A' and resid 856 through 865 removed outlier: 3.564A pdb=" N LEU A 860 " --> pdb=" O TRP A 856 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 903 Processing helix chain 'A' and resid 910 through 914 Processing helix chain 'A' and resid 915 through 929 Processing helix chain 'A' and resid 956 through 969 removed outlier: 3.593A pdb=" N ILE A 967 " --> pdb=" O ASP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 977 through 985 Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 995 through 1021 removed outlier: 3.524A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1048 removed outlier: 3.673A pdb=" N ARG A1033 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A1037 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1067 Processing helix chain 'A' and resid 1078 through 1080 No H-bonds generated for 'chain 'A' and resid 1078 through 1080' Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1116 through 1132 removed outlier: 3.775A pdb=" N ALA A1124 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A1132 " --> pdb=" O THR A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1157 removed outlier: 3.879A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1184 Processing helix chain 'A' and resid 1222 through 1234 removed outlier: 3.549A pdb=" N VAL A1232 " --> pdb=" O ILE A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1274 Processing helix chain 'A' and resid 1285 through 1301 removed outlier: 3.936A pdb=" N THR A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1310 through 1328 Processing helix chain 'A' and resid 1340 through 1356 removed outlier: 4.024A pdb=" N MET A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1379 Processing helix chain 'A' and resid 1384 through 1403 Processing helix chain 'A' and resid 1408 through 1413 removed outlier: 3.505A pdb=" N MET A1412 " --> pdb=" O ARG A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1449 removed outlier: 3.972A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.976A pdb=" N GLN A1473 " --> pdb=" O ARG A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1499 Processing helix chain 'A' and resid 1513 through 1529 Processing helix chain 'A' and resid 1530 through 1533 removed outlier: 4.193A pdb=" N GLU A1533 " --> pdb=" O CYS A1530 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1530 through 1533' Processing helix chain 'A' and resid 1542 through 1544 No H-bonds generated for 'chain 'A' and resid 1542 through 1544' Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 3.992A pdb=" N LEU A1550 " --> pdb=" O ASP A1546 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1558 " --> pdb=" O ASN A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1586 Processing helix chain 'A' and resid 1591 through 1606 Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 3.692A pdb=" N LYS A1621 " --> pdb=" O SER A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1683 through 1709 Processing helix chain 'A' and resid 1717 through 1765 Processing helix chain 'A' and resid 1954 through 1984 removed outlier: 3.920A pdb=" N ASN A1980 " --> pdb=" O GLU A1976 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A1982 " --> pdb=" O PHE A1978 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1983 " --> pdb=" O LYS A1979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1998 Processing helix chain 'A' and resid 2003 through 2021 Processing helix chain 'A' and resid 2030 through 2035 removed outlier: 3.604A pdb=" N LEU A2035 " --> pdb=" O ARG A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2037 through 2047 Processing helix chain 'A' and resid 2052 through 2064 Processing helix chain 'A' and resid 2076 through 2086 Processing helix chain 'A' and resid 2100 through 2112 removed outlier: 3.778A pdb=" N PHE A2111 " --> pdb=" O SER A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2126 No H-bonds generated for 'chain 'A' and resid 2124 through 2126' Processing helix chain 'A' and resid 2127 through 2132 Processing helix chain 'A' and resid 2171 through 2177 removed outlier: 3.686A pdb=" N ARG A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2202 Processing helix chain 'A' and resid 2203 through 2216 removed outlier: 3.534A pdb=" N ASP A2207 " --> pdb=" O ARG A2203 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2239 removed outlier: 3.543A pdb=" N ARG A2225 " --> pdb=" O GLN A2221 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A2226 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A2227 " --> pdb=" O ARG A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2241 through 2243 No H-bonds generated for 'chain 'A' and resid 2241 through 2243' Processing helix chain 'A' and resid 2244 through 2268 removed outlier: 3.758A pdb=" N ILE A2248 " --> pdb=" O ASP A2244 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A2251 " --> pdb=" O THR A2247 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A2259 " --> pdb=" O LEU A2255 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A2268 " --> pdb=" O ARG A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2300 removed outlier: 3.658A pdb=" N MET A2273 " --> pdb=" O THR A2269 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A2274 " --> pdb=" O ASP A2270 " (cutoff:3.500A) Proline residue: A2285 - end of helix Processing helix chain 'A' and resid 2301 through 2303 No H-bonds generated for 'chain 'A' and resid 2301 through 2303' Processing helix chain 'A' and resid 2310 through 2324 Processing helix chain 'A' and resid 2325 through 2329 removed outlier: 3.933A pdb=" N LYS A2329 " --> pdb=" O PRO A2326 " (cutoff:3.500A) Processing helix chain 'A' and resid 2335 through 2355 removed outlier: 3.913A pdb=" N SER A2339 " --> pdb=" O THR A2335 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A2355 " --> pdb=" O ASN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2361 through 2377 Processing helix chain 'A' and resid 2383 through 2392 Processing helix chain 'A' and resid 2393 through 2396 removed outlier: 3.854A pdb=" N ILE A2396 " --> pdb=" O GLY A2393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2393 through 2396' Processing helix chain 'A' and resid 2410 through 2422 removed outlier: 3.887A pdb=" N CYS A2422 " --> pdb=" O VAL A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2435 removed outlier: 3.644A pdb=" N ALA A2435 " --> pdb=" O ALA A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2443 removed outlier: 3.925A pdb=" N ILE A2441 " --> pdb=" O GLU A2437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2463 through 2478 removed outlier: 3.532A pdb=" N GLN A2467 " --> pdb=" O THR A2463 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2481 No H-bonds generated for 'chain 'A' and resid 2479 through 2481' Processing helix chain 'A' and resid 2482 through 2496 removed outlier: 3.550A pdb=" N ASN A2494 " --> pdb=" O PHE A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2505 removed outlier: 3.716A pdb=" N GLU A2504 " --> pdb=" O MET A2500 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A2505 " --> pdb=" O SER A2501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2500 through 2505' Processing helix chain 'A' and resid 2508 through 2513 removed outlier: 4.318A pdb=" N ILE A2512 " --> pdb=" O ASP A2508 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2545 removed outlier: 4.018A pdb=" N VAL A2537 " --> pdb=" O ALA A2533 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2570 removed outlier: 3.987A pdb=" N PHE A2559 " --> pdb=" O SER A2555 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASN A2560 " --> pdb=" O ALA A2556 " (cutoff:3.500A) Processing helix chain 'A' and resid 2584 through 2596 removed outlier: 3.604A pdb=" N HIS A2596 " --> pdb=" O GLU A2592 " (cutoff:3.500A) Processing helix chain 'A' and resid 2617 through 2624 removed outlier: 3.717A pdb=" N LEU A2621 " --> pdb=" O PRO A2617 " (cutoff:3.500A) Processing helix chain 'A' and resid 2634 through 2646 removed outlier: 3.841A pdb=" N ILE A2646 " --> pdb=" O THR A2642 " (cutoff:3.500A) Processing helix chain 'A' and resid 2647 through 2653 Processing helix chain 'A' and resid 2657 through 2675 Processing helix chain 'A' and resid 2676 through 2678 No H-bonds generated for 'chain 'A' and resid 2676 through 2678' Processing helix chain 'A' and resid 2690 through 2709 removed outlier: 3.814A pdb=" N LEU A2694 " --> pdb=" O GLY A2690 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2732 Processing helix chain 'A' and resid 2740 through 2755 removed outlier: 3.528A pdb=" N GLN A2744 " --> pdb=" O ASN A2740 " (cutoff:3.500A) Processing helix chain 'A' and resid 2756 through 2761 Processing helix chain 'A' and resid 2783 through 2793 removed outlier: 3.772A pdb=" N PHE A2787 " --> pdb=" O ARG A2783 " (cutoff:3.500A) Processing helix chain 'A' and resid 2799 through 2804 Processing helix chain 'A' and resid 2808 through 2828 removed outlier: 3.500A pdb=" N VAL A2812 " --> pdb=" O ASN A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2858 through 2873 removed outlier: 3.806A pdb=" N THR A2865 " --> pdb=" O THR A2861 " (cutoff:3.500A) Processing helix chain 'A' and resid 2889 through 2921 Processing helix chain 'A' and resid 2927 through 2939 Processing helix chain 'A' and resid 2943 through 2947 Processing helix chain 'A' and resid 2956 through 2981 Processing helix chain 'A' and resid 2984 through 2989 removed outlier: 4.143A pdb=" N ASN A2988 " --> pdb=" O LYS A2984 " (cutoff:3.500A) Processing helix chain 'A' and resid 2994 through 2996 No H-bonds generated for 'chain 'A' and resid 2994 through 2996' Processing helix chain 'A' and resid 2998 through 3014 removed outlier: 3.586A pdb=" N TYR A3002 " --> pdb=" O VAL A2998 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A3014 " --> pdb=" O VAL A3010 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3019 No H-bonds generated for 'chain 'A' and resid 3017 through 3019' Processing helix chain 'A' and resid 3113 through 3121 removed outlier: 3.546A pdb=" N PHE A3117 " --> pdb=" O ASP A3113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 211 removed outlier: 7.153A pdb=" N SER A 208 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 221 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE A 210 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLY A 220 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N THR A 233 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N SER A 222 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N PHE A 231 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 450 Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AA6, first strand: chain 'A' and resid 766 through 768 removed outlier: 6.506A pdb=" N MET A 767 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 793 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TRP A 845 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 795 " --> pdb=" O TRP A 845 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 847 " --> pdb=" O VAL A 795 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 797 " --> pdb=" O VAL A 847 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 811 through 813 Processing sheet with id=AA8, first strand: chain 'A' and resid 869 through 872 removed outlier: 3.744A pdb=" N GLU A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1082 through 1085 removed outlier: 3.503A pdb=" N GLU A1089 " --> pdb=" O SER A1085 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1160 through 1166 removed outlier: 3.685A pdb=" N VAL A1254 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A1137 " --> pdb=" O VAL A1279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1194 through 1195 Processing sheet with id=AB3, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.647A pdb=" N ILE A1427 " --> pdb=" O SER A1419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1502 through 1504 removed outlier: 6.666A pdb=" N SER A1502 " --> pdb=" O ALA A1536 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A1538 " --> pdb=" O SER A1502 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR A1504 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASP A1540 " --> pdb=" O TYR A1504 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A1535 " --> pdb=" O HIS A1608 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A1610 " --> pdb=" O ILE A1535 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE A1537 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR A1612 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET A1539 " --> pdb=" O THR A1612 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU A1479 " --> pdb=" O ASN A1637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2092 through 2095 removed outlier: 6.599A pdb=" N THR A2092 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN A2118 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A2094 " --> pdb=" O GLN A2118 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A2115 " --> pdb=" O PHE A2160 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N SER A2162 " --> pdb=" O LEU A2115 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A2117 " --> pdb=" O SER A2162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A2181 " --> pdb=" O LEU A2070 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2136 through 2138 Processing sheet with id=AB7, first strand: chain 'A' and resid 2548 through 2551 removed outlier: 6.439A pdb=" N VAL A2576 " --> pdb=" O PHE A2607 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR A2609 " --> pdb=" O VAL A2576 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A2578 " --> pdb=" O THR A2609 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU A2611 " --> pdb=" O LEU A2578 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2765 through 2767 removed outlier: 3.785A pdb=" N ALA A2767 " --> pdb=" O ILE A2776 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2990 through 2992 Processing sheet with id=AC1, first strand: chain 'A' and resid 3050 through 3052 removed outlier: 3.855A pdb=" N PHE A3102 " --> pdb=" O VAL A3091 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A3123 " --> pdb=" O GLN A3048 " (cutoff:3.500A) 1251 hydrogen bonds defined for protein. 3651 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: 15.60 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7339 1.34 - 1.46: 3206 1.46 - 1.57: 12890 1.57 - 1.69: 14 1.69 - 1.81: 194 Bond restraints: 23643 Sorted by residual: bond pdb=" N GLU A1312 " pdb=" CA GLU A1312 " ideal model delta sigma weight residual 1.462 1.491 -0.029 8.50e-03 1.38e+04 1.18e+01 bond pdb=" N ILE A 930 " pdb=" CA ILE A 930 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N GLY A 811 " pdb=" CA GLY A 811 " ideal model delta sigma weight residual 1.448 1.476 -0.028 8.80e-03 1.29e+04 1.01e+01 bond pdb=" N VAL A1319 " pdb=" CA VAL A1319 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N GLY A 823 " pdb=" CA GLY A 823 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.06e-02 8.90e+03 8.45e+00 ... (remaining 23638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 31388 1.82 - 3.65: 588 3.65 - 5.47: 80 5.47 - 7.29: 12 7.29 - 9.12: 2 Bond angle restraints: 32070 Sorted by residual: angle pdb=" CA GLY A 811 " pdb=" C GLY A 811 " pdb=" O GLY A 811 " ideal model delta sigma weight residual 122.37 118.12 4.25 7.30e-01 1.88e+00 3.39e+01 angle pdb=" C ASP A 478 " pdb=" CA ASP A 478 " pdb=" CB ASP A 478 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" CA GLY A 823 " pdb=" C GLY A 823 " pdb=" O GLY A 823 " ideal model delta sigma weight residual 122.28 117.78 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N GLU A 855 " pdb=" CA GLU A 855 " pdb=" C GLU A 855 " ideal model delta sigma weight residual 113.43 108.42 5.01 1.26e+00 6.30e-01 1.58e+01 angle pdb=" N ILE A2553 " pdb=" CA ILE A2553 " pdb=" C ILE A2553 " ideal model delta sigma weight residual 113.53 109.87 3.66 9.80e-01 1.04e+00 1.40e+01 ... (remaining 32065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 14040 35.33 - 70.66: 249 70.66 - 105.99: 36 105.99 - 141.33: 2 141.33 - 176.66: 2 Dihedral angle restraints: 14329 sinusoidal: 5941 harmonic: 8388 Sorted by residual: dihedral pdb=" C5' ADP A3201 " pdb=" O5' ADP A3201 " pdb=" PA ADP A3201 " pdb=" O2A ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 116.66 -176.66 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A3201 " pdb=" O3A ADP A3201 " pdb=" PA ADP A3201 " pdb=" PB ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 94.28 -154.28 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP A3201 " pdb=" O3A ADP A3201 " pdb=" PB ADP A3201 " pdb=" PA ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 75.11 -135.11 1 2.00e+01 2.50e-03 4.10e+01 ... (remaining 14326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2614 0.040 - 0.080: 724 0.080 - 0.119: 233 0.119 - 0.159: 36 0.159 - 0.199: 3 Chirality restraints: 3610 Sorted by residual: chirality pdb=" CB ILE A2715 " pdb=" CA ILE A2715 " pdb=" CG1 ILE A2715 " pdb=" CG2 ILE A2715 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CB ILE A1481 " pdb=" CA ILE A1481 " pdb=" CG1 ILE A1481 " pdb=" CG2 ILE A1481 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA MET A1318 " pdb=" N MET A1318 " pdb=" C MET A1318 " pdb=" CB MET A1318 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3607 not shown) Planarity restraints: 4099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1680 " 0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO A1681 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A1681 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1681 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2716 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A2717 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A2717 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2717 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2654 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A2655 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2655 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2655 " 0.026 5.00e-02 4.00e+02 ... (remaining 4096 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3473 2.76 - 3.29: 23607 3.29 - 3.83: 38712 3.83 - 4.36: 44324 4.36 - 4.90: 76435 Nonbonded interactions: 186551 Sorted by model distance: nonbonded pdb=" O LYS A1579 " pdb=" NE2 GLN A1583 " model vdw 2.224 3.120 nonbonded pdb=" O THR A1573 " pdb=" OG1 THR A1576 " model vdw 2.236 3.040 nonbonded pdb=" O MET A 52 " pdb=" OG SER A 55 " model vdw 2.250 3.040 nonbonded pdb=" OG SER A2492 " pdb=" OE1 GLU A2497 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP A1540 " pdb=" OG1 THR A1612 " model vdw 2.268 3.040 ... (remaining 186546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 62.310 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23643 Z= 0.186 Angle : 0.586 9.117 32070 Z= 0.341 Chirality : 0.041 0.199 3610 Planarity : 0.004 0.076 4099 Dihedral : 14.750 176.657 8879 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % 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 (0.17), residues: 2852 helix: 1.51 (0.14), residues: 1566 sheet: -1.45 (0.35), residues: 224 loop : -1.01 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 246 HIS 0.004 0.001 HIS A2601 PHE 0.013 0.001 PHE A 61 TYR 0.019 0.001 TYR A1675 ARG 0.006 0.000 ARG A 33 Details of bonding type rmsd hydrogen bonds : bond 0.14431 ( 1251) hydrogen bonds : angle 5.49896 ( 3651) covalent geometry : bond 0.00298 (23643) covalent geometry : angle 0.58587 (32070) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 387 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7668 (mm) cc_final: 0.7036 (tp) REVERT: A 134 MET cc_start: 0.6079 (mpp) cc_final: 0.5850 (tpt) REVERT: A 1052 ARG cc_start: 0.7205 (mtm180) cc_final: 0.6645 (ptt90) REVERT: A 1200 LEU cc_start: 0.8803 (mm) cc_final: 0.8335 (tp) REVERT: A 1310 TYR cc_start: 0.7027 (m-80) cc_final: 0.6702 (m-80) REVERT: A 1386 GLU cc_start: 0.7905 (pm20) cc_final: 0.7654 (pm20) REVERT: A 1575 MET cc_start: 0.8018 (mmm) cc_final: 0.7728 (mmt) REVERT: A 1653 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 1658 MET cc_start: 0.8209 (tpp) cc_final: 0.7386 (ttm) REVERT: A 1726 ASN cc_start: 0.8448 (m-40) cc_final: 0.8091 (m-40) REVERT: A 1968 ARG cc_start: 0.6617 (mmt180) cc_final: 0.5163 (ttm110) REVERT: A 2200 LYS cc_start: 0.8211 (tppt) cc_final: 0.7931 (ttpp) REVERT: A 2505 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7639 (mt0) REVERT: A 2545 ASN cc_start: 0.8753 (m-40) cc_final: 0.8549 (m-40) REVERT: A 2639 MET cc_start: 0.8548 (mtp) cc_final: 0.7929 (mtp) REVERT: A 3112 GLU cc_start: 0.7312 (mp0) cc_final: 0.6721 (mp0) outliers start: 3 outliers final: 0 residues processed: 388 average time/residue: 0.4202 time to fit residues: 248.8196 Evaluate side-chains 217 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 6.9990 chunk 216 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 0.0770 chunk 166 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 293 GLN A 484 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 GLN A1166 ASN A1297 ASN A1559 ASN A1583 GLN A1592 HIS A1742 GLN A1743 GLN A1745 HIS A2019 GLN A2022 ASN A2084 ASN ** A2236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2351 ASN A2362 HIS A2450 GLN A2511 HIS A3094 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093404 restraints weight = 42744.009| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.16 r_work: 0.3139 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23643 Z= 0.234 Angle : 0.632 10.485 32070 Z= 0.320 Chirality : 0.044 0.238 3610 Planarity : 0.004 0.051 4099 Dihedral : 7.210 159.924 3181 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 1.22 % Allowed : 7.81 % Favored : 90.97 % 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: 0.28 (0.16), residues: 2852 helix: 1.27 (0.13), residues: 1596 sheet: -1.63 (0.32), residues: 247 loop : -1.04 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 68 HIS 0.016 0.001 HIS A 104 PHE 0.032 0.002 PHE A2295 TYR 0.016 0.002 TYR A2929 ARG 0.006 0.001 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1251) hydrogen bonds : angle 4.41478 ( 3651) covalent geometry : bond 0.00560 (23643) covalent geometry : angle 0.63212 (32070) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.6762 (mpp) cc_final: 0.6313 (tpt) REVERT: A 860 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (mt) REVERT: A 917 ASP cc_start: 0.8448 (t0) cc_final: 0.8148 (t0) REVERT: A 1200 LEU cc_start: 0.8785 (mm) cc_final: 0.8349 (tp) REVERT: A 1310 TYR cc_start: 0.7288 (m-80) cc_final: 0.6664 (m-80) REVERT: A 1574 LEU cc_start: 0.8737 (pp) cc_final: 0.8430 (pp) REVERT: A 1575 MET cc_start: 0.8232 (mmm) cc_final: 0.7955 (mmm) REVERT: A 1584 LYS cc_start: 0.8583 (tptp) cc_final: 0.8265 (ttpt) REVERT: A 1968 ARG cc_start: 0.6430 (mmt180) cc_final: 0.5120 (ttm110) REVERT: A 1979 LYS cc_start: 0.6827 (mmtm) cc_final: 0.5674 (tttt) REVERT: A 2200 LYS cc_start: 0.8582 (tppt) cc_final: 0.8310 (ttpp) REVERT: A 2274 GLN cc_start: 0.6959 (mp10) cc_final: 0.6672 (mp10) REVERT: A 2545 ASN cc_start: 0.8827 (m-40) cc_final: 0.8584 (m-40) REVERT: A 2610 MET cc_start: 0.7932 (tpt) cc_final: 0.7720 (tpp) REVERT: A 3112 GLU cc_start: 0.7481 (mp0) cc_final: 0.7084 (mp0) outliers start: 31 outliers final: 18 residues processed: 249 average time/residue: 0.5307 time to fit residues: 210.4613 Evaluate side-chains 221 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1530 CYS Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2732 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 283 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 532 ASN A 762 ASN A2019 GLN A2118 GLN A2254 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094491 restraints weight = 42388.341| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.24 r_work: 0.3163 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23643 Z= 0.129 Angle : 0.541 9.984 32070 Z= 0.272 Chirality : 0.040 0.255 3610 Planarity : 0.004 0.044 4099 Dihedral : 6.841 144.487 3181 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.10 % Allowed : 10.09 % Favored : 88.81 % 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: 0.45 (0.16), residues: 2852 helix: 1.45 (0.13), residues: 1592 sheet: -1.53 (0.33), residues: 248 loop : -1.03 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 779 HIS 0.011 0.001 HIS A1745 PHE 0.019 0.001 PHE A2295 TYR 0.019 0.001 TYR A2294 ARG 0.005 0.000 ARG A2110 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 1251) hydrogen bonds : angle 4.11957 ( 3651) covalent geometry : bond 0.00290 (23643) covalent geometry : angle 0.54103 (32070) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6493 (pp20) REVERT: A 134 MET cc_start: 0.6411 (mpp) cc_final: 0.6173 (tpt) REVERT: A 417 TYR cc_start: 0.8949 (t80) cc_final: 0.8150 (t80) REVERT: A 1200 LEU cc_start: 0.8703 (mm) cc_final: 0.8297 (tp) REVERT: A 1310 TYR cc_start: 0.7314 (m-80) cc_final: 0.6666 (m-80) REVERT: A 1575 MET cc_start: 0.8253 (mmm) cc_final: 0.7954 (mmt) REVERT: A 1584 LYS cc_start: 0.8557 (tptp) cc_final: 0.8300 (tttt) REVERT: A 1603 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8684 (p) REVERT: A 1657 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8664 (mtmm) REVERT: A 1726 ASN cc_start: 0.8673 (m-40) cc_final: 0.8313 (m-40) REVERT: A 1968 ARG cc_start: 0.6500 (mmt180) cc_final: 0.4839 (ttm-80) REVERT: A 1979 LYS cc_start: 0.6741 (mmtm) cc_final: 0.5654 (tttt) REVERT: A 1998 TYR cc_start: 0.8816 (m-80) cc_final: 0.8116 (m-80) REVERT: A 2165 ASP cc_start: 0.7908 (p0) cc_final: 0.7599 (p0) REVERT: A 2200 LYS cc_start: 0.8665 (tppt) cc_final: 0.8398 (ttpp) REVERT: A 2274 GLN cc_start: 0.6982 (mp10) cc_final: 0.6674 (mp10) REVERT: A 2545 ASN cc_start: 0.8811 (m-40) cc_final: 0.8562 (m-40) REVERT: A 2559 PHE cc_start: 0.7423 (m-10) cc_final: 0.7141 (m-10) REVERT: A 3112 GLU cc_start: 0.7351 (mp0) cc_final: 0.7020 (mp0) outliers start: 28 outliers final: 17 residues processed: 246 average time/residue: 0.3726 time to fit residues: 146.0026 Evaluate side-chains 233 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2118 GLN Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2733 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 23 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 247 optimal weight: 0.0770 chunk 258 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 844 GLN A2022 ASN A2118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.095588 restraints weight = 42727.944| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.15 r_work: 0.3183 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23643 Z= 0.120 Angle : 0.528 10.417 32070 Z= 0.264 Chirality : 0.040 0.254 3610 Planarity : 0.004 0.045 4099 Dihedral : 6.611 145.916 3181 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 1.53 % Allowed : 11.07 % Favored : 87.40 % 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: 0.59 (0.16), residues: 2852 helix: 1.57 (0.13), residues: 1594 sheet: -1.39 (0.33), residues: 247 loop : -1.02 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 246 HIS 0.015 0.001 HIS A 104 PHE 0.027 0.001 PHE A 79 TYR 0.017 0.001 TYR A2294 ARG 0.004 0.000 ARG A1389 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 1251) hydrogen bonds : angle 3.98171 ( 3651) covalent geometry : bond 0.00268 (23643) covalent geometry : angle 0.52793 (32070) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6363 (pp20) REVERT: A 134 MET cc_start: 0.6382 (mpp) cc_final: 0.6132 (tpt) REVERT: A 510 GLU cc_start: 0.8138 (tp30) cc_final: 0.7916 (tp30) REVERT: A 808 HIS cc_start: 0.8270 (m170) cc_final: 0.8069 (m-70) REVERT: A 1200 LEU cc_start: 0.8694 (mm) cc_final: 0.8263 (tp) REVERT: A 1310 TYR cc_start: 0.7265 (m-80) cc_final: 0.6741 (m-80) REVERT: A 1389 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7480 (ptm160) REVERT: A 1575 MET cc_start: 0.8219 (mmm) cc_final: 0.7917 (mmt) REVERT: A 1584 LYS cc_start: 0.8512 (tptp) cc_final: 0.8277 (ttpt) REVERT: A 1603 VAL cc_start: 0.8965 (t) cc_final: 0.8634 (p) REVERT: A 1657 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8668 (mtmm) REVERT: A 1726 ASN cc_start: 0.8652 (m-40) cc_final: 0.8324 (m-40) REVERT: A 1744 MET cc_start: 0.7545 (tmm) cc_final: 0.7236 (ppp) REVERT: A 1968 ARG cc_start: 0.6545 (mmt180) cc_final: 0.4899 (ttm-80) REVERT: A 1979 LYS cc_start: 0.6707 (mmtm) cc_final: 0.5545 (ttmm) REVERT: A 1998 TYR cc_start: 0.8822 (m-80) cc_final: 0.8160 (m-80) REVERT: A 2165 ASP cc_start: 0.7940 (p0) cc_final: 0.7627 (p0) REVERT: A 2200 LYS cc_start: 0.8633 (tppt) cc_final: 0.8386 (ttpp) REVERT: A 2228 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7461 (mt-10) REVERT: A 2545 ASN cc_start: 0.8802 (m-40) cc_final: 0.8473 (m-40) REVERT: A 2714 ASN cc_start: 0.8379 (m-40) cc_final: 0.8120 (p0) REVERT: A 2886 ASN cc_start: 0.8279 (m110) cc_final: 0.7941 (m-40) outliers start: 39 outliers final: 24 residues processed: 264 average time/residue: 0.3950 time to fit residues: 167.6640 Evaluate side-chains 237 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 269 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A1743 GLN A1745 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095121 restraints weight = 43218.224| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3143 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23643 Z= 0.188 Angle : 0.576 10.800 32070 Z= 0.287 Chirality : 0.042 0.287 3610 Planarity : 0.004 0.045 4099 Dihedral : 6.659 152.159 3181 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.73 % Allowed : 12.09 % Favored : 86.19 % 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: 0.45 (0.16), residues: 2852 helix: 1.46 (0.13), residues: 1596 sheet: -1.45 (0.33), residues: 248 loop : -1.08 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 246 HIS 0.010 0.001 HIS A 104 PHE 0.022 0.002 PHE A2295 TYR 0.017 0.001 TYR A2294 ARG 0.005 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 1251) hydrogen bonds : angle 4.05643 ( 3651) covalent geometry : bond 0.00448 (23643) covalent geometry : angle 0.57604 (32070) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6349 (pp20) REVERT: A 510 GLU cc_start: 0.8112 (tp30) cc_final: 0.7885 (tp30) REVERT: A 1200 LEU cc_start: 0.8677 (mm) cc_final: 0.8202 (tp) REVERT: A 1310 TYR cc_start: 0.7255 (m-80) cc_final: 0.6883 (m-80) REVERT: A 1389 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7543 (ptm160) REVERT: A 1575 MET cc_start: 0.8201 (mmm) cc_final: 0.7741 (mmm) REVERT: A 1584 LYS cc_start: 0.8504 (tptp) cc_final: 0.8281 (ttpt) REVERT: A 1657 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8768 (mtmm) REVERT: A 1968 ARG cc_start: 0.6411 (mmt180) cc_final: 0.5003 (ttm-80) REVERT: A 1979 LYS cc_start: 0.6924 (mmtm) cc_final: 0.5808 (tttt) REVERT: A 1998 TYR cc_start: 0.8868 (m-80) cc_final: 0.8206 (m-80) REVERT: A 2165 ASP cc_start: 0.7958 (p0) cc_final: 0.7692 (p0) REVERT: A 2200 LYS cc_start: 0.8660 (tppt) cc_final: 0.8431 (ttpp) REVERT: A 2228 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 2486 MET cc_start: 0.8530 (tpt) cc_final: 0.8200 (tpt) REVERT: A 2545 ASN cc_start: 0.8783 (m-40) cc_final: 0.8465 (m-40) REVERT: A 2886 ASN cc_start: 0.8345 (m110) cc_final: 0.8001 (m-40) outliers start: 44 outliers final: 31 residues processed: 249 average time/residue: 0.3539 time to fit residues: 142.4364 Evaluate side-chains 237 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 238 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 268 optimal weight: 0.0270 chunk 104 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.118754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094845 restraints weight = 42334.585| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23643 Z= 0.112 Angle : 0.535 11.786 32070 Z= 0.266 Chirality : 0.040 0.261 3610 Planarity : 0.004 0.045 4099 Dihedral : 6.541 159.182 3181 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 1.57 % Allowed : 12.56 % Favored : 85.87 % 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 (0.16), residues: 2852 helix: 1.63 (0.13), residues: 1592 sheet: -1.29 (0.34), residues: 238 loop : -1.02 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 779 HIS 0.009 0.001 HIS A1745 PHE 0.017 0.001 PHE A2295 TYR 0.018 0.001 TYR A2294 ARG 0.002 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1251) hydrogen bonds : angle 3.92562 ( 3651) covalent geometry : bond 0.00250 (23643) covalent geometry : angle 0.53537 (32070) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6301 (pp20) REVERT: A 917 ASP cc_start: 0.8394 (t0) cc_final: 0.8135 (t0) REVERT: A 1200 LEU cc_start: 0.8611 (mm) cc_final: 0.8211 (tp) REVERT: A 1310 TYR cc_start: 0.7273 (m-80) cc_final: 0.6876 (m-80) REVERT: A 1361 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 1389 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7549 (ptm160) REVERT: A 1498 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7857 (ttp) REVERT: A 1575 MET cc_start: 0.8163 (mmm) cc_final: 0.7831 (mmt) REVERT: A 1657 LYS cc_start: 0.8996 (mmmm) cc_final: 0.8729 (mtmm) REVERT: A 1744 MET cc_start: 0.7452 (ppp) cc_final: 0.7194 (ppp) REVERT: A 1968 ARG cc_start: 0.6413 (mmt180) cc_final: 0.4974 (ttm-80) REVERT: A 1979 LYS cc_start: 0.6869 (mmtm) cc_final: 0.5683 (tttt) REVERT: A 1998 TYR cc_start: 0.8814 (m-10) cc_final: 0.8239 (m-80) REVERT: A 2165 ASP cc_start: 0.7976 (p0) cc_final: 0.7730 (p0) REVERT: A 2200 LYS cc_start: 0.8658 (tppt) cc_final: 0.8416 (ttpp) REVERT: A 2486 MET cc_start: 0.8471 (tpt) cc_final: 0.8089 (tpt) REVERT: A 2545 ASN cc_start: 0.8805 (m-40) cc_final: 0.8478 (m-40) REVERT: A 2559 PHE cc_start: 0.7505 (m-10) cc_final: 0.7301 (m-10) REVERT: A 2639 MET cc_start: 0.8784 (mtp) cc_final: 0.8255 (mtp) REVERT: A 2886 ASN cc_start: 0.8332 (m110) cc_final: 0.8002 (m-40) outliers start: 40 outliers final: 28 residues processed: 249 average time/residue: 0.3449 time to fit residues: 138.4658 Evaluate side-chains 239 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.117293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093984 restraints weight = 42813.053| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.12 r_work: 0.3148 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23643 Z= 0.152 Angle : 0.551 12.102 32070 Z= 0.273 Chirality : 0.040 0.308 3610 Planarity : 0.004 0.047 4099 Dihedral : 6.522 170.734 3181 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 1.61 % Allowed : 13.30 % Favored : 85.09 % 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 (0.16), residues: 2852 helix: 1.58 (0.13), residues: 1593 sheet: -1.33 (0.34), residues: 242 loop : -0.96 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2869 HIS 0.010 0.001 HIS A1745 PHE 0.020 0.001 PHE A2295 TYR 0.017 0.001 TYR A2294 ARG 0.004 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1251) hydrogen bonds : angle 3.94808 ( 3651) covalent geometry : bond 0.00358 (23643) covalent geometry : angle 0.55123 (32070) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6154 (pp20) REVERT: A 917 ASP cc_start: 0.8458 (t0) cc_final: 0.8197 (t0) REVERT: A 1310 TYR cc_start: 0.7401 (m-80) cc_final: 0.6973 (m-80) REVERT: A 1389 ARG cc_start: 0.7959 (mtm110) cc_final: 0.7533 (ptm160) REVERT: A 1575 MET cc_start: 0.8197 (mmm) cc_final: 0.7853 (mmt) REVERT: A 1657 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8749 (mtmm) REVERT: A 1968 ARG cc_start: 0.6402 (mmt180) cc_final: 0.5046 (ttm-80) REVERT: A 1979 LYS cc_start: 0.6875 (mmtm) cc_final: 0.5660 (tttt) REVERT: A 1998 TYR cc_start: 0.8834 (m-10) cc_final: 0.8250 (m-80) REVERT: A 2165 ASP cc_start: 0.8057 (p0) cc_final: 0.7828 (p0) REVERT: A 2200 LYS cc_start: 0.8657 (tppt) cc_final: 0.8410 (ttpp) REVERT: A 2229 LYS cc_start: 0.6890 (mmtt) cc_final: 0.6539 (mmtt) REVERT: A 2486 MET cc_start: 0.8459 (tpt) cc_final: 0.8073 (tpt) REVERT: A 2545 ASN cc_start: 0.8824 (m-40) cc_final: 0.8494 (m-40) REVERT: A 2559 PHE cc_start: 0.7535 (m-10) cc_final: 0.7308 (m-10) REVERT: A 2886 ASN cc_start: 0.8340 (m110) cc_final: 0.7997 (m-40) outliers start: 41 outliers final: 34 residues processed: 238 average time/residue: 0.3557 time to fit residues: 136.1231 Evaluate side-chains 239 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 169 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 220 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A2022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.091879 restraints weight = 43003.656| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.22 r_work: 0.3108 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23643 Z= 0.221 Angle : 0.613 12.251 32070 Z= 0.304 Chirality : 0.043 0.320 3610 Planarity : 0.004 0.046 4099 Dihedral : 6.586 172.762 3181 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 1.92 % Allowed : 13.54 % Favored : 84.54 % 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: 0.47 (0.16), residues: 2852 helix: 1.43 (0.13), residues: 1593 sheet: -1.38 (0.34), residues: 231 loop : -1.01 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A2869 HIS 0.009 0.001 HIS A1745 PHE 0.023 0.002 PHE A2295 TYR 0.017 0.001 TYR A2294 ARG 0.006 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 1251) hydrogen bonds : angle 4.10205 ( 3651) covalent geometry : bond 0.00529 (23643) covalent geometry : angle 0.61266 (32070) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7511 (t0) REVERT: A 308 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: A 1310 TYR cc_start: 0.7646 (m-80) cc_final: 0.7175 (m-80) REVERT: A 1361 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 1389 ARG cc_start: 0.7968 (mtm110) cc_final: 0.7534 (ptm160) REVERT: A 1575 MET cc_start: 0.8224 (mmm) cc_final: 0.7883 (mmm) REVERT: A 1657 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8742 (mtmm) REVERT: A 1968 ARG cc_start: 0.6339 (mmt180) cc_final: 0.4987 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8861 (m-10) cc_final: 0.8206 (m-80) REVERT: A 2165 ASP cc_start: 0.8087 (p0) cc_final: 0.7825 (p0) REVERT: A 2200 LYS cc_start: 0.8738 (tppt) cc_final: 0.8482 (ttpp) REVERT: A 2229 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6651 (mmtt) REVERT: A 2486 MET cc_start: 0.8510 (tpt) cc_final: 0.8155 (tpt) REVERT: A 2545 ASN cc_start: 0.8905 (m-40) cc_final: 0.8480 (m-40) REVERT: A 2886 ASN cc_start: 0.8356 (m110) cc_final: 0.8008 (m-40) outliers start: 49 outliers final: 36 residues processed: 245 average time/residue: 0.3538 time to fit residues: 139.3589 Evaluate side-chains 237 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1345 THR Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 52 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 285 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 841 GLN A2022 ASN A3026 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093291 restraints weight = 42731.311| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.16 r_work: 0.3135 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23643 Z= 0.137 Angle : 0.565 12.524 32070 Z= 0.279 Chirality : 0.040 0.299 3610 Planarity : 0.004 0.044 4099 Dihedral : 6.345 161.521 3181 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 1.84 % Allowed : 13.74 % Favored : 84.42 % 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: 0.59 (0.16), residues: 2852 helix: 1.55 (0.13), residues: 1593 sheet: -1.31 (0.34), residues: 238 loop : -1.00 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2869 HIS 0.015 0.001 HIS A 104 PHE 0.029 0.001 PHE A1227 TYR 0.018 0.001 TYR A2294 ARG 0.004 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1251) hydrogen bonds : angle 3.97102 ( 3651) covalent geometry : bond 0.00320 (23643) covalent geometry : angle 0.56451 (32070) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7493 (t0) REVERT: A 308 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: A 841 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: A 917 ASP cc_start: 0.8290 (t0) cc_final: 0.8010 (t0) REVERT: A 1310 TYR cc_start: 0.7456 (m-80) cc_final: 0.6995 (m-80) REVERT: A 1361 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (tt) REVERT: A 1389 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7520 (ptm160) REVERT: A 1575 MET cc_start: 0.8223 (mmm) cc_final: 0.7874 (mmm) REVERT: A 1657 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8711 (mtmm) REVERT: A 1968 ARG cc_start: 0.6297 (mmt180) cc_final: 0.4971 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8771 (m-10) cc_final: 0.8256 (m-80) REVERT: A 2165 ASP cc_start: 0.8045 (p0) cc_final: 0.7790 (p0) REVERT: A 2200 LYS cc_start: 0.8708 (tppt) cc_final: 0.8464 (ttpp) REVERT: A 2486 MET cc_start: 0.8472 (tpt) cc_final: 0.8117 (tpt) REVERT: A 2545 ASN cc_start: 0.8908 (m-40) cc_final: 0.8479 (m-40) REVERT: A 2639 MET cc_start: 0.8799 (mtp) cc_final: 0.8282 (mtp) REVERT: A 2886 ASN cc_start: 0.8326 (m110) cc_final: 0.7970 (m-40) outliers start: 47 outliers final: 37 residues processed: 249 average time/residue: 0.3512 time to fit residues: 139.5321 Evaluate side-chains 241 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 841 GLN Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1603 VAL Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2092 THR Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 247 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 158 optimal weight: 0.4980 chunk 241 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A1745 HIS A2022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.117913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094292 restraints weight = 42569.712| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.21 r_work: 0.3155 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23643 Z= 0.115 Angle : 0.560 12.735 32070 Z= 0.275 Chirality : 0.040 0.310 3610 Planarity : 0.004 0.045 4099 Dihedral : 6.080 147.791 3181 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.33 % Allowed : 14.40 % Favored : 84.26 % 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: 0.70 (0.16), residues: 2852 helix: 1.65 (0.13), residues: 1592 sheet: -1.28 (0.34), residues: 230 loop : -0.98 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A2869 HIS 0.019 0.001 HIS A 104 PHE 0.025 0.001 PHE A1227 TYR 0.017 0.001 TYR A2294 ARG 0.006 0.000 ARG A 843 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 1251) hydrogen bonds : angle 3.88659 ( 3651) covalent geometry : bond 0.00258 (23643) covalent geometry : angle 0.56002 (32070) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5704 Ramachandran restraints generated. 2852 Oldfield, 0 Emsley, 2852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.7262 (tpt) cc_final: 0.6392 (mpp) REVERT: A 135 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7381 (t0) REVERT: A 308 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: A 695 VAL cc_start: 0.8987 (m) cc_final: 0.8774 (p) REVERT: A 917 ASP cc_start: 0.8226 (t0) cc_final: 0.7942 (t0) REVERT: A 1310 TYR cc_start: 0.7401 (m-80) cc_final: 0.6935 (m-80) REVERT: A 1361 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 1389 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7498 (ptm160) REVERT: A 1575 MET cc_start: 0.8240 (mmm) cc_final: 0.7886 (mmm) REVERT: A 1657 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8730 (mtmm) REVERT: A 1658 MET cc_start: 0.8297 (tpp) cc_final: 0.7383 (ttm) REVERT: A 1744 MET cc_start: 0.7731 (tmm) cc_final: 0.7451 (ppp) REVERT: A 1968 ARG cc_start: 0.6269 (mmt180) cc_final: 0.4944 (ttm-80) REVERT: A 1998 TYR cc_start: 0.8739 (m-10) cc_final: 0.8374 (m-80) REVERT: A 2165 ASP cc_start: 0.7993 (p0) cc_final: 0.7764 (p0) REVERT: A 2200 LYS cc_start: 0.8710 (tppt) cc_final: 0.8461 (ttpp) REVERT: A 2223 ARG cc_start: 0.8799 (tmm-80) cc_final: 0.8433 (tmm-80) REVERT: A 2545 ASN cc_start: 0.8893 (m-40) cc_final: 0.8480 (m-40) REVERT: A 2639 MET cc_start: 0.8763 (mtp) cc_final: 0.8288 (mtp) outliers start: 34 outliers final: 29 residues processed: 235 average time/residue: 0.3586 time to fit residues: 137.0123 Evaluate side-chains 231 residues out of total 2549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1361 LEU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1574 LEU Chi-restraints excluded: chain A residue 1587 LEU Chi-restraints excluded: chain A residue 1639 PHE Chi-restraints excluded: chain A residue 1745 HIS Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1964 LEU Chi-restraints excluded: chain A residue 2099 ASP Chi-restraints excluded: chain A residue 2145 THR Chi-restraints excluded: chain A residue 2178 VAL Chi-restraints excluded: chain A residue 2216 LEU Chi-restraints excluded: chain A residue 2269 THR Chi-restraints excluded: chain A residue 2331 VAL Chi-restraints excluded: chain A residue 2733 ILE Chi-restraints excluded: chain A residue 2887 ILE Chi-restraints excluded: chain A residue 2998 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 215 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 256 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS A 841 GLN A2022 ASN A2886 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094483 restraints weight = 42494.252| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.10 r_work: 0.3163 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23643 Z= 0.127 Angle : 0.561 12.655 32070 Z= 0.275 Chirality : 0.040 0.291 3610 Planarity : 0.004 0.045 4099 Dihedral : 5.908 135.134 3181 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.41 % Allowed : 14.40 % Favored : 84.18 % 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: 0.71 (0.16), residues: 2852 helix: 1.66 (0.13), residues: 1593 sheet: -1.30 (0.34), residues: 242 loop : -0.97 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A2869 HIS 0.016 0.001 HIS A1745 PHE 0.025 0.001 PHE A1227 TYR 0.028 0.001 TYR A 18 ARG 0.003 0.000 ARG A2187 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1251) hydrogen bonds : angle 3.87536 ( 3651) covalent geometry : bond 0.00292 (23643) covalent geometry : angle 0.56136 (32070) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12562.32 seconds wall clock time: 217 minutes 46.61 seconds (13066.61 seconds total)