Starting phenix.real_space_refine on Fri Sep 19 08:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qbb_52996/09_2025/9qbb_52996.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.899 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 14704 2.51 5 N 4022 2.21 5 O 4454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23257 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 23257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2911, 23257 Classifications: {'peptide': 2911} Link IDs: {'PTRANS': 119, 'TRANS': 2791} Chain breaks: 3 Time building chain proxies: 5.53, per 1000 atoms: 0.24 Number of scatterers: 23257 At special positions: 0 Unit cell: (161.766, 245.014, 105.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 4454 8.00 N 4022 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A3182 " - pdb=" SG CYS A3205 " distance=2.04 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: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5476 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 31 sheets defined 42.2% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 241 through 256 Processing helix chain 'A' and resid 263 through 283 Processing helix chain 'A' and resid 290 through 305 removed outlier: 3.873A pdb=" N TYR A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.731A pdb=" N ILE A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.993A pdb=" N PHE A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 379 Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.544A pdb=" N ASN A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.143A pdb=" N ALA A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 452 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 472 through 502 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.707A pdb=" N THR A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 551 removed outlier: 3.899A pdb=" N MET A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 579 through 584 removed outlier: 4.141A pdb=" N PHE A 582 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 614 through 631 Processing helix chain 'A' and resid 677 through 695 removed outlier: 3.544A pdb=" N ASP A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 removed outlier: 3.719A pdb=" N ASP A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.760A pdb=" N GLY A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 871 through 887 removed outlier: 4.582A pdb=" N VAL A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 909 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 952 through 966 removed outlier: 3.641A pdb=" N SER A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 997 Processing helix chain 'A' and resid 1037 through 1052 Processing helix chain 'A' and resid 1059 through 1078 removed outlier: 3.765A pdb=" N LYS A1078 " --> pdb=" O PHE A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1092 through 1104 removed outlier: 3.800A pdb=" N LEU A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1139 removed outlier: 3.637A pdb=" N PHE A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1158 through 1167 Processing helix chain 'A' and resid 1172 through 1185 Processing helix chain 'A' and resid 1200 through 1209 Processing helix chain 'A' and resid 1212 through 1230 removed outlier: 4.358A pdb=" N SER A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Proline residue: A1221 - end of helix Processing helix chain 'A' and resid 1237 through 1247 removed outlier: 3.606A pdb=" N LEU A1247 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1289 through 1312 removed outlier: 3.834A pdb=" N GLY A1293 " --> pdb=" O ASN A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1323 Processing helix chain 'A' and resid 1333 through 1347 Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.548A pdb=" N ALA A1368 " --> pdb=" O THR A1364 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1387 Processing helix chain 'A' and resid 1388 through 1391 removed outlier: 3.680A pdb=" N GLY A1391 " --> pdb=" O GLN A1388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1391' Processing helix chain 'A' and resid 1442 through 1459 removed outlier: 4.201A pdb=" N TYR A1446 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLN A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ARG A1452 " --> pdb=" O HIS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1479 Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.806A pdb=" N THR A1490 " --> pdb=" O LEU A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1515 Processing helix chain 'A' and resid 1521 through 1547 removed outlier: 3.637A pdb=" N THR A1547 " --> pdb=" O ASN A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1568 Processing helix chain 'A' and resid 1606 through 1619 Processing helix chain 'A' and resid 1621 through 1628 Processing helix chain 'A' and resid 1646 through 1654 removed outlier: 3.891A pdb=" N TRP A1650 " --> pdb=" O SER A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 removed outlier: 3.674A pdb=" N LEU A1676 " --> pdb=" O ARG A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1688 through 1696 Processing helix chain 'A' and resid 1720 through 1730 Processing helix chain 'A' and resid 1733 through 1747 removed outlier: 4.578A pdb=" N ASN A1739 " --> pdb=" O GLU A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1798 Processing helix chain 'A' and resid 1842 through 1856 removed outlier: 3.653A pdb=" N ARG A1846 " --> pdb=" O GLU A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1885 Processing helix chain 'A' and resid 1898 through 1920 removed outlier: 3.575A pdb=" N THR A1906 " --> pdb=" O LEU A1902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1944 Processing helix chain 'A' and resid 1946 through 1961 Processing helix chain 'A' and resid 1969 through 1981 Processing helix chain 'A' and resid 1985 through 2006 Processing helix chain 'A' and resid 2031 through 2036 Processing helix chain 'A' and resid 2041 through 2056 removed outlier: 3.590A pdb=" N GLN A2045 " --> pdb=" O GLU A2041 " (cutoff:3.500A) Processing helix chain 'A' and resid 2111 through 2120 Processing helix chain 'A' and resid 2127 through 2131 Processing helix chain 'A' and resid 2222 through 2233 Processing helix chain 'A' and resid 2379 through 2381 No H-bonds generated for 'chain 'A' and resid 2379 through 2381' Processing helix chain 'A' and resid 2409 through 2413 Processing helix chain 'A' and resid 2445 through 2452 Processing helix chain 'A' and resid 2458 through 2470 removed outlier: 3.812A pdb=" N ILE A2462 " --> pdb=" O ARG A2458 " (cutoff:3.500A) Processing helix chain 'A' and resid 2610 through 2617 Processing helix chain 'A' and resid 2642 through 2644 No H-bonds generated for 'chain 'A' and resid 2642 through 2644' Processing helix chain 'A' and resid 2742 through 2749 removed outlier: 4.074A pdb=" N GLN A2749 " --> pdb=" O GLN A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2787 Processing helix chain 'A' and resid 2822 through 2826 Processing helix chain 'A' and resid 2830 through 2843 Proline residue: A2839 - end of helix Processing helix chain 'A' and resid 2844 through 2848 removed outlier: 3.922A pdb=" N PHE A2848 " --> pdb=" O THR A2845 " (cutoff:3.500A) Processing helix chain 'A' and resid 2850 through 2854 Processing helix chain 'A' and resid 2868 through 2882 Processing helix chain 'A' and resid 2978 through 2987 removed outlier: 6.726A pdb=" N GLU A2984 " --> pdb=" O ARG A2980 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS A2985 " --> pdb=" O HIS A2981 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN A2987 " --> pdb=" O TRP A2983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3020 through 3023 removed outlier: 4.108A pdb=" N THR A3023 " --> pdb=" O TYR A3020 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3020 through 3023' Processing helix chain 'A' and resid 3037 through 3041 removed outlier: 4.377A pdb=" N GLY A3040 " --> pdb=" O PHE A3037 " (cutoff:3.500A) Processing helix chain 'A' and resid 3056 through 3070 Processing helix chain 'A' and resid 3072 through 3087 removed outlier: 3.522A pdb=" N VAL A3087 " --> pdb=" O MET A3083 " (cutoff:3.500A) Processing helix chain 'A' and resid 3095 through 3100 Processing helix chain 'A' and resid 3192 through 3195 Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 510 removed outlier: 6.250A pdb=" N ASN A 315 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR A 556 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS A 317 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 652 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE A 651 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA4, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 936 Processing sheet with id=AA6, first strand: chain 'A' and resid 1146 through 1149 removed outlier: 6.513A pdb=" N ILE A 971 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N HIS A1148 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE A 973 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 941 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 974 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 943 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 940 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N THR A1191 " --> pdb=" O ILE A 940 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN A 942 " --> pdb=" O THR A1191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA8, first strand: chain 'A' and resid 1269 through 1271 removed outlier: 3.776A pdb=" N SER A1269 " --> pdb=" O THR A1276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1465 through 1466 removed outlier: 3.679A pdb=" N TYR A1643 " --> pdb=" O HIS A1553 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1680 through 1682 Processing sheet with id=AB2, first strand: chain 'A' and resid 1814 through 1815 removed outlier: 4.255A pdb=" N GLU A1814 " --> pdb=" O ASN A1824 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2062 through 2063 removed outlier: 7.195A pdb=" N LEU A2070 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN A2267 " --> pdb=" O THR A2312 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL A2314 " --> pdb=" O ASN A2267 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A2269 " --> pdb=" O VAL A2314 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN A2330 " --> pdb=" O ARG A2349 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE A2351 " --> pdb=" O ASN A2330 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A2332 " --> pdb=" O ILE A2351 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY A2346 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS A2371 " --> pdb=" O GLY A2346 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A2348 " --> pdb=" O HIS A2371 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A2373 " --> pdb=" O ASN A2348 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A2350 " --> pdb=" O ILE A2373 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG A2418 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS A2371 " --> pdb=" O ARG A2418 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N HIS A2420 " --> pdb=" O HIS A2371 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A2373 " --> pdb=" O HIS A2420 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE A2417 " --> pdb=" O ALA A2429 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR A2426 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A2474 " --> pdb=" O LEU A2438 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A2440 " --> pdb=" O THR A2474 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU A2476 " --> pdb=" O ILE A2440 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A2442 " --> pdb=" O GLU A2476 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG A2478 " --> pdb=" O LEU A2442 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP A2444 " --> pdb=" O ARG A2478 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN A2480 " --> pdb=" O ASP A2444 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A2481 " --> pdb=" O THR A2484 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A2484 " --> pdb=" O GLY A2481 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A2485 " --> pdb=" O GLN A2498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A2519 " --> pdb=" O TYR A2497 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A2516 " --> pdb=" O GLN A2540 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE A2542 " --> pdb=" O THR A2516 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A2518 " --> pdb=" O ILE A2542 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A2565 " --> pdb=" O GLY A2625 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY A2625 " --> pdb=" O GLY A2565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2091 through 2096 removed outlier: 4.383A pdb=" N GLU A2095 " --> pdb=" O LYS A2080 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS A2080 " --> pdb=" O GLU A2095 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N THR A2202 " --> pdb=" O GLY A2079 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N MET A2081 " --> pdb=" O THR A2202 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A2204 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A2083 " --> pdb=" O ILE A2204 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A2291 " --> pdb=" O VAL A2302 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR A2304 " --> pdb=" O GLN A2289 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN A2289 " --> pdb=" O THR A2304 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2098 through 2101 removed outlier: 4.546A pdb=" N THR A2167 " --> pdb=" O ALA A2100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2098 through 2101 removed outlier: 4.546A pdb=" N THR A2167 " --> pdb=" O ALA A2100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A2195 " --> pdb=" O GLN A2164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2280 through 2283 Processing sheet with id=AB8, first strand: chain 'A' and resid 2361 through 2364 removed outlier: 5.637A pdb=" N LEU A2362 " --> pdb=" O GLN A2403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 2383 through 2384 removed outlier: 4.540A pdb=" N ILE A2393 " --> pdb=" O LYS A2384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2506 through 2508 removed outlier: 6.649A pdb=" N PHE A2506 " --> pdb=" O ILE A2527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 2552 through 2555 removed outlier: 4.458A pdb=" N THR A2552 " --> pdb=" O ARG A2599 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A2601 " --> pdb=" O THR A2552 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP A2554 " --> pdb=" O ALA A2601 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLN A2603 " --> pdb=" O ASP A2554 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP A2606 " --> pdb=" O ILE A2602 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2638 through 2640 Processing sheet with id=AC4, first strand: chain 'A' and resid 2647 through 2651 removed outlier: 3.579A pdb=" N VAL A2720 " --> pdb=" O LEU A2651 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A2721 " --> pdb=" O LEU A2679 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2702 through 2704 Processing sheet with id=AC6, first strand: chain 'A' and resid 2683 through 2686 removed outlier: 4.663A pdb=" N ILE A2713 " --> pdb=" O LYS A2684 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2731 through 2733 removed outlier: 6.764A pdb=" N ILE A2752 " --> pdb=" O THR A2816 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A2818 " --> pdb=" O ILE A2752 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A2754 " --> pdb=" O ARG A2818 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2738 through 2741 Processing sheet with id=AC9, first strand: chain 'A' and resid 2858 through 2860 Processing sheet with id=AD1, first strand: chain 'A' and resid 2908 through 2912 removed outlier: 6.296A pdb=" N MET A2909 " --> pdb=" O ILE A2973 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N SER A2975 " --> pdb=" O MET A2909 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR A2911 " --> pdb=" O SER A2975 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A2961 " --> pdb=" O MET A2972 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2936 through 2938 removed outlier: 6.799A pdb=" N LYS A2937 " --> pdb=" O LEU A2991 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N GLU A2993 " --> pdb=" O LYS A2937 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A3015 " --> pdb=" O SER A3033 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A3033 " --> pdb=" O VAL A3015 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 3104 through 3110 removed outlier: 7.133A pdb=" N TYR A3199 " --> pdb=" O VAL A3188 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A3188 " --> pdb=" O TYR A3199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A3201 " --> pdb=" O THR A3186 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 3133 through 3134 1052 hydrogen bonds defined for protein. 2976 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: 8.51 Time building geometry restraints manager: 2.84 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: 7729 1.34 - 1.46: 4680 1.46 - 1.58: 11169 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 23718 Sorted by residual: bond pdb=" N LEU A3124 " pdb=" CA LEU A3124 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.41e+00 bond pdb=" N VAL A1871 " pdb=" CA VAL A1871 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.02e+00 bond pdb=" N ILE A1899 " pdb=" CA ILE A1899 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.18e+00 bond pdb=" N VAL A1872 " pdb=" CA VAL A1872 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.41e-02 5.03e+03 7.04e+00 bond pdb=" N LEU A2427 " pdb=" CA LEU A2427 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.22e-02 6.72e+03 6.94e+00 ... (remaining 23713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 31318 1.99 - 3.97: 658 3.97 - 5.96: 121 5.96 - 7.94: 26 7.94 - 9.93: 13 Bond angle restraints: 32136 Sorted by residual: angle pdb=" N GLU A 288 " pdb=" CA GLU A 288 " pdb=" C GLU A 288 " ideal model delta sigma weight residual 112.72 108.01 4.71 1.14e+00 7.69e-01 1.71e+01 angle pdb=" CA THR A3122 " pdb=" C THR A3122 " pdb=" O THR A3122 " ideal model delta sigma weight residual 121.99 117.67 4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" CA LYS A2755 " pdb=" CB LYS A2755 " pdb=" CG LYS A2755 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C ASN A 289 " pdb=" CA ASN A 289 " pdb=" CB ASN A 289 " ideal model delta sigma weight residual 116.63 112.36 4.27 1.16e+00 7.43e-01 1.36e+01 angle pdb=" CB ARG A1993 " pdb=" CG ARG A1993 " pdb=" CD ARG A1993 " ideal model delta sigma weight residual 111.30 119.63 -8.33 2.30e+00 1.89e-01 1.31e+01 ... (remaining 32131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13192 17.99 - 35.98: 1024 35.98 - 53.97: 145 53.97 - 71.95: 22 71.95 - 89.94: 15 Dihedral angle restraints: 14398 sinusoidal: 5905 harmonic: 8493 Sorted by residual: dihedral pdb=" CB CYS A3182 " pdb=" SG CYS A3182 " pdb=" SG CYS A3205 " pdb=" CB CYS A3205 " ideal model delta sinusoidal sigma weight residual 93.00 179.27 -86.27 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CA ARG A2458 " pdb=" C ARG A2458 " pdb=" N PRO A2459 " pdb=" CA PRO A2459 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A2548 " pdb=" C ASP A2548 " pdb=" N HIS A2549 " pdb=" CA HIS A2549 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 14395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2743 0.049 - 0.099: 689 0.099 - 0.148: 175 0.148 - 0.197: 20 0.197 - 0.247: 1 Chirality restraints: 3628 Sorted by residual: chirality pdb=" CB VAL A1810 " pdb=" CA VAL A1810 " pdb=" CG1 VAL A1810 " pdb=" CG2 VAL A1810 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA LEU A3099 " pdb=" N LEU A3099 " pdb=" C LEU A3099 " pdb=" CB LEU A3099 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA ILE A3157 " pdb=" N ILE A3157 " pdb=" C ILE A3157 " pdb=" CB ILE A3157 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 3625 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A3100 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.67e+00 pdb=" NE ARG A3100 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A3100 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A3100 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A3100 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A3180 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C GLY A3180 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A3180 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A3181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 716 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO A 717 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.036 5.00e-02 4.00e+02 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 10117 2.93 - 3.42: 24396 3.42 - 3.91: 38498 3.91 - 4.41: 43339 4.41 - 4.90: 71420 Nonbonded interactions: 187770 Sorted by model distance: nonbonded pdb=" O LYS A3119 " pdb=" OG1 THR A3122 " model vdw 2.433 3.040 nonbonded pdb=" O TYR A2986 " pdb=" OD1 ASN A2987 " model vdw 2.485 3.040 nonbonded pdb=" N GLN A2485 " pdb=" OE1 GLN A2485 " model vdw 2.500 3.120 nonbonded pdb=" N ASP A2234 " pdb=" OD1 ASP A2234 " model vdw 2.515 3.120 nonbonded pdb=" N GLU A2690 " pdb=" OE1 GLU A2690 " model vdw 2.518 3.120 ... (remaining 187765 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23719 Z= 0.191 Angle : 0.721 9.928 32138 Z= 0.382 Chirality : 0.047 0.247 3628 Planarity : 0.005 0.125 4151 Dihedral : 12.624 89.943 8919 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.19 % Allowed : 9.98 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2903 helix: 1.39 (0.16), residues: 1131 sheet: -0.86 (0.23), residues: 549 loop : -1.71 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1993 TYR 0.023 0.001 TYR A1592 PHE 0.037 0.002 PHE A 433 TRP 0.018 0.001 TRP A2448 HIS 0.009 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00387 (23718) covalent geometry : angle 0.72123 (32136) SS BOND : bond 0.00873 ( 1) SS BOND : angle 1.19121 ( 2) hydrogen bonds : bond 0.13073 ( 1049) hydrogen bonds : angle 5.93418 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 771 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 HIS cc_start: 0.8138 (m-70) cc_final: 0.7903 (m-70) REVERT: A 324 SER cc_start: 0.8990 (m) cc_final: 0.8564 (p) REVERT: A 413 GLU cc_start: 0.8231 (mp0) cc_final: 0.7929 (mp0) REVERT: A 481 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8694 (tttp) REVERT: A 560 MET cc_start: 0.8811 (mtm) cc_final: 0.8385 (mtm) REVERT: A 604 ASN cc_start: 0.8206 (t0) cc_final: 0.7862 (t0) REVERT: A 642 THR cc_start: 0.9007 (m) cc_final: 0.8770 (t) REVERT: A 696 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8183 (ttm-80) REVERT: A 700 ASN cc_start: 0.8472 (t0) cc_final: 0.8128 (t0) REVERT: A 721 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8631 (mtpp) REVERT: A 758 ASP cc_start: 0.8666 (p0) cc_final: 0.8457 (p0) REVERT: A 953 ASN cc_start: 0.8554 (t0) cc_final: 0.8270 (t0) REVERT: A 1122 LYS cc_start: 0.9422 (mmtt) cc_final: 0.9094 (mmmt) REVERT: A 1335 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 1387 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 1548 ASN cc_start: 0.8779 (t0) cc_final: 0.8320 (t0) REVERT: A 1690 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7722 (tttt) REVERT: A 1850 LEU cc_start: 0.9115 (mt) cc_final: 0.8817 (mt) REVERT: A 1863 MET cc_start: 0.6245 (tmm) cc_final: 0.5866 (tpp) REVERT: A 1897 MET cc_start: 0.3821 (tpp) cc_final: 0.2443 (pmm) REVERT: A 2012 PHE cc_start: 0.6884 (t80) cc_final: 0.5871 (t80) REVERT: A 2027 MET cc_start: 0.7825 (mpp) cc_final: 0.7613 (ptp) REVERT: A 2084 ASP cc_start: 0.6122 (t0) cc_final: 0.5393 (p0) REVERT: A 2194 LEU cc_start: 0.7942 (pt) cc_final: 0.7671 (tt) REVERT: A 2202 THR cc_start: 0.8303 (m) cc_final: 0.8098 (p) REVERT: A 2249 GLN cc_start: 0.8410 (tt0) cc_final: 0.8205 (tt0) REVERT: A 2449 GLN cc_start: 0.8323 (tp40) cc_final: 0.7862 (mm-40) REVERT: A 2471 TRP cc_start: 0.8396 (m100) cc_final: 0.8149 (m100) REVERT: A 2500 GLN cc_start: 0.8062 (pm20) cc_final: 0.7591 (pm20) REVERT: A 2570 ASN cc_start: 0.8888 (m-40) cc_final: 0.8446 (p0) REVERT: A 2765 LEU cc_start: 0.8280 (mt) cc_final: 0.8060 (mt) REVERT: A 2776 ASP cc_start: 0.8386 (t0) cc_final: 0.8109 (t0) REVERT: A 2777 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7585 (mmmt) REVERT: A 2782 LYS cc_start: 0.8193 (mttp) cc_final: 0.7930 (mttm) REVERT: A 2800 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8210 (ttp-110) REVERT: A 2825 MET cc_start: 0.8189 (mmm) cc_final: 0.7788 (ptm) REVERT: A 2854 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8498 (mmtt) REVERT: A 2863 ASP cc_start: 0.8969 (m-30) cc_final: 0.8531 (m-30) REVERT: A 2944 LYS cc_start: 0.8308 (mttp) cc_final: 0.7829 (mppt) REVERT: A 2993 GLU cc_start: 0.7857 (tt0) cc_final: 0.7651 (tt0) REVERT: A 3009 ASN cc_start: 0.8799 (m-40) cc_final: 0.8580 (m110) REVERT: A 3013 MET cc_start: 0.8426 (mmm) cc_final: 0.8140 (mmm) REVERT: A 3041 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7449 (tp30) REVERT: A 3089 ASN cc_start: 0.8308 (p0) cc_final: 0.7990 (p0) REVERT: A 3091 GLU cc_start: 0.7043 (mp0) cc_final: 0.6699 (mp0) REVERT: A 3115 ARG cc_start: 0.8669 (ttt180) cc_final: 0.8371 (tpt-90) REVERT: A 3151 TYR cc_start: 0.8278 (m-80) cc_final: 0.7429 (m-80) REVERT: A 3193 TYR cc_start: 0.8765 (t80) cc_final: 0.7161 (t80) outliers start: 5 outliers final: 2 residues processed: 776 average time/residue: 0.1929 time to fit residues: 224.1942 Evaluate side-chains 562 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 560 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2140 TRP Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 3.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 463 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN ** A 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 HIS A1415 ASN A1510 HIS A1511 GLN A1541 GLN A1651 ASN A1772 GLN A1776 GLN ** A1778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 GLN A2133 HIS A2200 GLN A2287 GLN ** A2333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2347 ASN A2437 GLN ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2786 HIS A3009 ASN A3196 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109624 restraints weight = 36514.227| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.52 r_work: 0.3158 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23719 Z= 0.173 Angle : 0.649 9.108 32138 Z= 0.330 Chirality : 0.045 0.249 3628 Planarity : 0.004 0.049 4151 Dihedral : 4.025 25.176 3173 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.31 % Allowed : 14.61 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2903 helix: 1.59 (0.16), residues: 1135 sheet: -0.68 (0.22), residues: 557 loop : -1.65 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2216 TYR 0.024 0.001 TYR A1592 PHE 0.021 0.001 PHE A 433 TRP 0.014 0.001 TRP A2448 HIS 0.009 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00402 (23718) covalent geometry : angle 0.64877 (32136) SS BOND : bond 0.00299 ( 1) SS BOND : angle 1.25335 ( 2) hydrogen bonds : bond 0.04381 ( 1049) hydrogen bonds : angle 4.79161 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 569 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8971 (tp) cc_final: 0.8763 (pt) REVERT: A 261 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7215 (mmtp) REVERT: A 281 MET cc_start: 0.7961 (tmm) cc_final: 0.7391 (tpp) REVERT: A 324 SER cc_start: 0.9068 (m) cc_final: 0.8657 (p) REVERT: A 392 GLU cc_start: 0.8958 (tp30) cc_final: 0.8425 (tm-30) REVERT: A 604 ASN cc_start: 0.8110 (t0) cc_final: 0.7587 (t0) REVERT: A 642 THR cc_start: 0.9066 (m) cc_final: 0.8737 (t) REVERT: A 673 SER cc_start: 0.8884 (m) cc_final: 0.8643 (m) REVERT: A 696 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7864 (ttm-80) REVERT: A 700 ASN cc_start: 0.8322 (t0) cc_final: 0.8008 (t0) REVERT: A 721 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8574 (mtpp) REVERT: A 794 LYS cc_start: 0.8796 (tppt) cc_final: 0.8189 (tptp) REVERT: A 815 THR cc_start: 0.9114 (m) cc_final: 0.8908 (m) REVERT: A 951 ASN cc_start: 0.8220 (t0) cc_final: 0.7882 (t0) REVERT: A 953 ASN cc_start: 0.8743 (t0) cc_final: 0.8420 (t0) REVERT: A 1087 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 1335 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 1466 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: A 1491 GLU cc_start: 0.8494 (pm20) cc_final: 0.8060 (pm20) REVERT: A 1548 ASN cc_start: 0.8773 (t0) cc_final: 0.8434 (t0) REVERT: A 1690 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7799 (tttt) REVERT: A 1694 ASP cc_start: 0.8721 (m-30) cc_final: 0.8417 (m-30) REVERT: A 1863 MET cc_start: 0.6484 (tmm) cc_final: 0.6100 (tpp) REVERT: A 1918 PHE cc_start: 0.8934 (m-80) cc_final: 0.8733 (t80) REVERT: A 2012 PHE cc_start: 0.6934 (t80) cc_final: 0.5956 (t80) REVERT: A 2027 MET cc_start: 0.8097 (mpp) cc_final: 0.7714 (ptp) REVERT: A 2084 ASP cc_start: 0.7112 (t0) cc_final: 0.6267 (p0) REVERT: A 2142 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8119 (mmm160) REVERT: A 2191 ARG cc_start: 0.8821 (mmp80) cc_final: 0.8555 (mmp80) REVERT: A 2303 MET cc_start: 0.7753 (mmm) cc_final: 0.7364 (mmm) REVERT: A 2403 GLN cc_start: 0.7845 (pm20) cc_final: 0.7633 (pm20) REVERT: A 2449 GLN cc_start: 0.8558 (tp40) cc_final: 0.8089 (mm-40) REVERT: A 2471 TRP cc_start: 0.8586 (m100) cc_final: 0.8362 (m100) REVERT: A 2500 GLN cc_start: 0.8213 (pm20) cc_final: 0.7741 (pm20) REVERT: A 2503 TYR cc_start: 0.9239 (m-80) cc_final: 0.8349 (m-10) REVERT: A 2570 ASN cc_start: 0.8964 (m-40) cc_final: 0.8509 (p0) REVERT: A 2646 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8357 (pt0) REVERT: A 2677 GLU cc_start: 0.7431 (pm20) cc_final: 0.5840 (pm20) REVERT: A 2702 LEU cc_start: 0.9106 (mp) cc_final: 0.8900 (mp) REVERT: A 2709 ARG cc_start: 0.8601 (mtp180) cc_final: 0.8304 (mtp180) REVERT: A 2723 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7485 (ttp80) REVERT: A 2776 ASP cc_start: 0.8407 (t0) cc_final: 0.8192 (t0) REVERT: A 2777 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7730 (mmmt) REVERT: A 2796 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 2800 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8240 (ttp-110) REVERT: A 2825 MET cc_start: 0.7900 (mmm) cc_final: 0.7478 (ttt) REVERT: A 2854 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8630 (mmtt) REVERT: A 2875 TYR cc_start: 0.8612 (t80) cc_final: 0.8352 (t80) REVERT: A 2944 LYS cc_start: 0.8611 (mttp) cc_final: 0.8070 (mppt) REVERT: A 2991 LEU cc_start: 0.9438 (mp) cc_final: 0.9208 (mt) REVERT: A 3007 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8261 (ttt90) REVERT: A 3013 MET cc_start: 0.8336 (mmm) cc_final: 0.8088 (mmm) REVERT: A 3091 GLU cc_start: 0.7138 (mp0) cc_final: 0.6749 (mp0) REVERT: A 3151 TYR cc_start: 0.8385 (m-80) cc_final: 0.7532 (m-80) REVERT: A 3160 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8155 (mmm) REVERT: A 3189 ASP cc_start: 0.8692 (t0) cc_final: 0.8483 (t0) REVERT: A 3193 TYR cc_start: 0.8759 (t80) cc_final: 0.7152 (t80) outliers start: 60 outliers final: 37 residues processed: 596 average time/residue: 0.1794 time to fit residues: 163.4824 Evaluate side-chains 564 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 523 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1511 GLN Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2147 ILE Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2796 SER Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3002 VAL Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3030 VAL Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3160 MET Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 210 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 58 optimal weight: 0.0270 chunk 183 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN A1210 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1510 HIS A1511 GLN ** A1625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 GLN ** A1794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 ASN A2133 HIS A2249 GLN ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2333 HIS ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2437 GLN ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2498 GLN A2603 GLN ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3009 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.164390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110205 restraints weight = 36262.394| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.52 r_work: 0.3164 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23719 Z= 0.131 Angle : 0.597 11.734 32138 Z= 0.300 Chirality : 0.043 0.253 3628 Planarity : 0.004 0.046 4151 Dihedral : 3.930 26.557 3171 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.43 % Allowed : 15.69 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2903 helix: 1.65 (0.16), residues: 1136 sheet: -0.57 (0.22), residues: 556 loop : -1.65 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2216 TYR 0.015 0.001 TYR A1592 PHE 0.023 0.001 PHE A1120 TRP 0.011 0.001 TRP A3063 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00300 (23718) covalent geometry : angle 0.59730 (32136) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.05645 ( 2) hydrogen bonds : bond 0.03878 ( 1049) hydrogen bonds : angle 4.55233 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 549 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7403 (mmtp) REVERT: A 281 MET cc_start: 0.7858 (tmm) cc_final: 0.7121 (tpt) REVERT: A 324 SER cc_start: 0.9074 (m) cc_final: 0.8674 (p) REVERT: A 392 GLU cc_start: 0.8968 (tp30) cc_final: 0.8415 (tm-30) REVERT: A 604 ASN cc_start: 0.8151 (t0) cc_final: 0.7633 (t0) REVERT: A 642 THR cc_start: 0.9065 (m) cc_final: 0.8719 (t) REVERT: A 673 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8697 (m) REVERT: A 696 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7895 (ttm-80) REVERT: A 700 ASN cc_start: 0.8282 (t0) cc_final: 0.7926 (t0) REVERT: A 721 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8551 (mtpp) REVERT: A 794 LYS cc_start: 0.8844 (tppt) cc_final: 0.8615 (tptp) REVERT: A 951 ASN cc_start: 0.8045 (t0) cc_final: 0.7667 (t0) REVERT: A 953 ASN cc_start: 0.8713 (t0) cc_final: 0.8397 (t0) REVERT: A 957 MET cc_start: 0.9215 (tpp) cc_final: 0.8964 (tpp) REVERT: A 1087 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7831 (pp) REVERT: A 1289 ASN cc_start: 0.9110 (t0) cc_final: 0.8501 (t0) REVERT: A 1335 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 1466 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: A 1491 GLU cc_start: 0.8507 (pm20) cc_final: 0.8126 (pm20) REVERT: A 1548 ASN cc_start: 0.8749 (t0) cc_final: 0.8399 (t0) REVERT: A 1690 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7780 (tttt) REVERT: A 1694 ASP cc_start: 0.8791 (m-30) cc_final: 0.8490 (m-30) REVERT: A 1948 MET cc_start: 0.8044 (pmm) cc_final: 0.7838 (ppp) REVERT: A 2012 PHE cc_start: 0.6856 (t80) cc_final: 0.5874 (t80) REVERT: A 2027 MET cc_start: 0.7904 (mpp) cc_final: 0.7643 (ptp) REVERT: A 2084 ASP cc_start: 0.7107 (t0) cc_final: 0.6219 (p0) REVERT: A 2142 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8209 (mmm160) REVERT: A 2179 ARG cc_start: 0.7375 (tpp80) cc_final: 0.7143 (tpp80) REVERT: A 2240 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7781 (mtp85) REVERT: A 2403 GLN cc_start: 0.7984 (pm20) cc_final: 0.7745 (pm20) REVERT: A 2449 GLN cc_start: 0.8591 (tp40) cc_final: 0.8026 (mm-40) REVERT: A 2471 TRP cc_start: 0.8601 (m100) cc_final: 0.8392 (m100) REVERT: A 2498 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: A 2503 TYR cc_start: 0.9213 (m-80) cc_final: 0.8345 (m-10) REVERT: A 2570 ASN cc_start: 0.8930 (m-40) cc_final: 0.8421 (p0) REVERT: A 2646 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8386 (pt0) REVERT: A 2677 GLU cc_start: 0.7446 (pm20) cc_final: 0.6962 (pm20) REVERT: A 2702 LEU cc_start: 0.9060 (mp) cc_final: 0.8796 (mp) REVERT: A 2709 ARG cc_start: 0.8667 (mtp180) cc_final: 0.8297 (mtp180) REVERT: A 2776 ASP cc_start: 0.8425 (t0) cc_final: 0.8152 (t0) REVERT: A 2777 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7676 (mmmt) REVERT: A 2800 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8101 (ttm-80) REVERT: A 2825 MET cc_start: 0.7905 (mmm) cc_final: 0.7499 (ttt) REVERT: A 2854 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8548 (mmtt) REVERT: A 2875 TYR cc_start: 0.8717 (t80) cc_final: 0.8517 (t80) REVERT: A 2944 LYS cc_start: 0.8606 (mttp) cc_final: 0.7965 (mppt) REVERT: A 2991 LEU cc_start: 0.9430 (mp) cc_final: 0.9195 (mt) REVERT: A 2993 GLU cc_start: 0.7927 (tt0) cc_final: 0.7447 (tp30) REVERT: A 3007 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8292 (ttt90) REVERT: A 3013 MET cc_start: 0.8302 (mmm) cc_final: 0.8046 (mmm) REVERT: A 3059 GLU cc_start: 0.8722 (tp30) cc_final: 0.8516 (tt0) REVERT: A 3062 MET cc_start: 0.8788 (mmm) cc_final: 0.8380 (mmm) REVERT: A 3089 ASN cc_start: 0.8617 (p0) cc_final: 0.8348 (p0) REVERT: A 3091 GLU cc_start: 0.7312 (mp0) cc_final: 0.6873 (mp0) REVERT: A 3151 TYR cc_start: 0.8283 (m-80) cc_final: 0.7407 (m-80) REVERT: A 3160 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: A 3189 ASP cc_start: 0.8694 (t0) cc_final: 0.8398 (t0) REVERT: A 3193 TYR cc_start: 0.8681 (t80) cc_final: 0.7217 (t80) outliers start: 63 outliers final: 39 residues processed: 575 average time/residue: 0.1768 time to fit residues: 156.4813 Evaluate side-chains 557 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 513 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2147 ILE Chi-restraints excluded: chain A residue 2248 VAL Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2324 ILE Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2498 GLN Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2745 GLN Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2812 SER Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3002 VAL Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3030 VAL Chi-restraints excluded: chain A residue 3043 MET Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3160 MET Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 68 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1489 GLN ** A1619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1651 ASN ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS A2249 GLN ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2412 HIS A2437 GLN ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2498 GLN ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3009 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109122 restraints weight = 36566.238| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.56 r_work: 0.3151 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23719 Z= 0.133 Angle : 0.590 14.768 32138 Z= 0.295 Chirality : 0.043 0.259 3628 Planarity : 0.004 0.046 4151 Dihedral : 3.913 26.734 3171 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.51 % Allowed : 15.73 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2903 helix: 1.68 (0.16), residues: 1135 sheet: -0.45 (0.23), residues: 536 loop : -1.59 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2216 TYR 0.017 0.001 TYR A1592 PHE 0.017 0.001 PHE A2072 TRP 0.014 0.001 TRP A3063 HIS 0.006 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00306 (23718) covalent geometry : angle 0.59045 (32136) SS BOND : bond 0.00153 ( 1) SS BOND : angle 1.08895 ( 2) hydrogen bonds : bond 0.03695 ( 1049) hydrogen bonds : angle 4.44202 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 541 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.9098 (mtt) cc_final: 0.8829 (mtt) REVERT: A 261 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7469 (mmtp) REVERT: A 281 MET cc_start: 0.7757 (tmm) cc_final: 0.7465 (tpt) REVERT: A 294 ILE cc_start: 0.5115 (mp) cc_final: 0.4911 (mp) REVERT: A 324 SER cc_start: 0.9103 (m) cc_final: 0.8762 (p) REVERT: A 392 GLU cc_start: 0.8979 (tp30) cc_final: 0.8425 (tm-30) REVERT: A 604 ASN cc_start: 0.8089 (t0) cc_final: 0.7543 (t0) REVERT: A 642 THR cc_start: 0.9064 (m) cc_final: 0.8715 (t) REVERT: A 696 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7875 (ttm-80) REVERT: A 700 ASN cc_start: 0.8290 (t0) cc_final: 0.7944 (t0) REVERT: A 953 ASN cc_start: 0.8708 (t0) cc_final: 0.8401 (t0) REVERT: A 1087 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 1120 PHE cc_start: 0.7616 (m-80) cc_final: 0.7048 (m-80) REVERT: A 1122 LYS cc_start: 0.9335 (tppt) cc_final: 0.9044 (tppt) REVERT: A 1135 ILE cc_start: 0.9556 (mt) cc_final: 0.9141 (tp) REVERT: A 1289 ASN cc_start: 0.9073 (t0) cc_final: 0.8470 (t0) REVERT: A 1335 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8250 (tm-30) REVERT: A 1466 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: A 1491 GLU cc_start: 0.8502 (pm20) cc_final: 0.8124 (pm20) REVERT: A 1548 ASN cc_start: 0.8726 (t0) cc_final: 0.8359 (t0) REVERT: A 1624 LEU cc_start: 0.9162 (tt) cc_final: 0.8951 (tp) REVERT: A 1647 ASP cc_start: 0.8287 (m-30) cc_final: 0.8040 (m-30) REVERT: A 1712 GLN cc_start: 0.8451 (mt0) cc_final: 0.8139 (pt0) REVERT: A 1729 ARG cc_start: 0.9145 (ttm-80) cc_final: 0.8916 (ttm-80) REVERT: A 1918 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8069 (t80) REVERT: A 2012 PHE cc_start: 0.6921 (t80) cc_final: 0.5910 (t80) REVERT: A 2084 ASP cc_start: 0.7095 (t0) cc_final: 0.6241 (p0) REVERT: A 2179 ARG cc_start: 0.7481 (tpp80) cc_final: 0.7256 (tpp80) REVERT: A 2240 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7844 (mtp85) REVERT: A 2403 GLN cc_start: 0.8143 (pm20) cc_final: 0.7902 (pm20) REVERT: A 2412 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.7211 (m170) REVERT: A 2448 TRP cc_start: 0.9079 (t-100) cc_final: 0.8654 (t60) REVERT: A 2449 GLN cc_start: 0.8603 (tp40) cc_final: 0.7972 (mm-40) REVERT: A 2471 TRP cc_start: 0.8675 (m100) cc_final: 0.8408 (m100) REVERT: A 2498 GLN cc_start: 0.8497 (tp40) cc_final: 0.8143 (tp40) REVERT: A 2503 TYR cc_start: 0.9233 (m-80) cc_final: 0.8431 (m-10) REVERT: A 2570 ASN cc_start: 0.8928 (m-40) cc_final: 0.8404 (p0) REVERT: A 2646 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8311 (pt0) REVERT: A 2672 LYS cc_start: 0.8962 (mttt) cc_final: 0.8598 (mttt) REVERT: A 2677 GLU cc_start: 0.7422 (pm20) cc_final: 0.6857 (pm20) REVERT: A 2702 LEU cc_start: 0.9052 (mp) cc_final: 0.8761 (mp) REVERT: A 2709 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8277 (mtp180) REVERT: A 2776 ASP cc_start: 0.8446 (t0) cc_final: 0.8179 (t0) REVERT: A 2777 LYS cc_start: 0.7885 (mmtt) cc_final: 0.7635 (mmmt) REVERT: A 2800 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8099 (ttm-80) REVERT: A 2825 MET cc_start: 0.7914 (mmm) cc_final: 0.7527 (ttt) REVERT: A 2854 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8580 (mmtt) REVERT: A 2941 MET cc_start: 0.8495 (mpp) cc_final: 0.7963 (mpp) REVERT: A 2944 LYS cc_start: 0.8666 (mttp) cc_final: 0.8142 (mppt) REVERT: A 2993 GLU cc_start: 0.7946 (tt0) cc_final: 0.7468 (tp30) REVERT: A 3013 MET cc_start: 0.8361 (mmm) cc_final: 0.8072 (mmm) REVERT: A 3062 MET cc_start: 0.8822 (mmm) cc_final: 0.8351 (mmm) REVERT: A 3151 TYR cc_start: 0.8328 (m-80) cc_final: 0.7513 (m-80) REVERT: A 3160 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7988 (mmm) REVERT: A 3189 ASP cc_start: 0.8714 (t0) cc_final: 0.8340 (t0) REVERT: A 3193 TYR cc_start: 0.8722 (t80) cc_final: 0.7287 (t80) outliers start: 65 outliers final: 43 residues processed: 569 average time/residue: 0.1716 time to fit residues: 151.8831 Evaluate side-chains 548 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 500 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 1918 PHE Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2147 ILE Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2412 HIS Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2745 GLN Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 2975 SER Chi-restraints excluded: chain A residue 3002 VAL Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3030 VAL Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3160 MET Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 51 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 202 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 142 optimal weight: 0.0060 chunk 158 optimal weight: 0.0060 chunk 276 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 75 optimal weight: 0.5980 chunk 261 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3009 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111311 restraints weight = 36033.081| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.97 r_work: 0.3167 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23719 Z= 0.107 Angle : 0.578 11.928 32138 Z= 0.286 Chirality : 0.042 0.266 3628 Planarity : 0.004 0.045 4151 Dihedral : 3.834 26.607 3171 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.08 % Allowed : 16.77 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2903 helix: 1.64 (0.16), residues: 1148 sheet: -0.33 (0.23), residues: 528 loop : -1.61 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3007 TYR 0.011 0.001 TYR A1592 PHE 0.016 0.001 PHE A2072 TRP 0.020 0.001 TRP A3063 HIS 0.013 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00236 (23718) covalent geometry : angle 0.57822 (32136) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.02581 ( 2) hydrogen bonds : bond 0.03429 ( 1049) hydrogen bonds : angle 4.33816 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 535 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7691 (tmm) cc_final: 0.7293 (tmm) REVERT: A 324 SER cc_start: 0.9117 (m) cc_final: 0.8768 (p) REVERT: A 392 GLU cc_start: 0.9003 (tp30) cc_final: 0.8411 (tm-30) REVERT: A 604 ASN cc_start: 0.8069 (t0) cc_final: 0.7453 (t0) REVERT: A 642 THR cc_start: 0.9056 (m) cc_final: 0.8724 (t) REVERT: A 696 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7839 (ttm-80) REVERT: A 721 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8545 (mtpp) REVERT: A 953 ASN cc_start: 0.8660 (t0) cc_final: 0.8286 (t0) REVERT: A 957 MET cc_start: 0.9213 (tpp) cc_final: 0.8995 (tpp) REVERT: A 1075 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 1087 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7833 (pp) REVERT: A 1120 PHE cc_start: 0.7520 (m-80) cc_final: 0.6995 (m-80) REVERT: A 1122 LYS cc_start: 0.9318 (tppt) cc_final: 0.9090 (tppt) REVERT: A 1135 ILE cc_start: 0.9529 (mt) cc_final: 0.9156 (tp) REVERT: A 1289 ASN cc_start: 0.9019 (t0) cc_final: 0.8445 (t0) REVERT: A 1335 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 1466 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 1491 GLU cc_start: 0.8515 (pm20) cc_final: 0.8142 (pm20) REVERT: A 1548 ASN cc_start: 0.8773 (t0) cc_final: 0.8395 (t0) REVERT: A 1647 ASP cc_start: 0.8208 (m-30) cc_final: 0.8000 (m-30) REVERT: A 1671 ASP cc_start: 0.8617 (m-30) cc_final: 0.8392 (t0) REVERT: A 1712 GLN cc_start: 0.8433 (mt0) cc_final: 0.8148 (pt0) REVERT: A 1760 MET cc_start: 0.9125 (mpp) cc_final: 0.8904 (mpp) REVERT: A 1918 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: A 2012 PHE cc_start: 0.6923 (t80) cc_final: 0.5906 (t80) REVERT: A 2084 ASP cc_start: 0.7087 (t0) cc_final: 0.6164 (p0) REVERT: A 2179 ARG cc_start: 0.7523 (tpp80) cc_final: 0.7178 (tpp80) REVERT: A 2240 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7921 (mtp85) REVERT: A 2403 GLN cc_start: 0.8241 (pm20) cc_final: 0.8019 (pm20) REVERT: A 2412 HIS cc_start: 0.7610 (m170) cc_final: 0.7393 (m170) REVERT: A 2448 TRP cc_start: 0.9090 (t-100) cc_final: 0.8616 (t60) REVERT: A 2449 GLN cc_start: 0.8599 (tp40) cc_final: 0.7982 (mm110) REVERT: A 2465 ARG cc_start: 0.9283 (mmm-85) cc_final: 0.8914 (mtp85) REVERT: A 2471 TRP cc_start: 0.8664 (m100) cc_final: 0.8381 (m100) REVERT: A 2480 GLN cc_start: 0.8854 (tp40) cc_final: 0.8443 (tt0) REVERT: A 2498 GLN cc_start: 0.8241 (tp40) cc_final: 0.7999 (tp40) REVERT: A 2503 TYR cc_start: 0.9233 (m-80) cc_final: 0.8469 (m-80) REVERT: A 2570 ASN cc_start: 0.8907 (m-40) cc_final: 0.8350 (p0) REVERT: A 2620 ASN cc_start: 0.8420 (m-40) cc_final: 0.8219 (m-40) REVERT: A 2641 LEU cc_start: 0.8817 (mm) cc_final: 0.8587 (mm) REVERT: A 2646 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8323 (pt0) REVERT: A 2672 LYS cc_start: 0.8934 (mttt) cc_final: 0.8589 (mttt) REVERT: A 2675 GLU cc_start: 0.6804 (mp0) cc_final: 0.6560 (pm20) REVERT: A 2677 GLU cc_start: 0.7314 (pm20) cc_final: 0.6912 (pm20) REVERT: A 2702 LEU cc_start: 0.9083 (mp) cc_final: 0.8765 (mp) REVERT: A 2709 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8278 (mtp180) REVERT: A 2776 ASP cc_start: 0.8463 (t0) cc_final: 0.8169 (t0) REVERT: A 2777 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7616 (mmmt) REVERT: A 2789 MET cc_start: 0.7968 (mmm) cc_final: 0.7593 (mmt) REVERT: A 2800 ARG cc_start: 0.8574 (ttm110) cc_final: 0.7860 (ttm-80) REVERT: A 2825 MET cc_start: 0.7935 (mmm) cc_final: 0.7556 (ttt) REVERT: A 2854 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8556 (mmtt) REVERT: A 2941 MET cc_start: 0.8455 (mpp) cc_final: 0.7945 (mpp) REVERT: A 2944 LYS cc_start: 0.8690 (mttp) cc_final: 0.8153 (mppt) REVERT: A 2993 GLU cc_start: 0.7986 (tt0) cc_final: 0.7496 (tp30) REVERT: A 3007 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7909 (mtp85) REVERT: A 3013 MET cc_start: 0.8390 (mmm) cc_final: 0.8078 (mmm) REVERT: A 3014 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7898 (mm110) REVERT: A 3074 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7684 (t) REVERT: A 3122 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7750 (p) REVERT: A 3151 TYR cc_start: 0.8280 (m-80) cc_final: 0.7425 (m-80) REVERT: A 3189 ASP cc_start: 0.8692 (t0) cc_final: 0.8352 (t0) REVERT: A 3193 TYR cc_start: 0.8683 (t80) cc_final: 0.7253 (t80) outliers start: 54 outliers final: 36 residues processed: 558 average time/residue: 0.1722 time to fit residues: 150.0200 Evaluate side-chains 541 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 500 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 1918 PHE Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2147 ILE Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2745 GLN Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 2975 SER Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3030 VAL Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 178 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 158 optimal weight: 0.0470 chunk 70 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 199 optimal weight: 0.5980 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS A1210 HIS A1619 GLN A1625 GLN ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2549 HIS ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.160705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105922 restraints weight = 36326.357| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.48 r_work: 0.3103 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23719 Z= 0.188 Angle : 0.614 11.299 32138 Z= 0.309 Chirality : 0.044 0.262 3628 Planarity : 0.004 0.051 4151 Dihedral : 4.019 26.552 3171 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.89 % Allowed : 16.69 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2903 helix: 1.70 (0.16), residues: 1136 sheet: -0.42 (0.23), residues: 554 loop : -1.57 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2805 TYR 0.023 0.001 TYR A1592 PHE 0.013 0.001 PHE A2072 TRP 0.015 0.001 TRP A3063 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00439 (23718) covalent geometry : angle 0.61379 (32136) SS BOND : bond 0.00145 ( 1) SS BOND : angle 1.10415 ( 2) hydrogen bonds : bond 0.03951 ( 1049) hydrogen bonds : angle 4.43576 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 515 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8595 (tmm-80) REVERT: A 252 MET cc_start: 0.8869 (mtt) cc_final: 0.8652 (mtt) REVERT: A 261 LYS cc_start: 0.7811 (mttm) cc_final: 0.6970 (mptt) REVERT: A 281 MET cc_start: 0.7725 (tmm) cc_final: 0.7210 (tpt) REVERT: A 294 ILE cc_start: 0.5096 (OUTLIER) cc_final: 0.4817 (mp) REVERT: A 304 GLU cc_start: 0.7930 (pp20) cc_final: 0.7324 (pp20) REVERT: A 324 SER cc_start: 0.9115 (m) cc_final: 0.8789 (p) REVERT: A 392 GLU cc_start: 0.9007 (tp30) cc_final: 0.8448 (tm-30) REVERT: A 570 PHE cc_start: 0.8072 (t80) cc_final: 0.7817 (t80) REVERT: A 604 ASN cc_start: 0.8131 (t0) cc_final: 0.7549 (t0) REVERT: A 642 THR cc_start: 0.9049 (m) cc_final: 0.8678 (t) REVERT: A 696 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8086 (ttm-80) REVERT: A 951 ASN cc_start: 0.8296 (t0) cc_final: 0.7796 (t0) REVERT: A 953 ASN cc_start: 0.8651 (t0) cc_final: 0.8298 (t0) REVERT: A 957 MET cc_start: 0.9249 (tpp) cc_final: 0.8985 (tpp) REVERT: A 1075 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 1087 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7868 (pp) REVERT: A 1120 PHE cc_start: 0.7584 (m-80) cc_final: 0.7015 (m-80) REVERT: A 1122 LYS cc_start: 0.9332 (tppt) cc_final: 0.9099 (tppt) REVERT: A 1135 ILE cc_start: 0.9568 (mt) cc_final: 0.9149 (tp) REVERT: A 1335 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 1373 LEU cc_start: 0.9245 (tp) cc_final: 0.9028 (tp) REVERT: A 1491 GLU cc_start: 0.8556 (pm20) cc_final: 0.8184 (pm20) REVERT: A 1647 ASP cc_start: 0.8386 (m-30) cc_final: 0.8174 (m-30) REVERT: A 1671 ASP cc_start: 0.8675 (m-30) cc_final: 0.8418 (t0) REVERT: A 2012 PHE cc_start: 0.6999 (t80) cc_final: 0.5976 (t80) REVERT: A 2070 LEU cc_start: 0.9029 (pp) cc_final: 0.8558 (mm) REVERT: A 2084 ASP cc_start: 0.7292 (t0) cc_final: 0.6315 (p0) REVERT: A 2133 HIS cc_start: 0.8416 (m170) cc_final: 0.8174 (m-70) REVERT: A 2179 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7258 (tpp80) REVERT: A 2236 LYS cc_start: 0.8066 (tttp) cc_final: 0.7811 (tptp) REVERT: A 2240 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7831 (mtp85) REVERT: A 2292 MET cc_start: 0.8149 (mmm) cc_final: 0.7853 (tpp) REVERT: A 2348 ASN cc_start: 0.8126 (m-40) cc_final: 0.7834 (m-40) REVERT: A 2412 HIS cc_start: 0.7788 (m170) cc_final: 0.7542 (m170) REVERT: A 2448 TRP cc_start: 0.9183 (t-100) cc_final: 0.8729 (t60) REVERT: A 2449 GLN cc_start: 0.8584 (tp40) cc_final: 0.8001 (mm110) REVERT: A 2471 TRP cc_start: 0.8636 (m100) cc_final: 0.8224 (m100) REVERT: A 2480 GLN cc_start: 0.8787 (tp40) cc_final: 0.8411 (tt0) REVERT: A 2498 GLN cc_start: 0.8354 (tp40) cc_final: 0.8054 (tp40) REVERT: A 2503 TYR cc_start: 0.9219 (m-80) cc_final: 0.8403 (m-10) REVERT: A 2570 ASN cc_start: 0.8880 (m-40) cc_final: 0.8331 (p0) REVERT: A 2672 LYS cc_start: 0.9030 (mttt) cc_final: 0.8657 (mttt) REVERT: A 2677 GLU cc_start: 0.7425 (pm20) cc_final: 0.6975 (pm20) REVERT: A 2702 LEU cc_start: 0.9104 (mp) cc_final: 0.8804 (mp) REVERT: A 2709 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8410 (mtp180) REVERT: A 2750 GLU cc_start: 0.8467 (pp20) cc_final: 0.7781 (pp20) REVERT: A 2776 ASP cc_start: 0.8458 (t0) cc_final: 0.8233 (t0) REVERT: A 2777 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7663 (mmmt) REVERT: A 2800 ARG cc_start: 0.8502 (ttm110) cc_final: 0.7985 (ttm-80) REVERT: A 2807 GLN cc_start: 0.7096 (pp30) cc_final: 0.6867 (pp30) REVERT: A 2825 MET cc_start: 0.7976 (mmm) cc_final: 0.7584 (ttt) REVERT: A 2854 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8532 (mmtt) REVERT: A 2941 MET cc_start: 0.8505 (mpp) cc_final: 0.7997 (mpp) REVERT: A 2956 ASP cc_start: 0.8312 (m-30) cc_final: 0.8083 (m-30) REVERT: A 2993 GLU cc_start: 0.7974 (tt0) cc_final: 0.7421 (tp30) REVERT: A 3014 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7925 (mm110) REVERT: A 3058 GLU cc_start: 0.8205 (pm20) cc_final: 0.7899 (pm20) REVERT: A 3074 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 3151 TYR cc_start: 0.8433 (m-80) cc_final: 0.7770 (m-80) REVERT: A 3189 ASP cc_start: 0.8720 (t0) cc_final: 0.8271 (t0) REVERT: A 3193 TYR cc_start: 0.8803 (t80) cc_final: 0.7397 (t80) outliers start: 75 outliers final: 47 residues processed: 555 average time/residue: 0.1734 time to fit residues: 148.6523 Evaluate side-chains 536 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 486 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1074 PHE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1522 LYS Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2463 LEU Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2745 GLN Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2812 SER Chi-restraints excluded: chain A residue 2871 ILE Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 2975 SER Chi-restraints excluded: chain A residue 3002 VAL Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3030 VAL Chi-restraints excluded: chain A residue 3038 ILE Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 8 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS A1511 GLN ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106845 restraints weight = 36266.517| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.49 r_work: 0.3118 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23719 Z= 0.150 Angle : 0.615 11.128 32138 Z= 0.306 Chirality : 0.044 0.279 3628 Planarity : 0.004 0.044 4151 Dihedral : 4.011 26.383 3171 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.47 % Allowed : 17.42 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2903 helix: 1.72 (0.16), residues: 1130 sheet: -0.39 (0.23), residues: 542 loop : -1.59 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3007 TYR 0.018 0.001 TYR A1592 PHE 0.016 0.001 PHE A 433 TRP 0.017 0.001 TRP A3063 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00349 (23718) covalent geometry : angle 0.61488 (32136) SS BOND : bond 0.00211 ( 1) SS BOND : angle 1.08826 ( 2) hydrogen bonds : bond 0.03696 ( 1049) hydrogen bonds : angle 4.36719 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 507 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7700 (tmm) cc_final: 0.7405 (tmm) REVERT: A 324 SER cc_start: 0.9099 (m) cc_final: 0.8781 (p) REVERT: A 392 GLU cc_start: 0.9004 (tp30) cc_final: 0.8435 (tm-30) REVERT: A 604 ASN cc_start: 0.8175 (t0) cc_final: 0.7615 (t0) REVERT: A 642 THR cc_start: 0.9056 (m) cc_final: 0.8696 (t) REVERT: A 696 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8041 (ttm-80) REVERT: A 953 ASN cc_start: 0.8640 (t0) cc_final: 0.8305 (t0) REVERT: A 1075 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 1087 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 1120 PHE cc_start: 0.7557 (m-80) cc_final: 0.7059 (m-80) REVERT: A 1122 LYS cc_start: 0.9319 (tppt) cc_final: 0.9076 (tppt) REVERT: A 1135 ILE cc_start: 0.9555 (mt) cc_final: 0.9127 (tp) REVERT: A 1335 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 1373 LEU cc_start: 0.9212 (tp) cc_final: 0.8980 (tp) REVERT: A 1491 GLU cc_start: 0.8560 (pm20) cc_final: 0.8228 (pm20) REVERT: A 1671 ASP cc_start: 0.8665 (m-30) cc_final: 0.8442 (t0) REVERT: A 2012 PHE cc_start: 0.7065 (t80) cc_final: 0.6045 (t80) REVERT: A 2084 ASP cc_start: 0.7328 (t0) cc_final: 0.6547 (p0) REVERT: A 2179 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7371 (tpp80) REVERT: A 2240 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7790 (mtp85) REVERT: A 2292 MET cc_start: 0.8218 (mmm) cc_final: 0.7933 (tpp) REVERT: A 2303 MET cc_start: 0.7753 (mmt) cc_final: 0.7416 (mmt) REVERT: A 2348 ASN cc_start: 0.8157 (m-40) cc_final: 0.7875 (m-40) REVERT: A 2412 HIS cc_start: 0.7899 (m170) cc_final: 0.7676 (m170) REVERT: A 2448 TRP cc_start: 0.9144 (t-100) cc_final: 0.8634 (t60) REVERT: A 2449 GLN cc_start: 0.8558 (tp40) cc_final: 0.7965 (mm110) REVERT: A 2465 ARG cc_start: 0.9270 (mmm-85) cc_final: 0.8993 (mtt180) REVERT: A 2480 GLN cc_start: 0.8747 (tp40) cc_final: 0.8346 (tt0) REVERT: A 2498 GLN cc_start: 0.8338 (tp40) cc_final: 0.8129 (tp40) REVERT: A 2503 TYR cc_start: 0.9246 (m-80) cc_final: 0.8433 (m-80) REVERT: A 2535 GLN cc_start: 0.8690 (pm20) cc_final: 0.8283 (pm20) REVERT: A 2570 ASN cc_start: 0.8880 (m-40) cc_final: 0.8294 (p0) REVERT: A 2672 LYS cc_start: 0.9031 (mttt) cc_final: 0.8657 (mttt) REVERT: A 2677 GLU cc_start: 0.7311 (pm20) cc_final: 0.6883 (pm20) REVERT: A 2702 LEU cc_start: 0.9114 (mp) cc_final: 0.8812 (mp) REVERT: A 2709 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8420 (mtp180) REVERT: A 2750 GLU cc_start: 0.8463 (pp20) cc_final: 0.7800 (pp20) REVERT: A 2776 ASP cc_start: 0.8445 (t0) cc_final: 0.8218 (t0) REVERT: A 2777 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7645 (mmmt) REVERT: A 2800 ARG cc_start: 0.8555 (ttm110) cc_final: 0.7972 (ttm-80) REVERT: A 2807 GLN cc_start: 0.7169 (pp30) cc_final: 0.6721 (pp30) REVERT: A 2818 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7503 (tpp80) REVERT: A 2825 MET cc_start: 0.7913 (mmm) cc_final: 0.7523 (ttt) REVERT: A 2854 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8556 (mmtt) REVERT: A 2941 MET cc_start: 0.8497 (mpp) cc_final: 0.7992 (mpp) REVERT: A 2944 LYS cc_start: 0.8744 (mttp) cc_final: 0.8189 (mppt) REVERT: A 2956 ASP cc_start: 0.8332 (m-30) cc_final: 0.8128 (m-30) REVERT: A 2993 GLU cc_start: 0.8036 (tt0) cc_final: 0.7485 (tp30) REVERT: A 3013 MET cc_start: 0.8229 (mmp) cc_final: 0.7848 (mmm) REVERT: A 3014 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7931 (mm110) REVERT: A 3062 MET cc_start: 0.8966 (mmm) cc_final: 0.8346 (mmm) REVERT: A 3074 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 3084 ASP cc_start: 0.8882 (t0) cc_final: 0.8635 (t0) REVERT: A 3122 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 3151 TYR cc_start: 0.8422 (m-80) cc_final: 0.7763 (m-80) REVERT: A 3189 ASP cc_start: 0.8740 (t0) cc_final: 0.8322 (t0) REVERT: A 3193 TYR cc_start: 0.8784 (t80) cc_final: 0.7407 (t80) outliers start: 64 outliers final: 44 residues processed: 543 average time/residue: 0.1749 time to fit residues: 147.8083 Evaluate side-chains 541 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 494 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2863 ASP Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 168 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 238 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** A1848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS ** A2330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.161209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.106873 restraints weight = 36109.981| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.46 r_work: 0.3119 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23719 Z= 0.145 Angle : 0.618 10.124 32138 Z= 0.308 Chirality : 0.044 0.285 3628 Planarity : 0.004 0.044 4151 Dihedral : 4.010 26.171 3171 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.35 % Allowed : 17.62 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2903 helix: 1.65 (0.15), residues: 1137 sheet: -0.28 (0.23), residues: 525 loop : -1.59 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3007 TYR 0.017 0.001 TYR A1592 PHE 0.031 0.001 PHE A1918 TRP 0.016 0.001 TRP A3063 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00337 (23718) covalent geometry : angle 0.61816 (32136) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.06354 ( 2) hydrogen bonds : bond 0.03695 ( 1049) hydrogen bonds : angle 4.34430 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 505 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.9009 (mtt) cc_final: 0.8692 (mtt) REVERT: A 281 MET cc_start: 0.7745 (tmm) cc_final: 0.7476 (tmm) REVERT: A 324 SER cc_start: 0.9097 (m) cc_final: 0.8780 (p) REVERT: A 392 GLU cc_start: 0.8971 (tp30) cc_final: 0.8398 (tm-30) REVERT: A 604 ASN cc_start: 0.8162 (t0) cc_final: 0.7549 (t0) REVERT: A 642 THR cc_start: 0.9051 (m) cc_final: 0.8688 (t) REVERT: A 696 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8062 (ttm-80) REVERT: A 953 ASN cc_start: 0.8659 (t0) cc_final: 0.8283 (t0) REVERT: A 1087 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7818 (pp) REVERT: A 1120 PHE cc_start: 0.7502 (m-80) cc_final: 0.7011 (m-80) REVERT: A 1122 LYS cc_start: 0.9321 (tppt) cc_final: 0.9072 (tppt) REVERT: A 1135 ILE cc_start: 0.9550 (mt) cc_final: 0.9121 (tp) REVERT: A 1335 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8283 (tm-30) REVERT: A 1373 LEU cc_start: 0.9214 (tp) cc_final: 0.8986 (tp) REVERT: A 1491 GLU cc_start: 0.8509 (pm20) cc_final: 0.8178 (pm20) REVERT: A 1671 ASP cc_start: 0.8665 (m-30) cc_final: 0.8340 (t0) REVERT: A 1729 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8901 (ttm-80) REVERT: A 1918 PHE cc_start: 0.8797 (t80) cc_final: 0.8562 (m-80) REVERT: A 2012 PHE cc_start: 0.7164 (t80) cc_final: 0.6120 (t80) REVERT: A 2070 LEU cc_start: 0.8985 (pp) cc_final: 0.8567 (mm) REVERT: A 2084 ASP cc_start: 0.7313 (t0) cc_final: 0.6532 (p0) REVERT: A 2133 HIS cc_start: 0.8419 (m170) cc_final: 0.8201 (m-70) REVERT: A 2179 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7291 (tpp80) REVERT: A 2240 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7759 (mtp85) REVERT: A 2292 MET cc_start: 0.8246 (mmm) cc_final: 0.7980 (tpp) REVERT: A 2303 MET cc_start: 0.7775 (mmt) cc_final: 0.7401 (mmt) REVERT: A 2348 ASN cc_start: 0.8219 (m-40) cc_final: 0.7899 (m-40) REVERT: A 2382 GLU cc_start: 0.8908 (mp0) cc_final: 0.8663 (mp0) REVERT: A 2412 HIS cc_start: 0.7920 (m170) cc_final: 0.7694 (m170) REVERT: A 2448 TRP cc_start: 0.9125 (t-100) cc_final: 0.8652 (t60) REVERT: A 2449 GLN cc_start: 0.8564 (tp40) cc_final: 0.7966 (mm110) REVERT: A 2480 GLN cc_start: 0.8745 (tp40) cc_final: 0.8351 (tt0) REVERT: A 2498 GLN cc_start: 0.8362 (tp40) cc_final: 0.8145 (tp40) REVERT: A 2503 TYR cc_start: 0.9242 (m-80) cc_final: 0.8419 (m-80) REVERT: A 2672 LYS cc_start: 0.9016 (mttt) cc_final: 0.8644 (mttt) REVERT: A 2677 GLU cc_start: 0.7297 (pm20) cc_final: 0.6844 (pm20) REVERT: A 2702 LEU cc_start: 0.9122 (mp) cc_final: 0.8820 (mp) REVERT: A 2709 ARG cc_start: 0.8686 (mtp180) cc_final: 0.8405 (mtp180) REVERT: A 2750 GLU cc_start: 0.8474 (pp20) cc_final: 0.7788 (pp20) REVERT: A 2777 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7549 (mmmt) REVERT: A 2800 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8031 (ttm-80) REVERT: A 2807 GLN cc_start: 0.7039 (pp30) cc_final: 0.6663 (pp30) REVERT: A 2818 ARG cc_start: 0.7859 (mmt-90) cc_final: 0.7457 (tpp80) REVERT: A 2825 MET cc_start: 0.7905 (mmm) cc_final: 0.7537 (ttt) REVERT: A 2854 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8523 (mmtt) REVERT: A 2860 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 2941 MET cc_start: 0.8517 (mpp) cc_final: 0.8047 (mpp) REVERT: A 2944 LYS cc_start: 0.8741 (mttp) cc_final: 0.8192 (mppt) REVERT: A 2956 ASP cc_start: 0.8326 (m-30) cc_final: 0.8123 (m-30) REVERT: A 2993 GLU cc_start: 0.8001 (tt0) cc_final: 0.7434 (tp30) REVERT: A 3013 MET cc_start: 0.8183 (mmp) cc_final: 0.7968 (mmp) REVERT: A 3014 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7954 (mm110) REVERT: A 3062 MET cc_start: 0.8975 (mmm) cc_final: 0.8346 (mmm) REVERT: A 3074 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 3084 ASP cc_start: 0.8941 (t0) cc_final: 0.8637 (t0) REVERT: A 3122 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7820 (p) REVERT: A 3151 TYR cc_start: 0.8412 (m-80) cc_final: 0.7766 (m-80) REVERT: A 3189 ASP cc_start: 0.8686 (t0) cc_final: 0.8261 (t0) REVERT: A 3193 TYR cc_start: 0.8773 (t80) cc_final: 0.7401 (t80) outliers start: 61 outliers final: 50 residues processed: 535 average time/residue: 0.1824 time to fit residues: 150.3865 Evaluate side-chains 546 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 493 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2091 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2269 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2561 VAL Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2812 SER Chi-restraints excluded: chain A residue 2863 ASP Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3079 ASP Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3145 SER Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 98 optimal weight: 0.0070 chunk 289 optimal weight: 0.0020 chunk 229 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 81 optimal weight: 0.0070 chunk 164 optimal weight: 5.9990 chunk 172 optimal weight: 0.0980 chunk 105 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 ASN A2330 ASN A2348 ASN ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS A2807 GLN ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110399 restraints weight = 36400.508| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.53 r_work: 0.3179 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23719 Z= 0.112 Angle : 0.628 13.500 32138 Z= 0.308 Chirality : 0.043 0.297 3628 Planarity : 0.004 0.045 4151 Dihedral : 3.940 27.624 3171 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.97 % Allowed : 18.77 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2903 helix: 1.70 (0.16), residues: 1130 sheet: -0.23 (0.23), residues: 531 loop : -1.53 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2216 TYR 0.014 0.001 TYR A1592 PHE 0.022 0.001 PHE A1918 TRP 0.021 0.001 TRP A3063 HIS 0.006 0.001 HIS A2727 Details of bonding type rmsd covalent geometry : bond 0.00246 (23718) covalent geometry : angle 0.62845 (32136) SS BOND : bond 0.00161 ( 1) SS BOND : angle 1.17455 ( 2) hydrogen bonds : bond 0.03329 ( 1049) hydrogen bonds : angle 4.26920 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 522 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8558 (tp30) cc_final: 0.8174 (tp30) REVERT: A 250 ARG cc_start: 0.8988 (ptm-80) cc_final: 0.8787 (tmm-80) REVERT: A 252 MET cc_start: 0.8978 (mtt) cc_final: 0.8736 (mtt) REVERT: A 281 MET cc_start: 0.7782 (tmm) cc_final: 0.7563 (tmm) REVERT: A 324 SER cc_start: 0.9116 (m) cc_final: 0.8785 (p) REVERT: A 604 ASN cc_start: 0.8042 (t0) cc_final: 0.7442 (t0) REVERT: A 642 THR cc_start: 0.9036 (m) cc_final: 0.8703 (t) REVERT: A 696 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7944 (ttm-80) REVERT: A 951 ASN cc_start: 0.8030 (t0) cc_final: 0.7381 (p0) REVERT: A 953 ASN cc_start: 0.8617 (t0) cc_final: 0.7898 (t0) REVERT: A 1087 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.7785 (pp) REVERT: A 1120 PHE cc_start: 0.7390 (m-80) cc_final: 0.6939 (m-80) REVERT: A 1122 LYS cc_start: 0.9315 (tppt) cc_final: 0.9069 (tppt) REVERT: A 1335 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 1491 GLU cc_start: 0.8557 (pm20) cc_final: 0.8249 (pm20) REVERT: A 1671 ASP cc_start: 0.8642 (m-30) cc_final: 0.8341 (t0) REVERT: A 1918 PHE cc_start: 0.8925 (t80) cc_final: 0.8627 (m-80) REVERT: A 2012 PHE cc_start: 0.7042 (t80) cc_final: 0.6018 (t80) REVERT: A 2070 LEU cc_start: 0.8965 (pp) cc_final: 0.8565 (mm) REVERT: A 2084 ASP cc_start: 0.7314 (t0) cc_final: 0.6469 (p0) REVERT: A 2133 HIS cc_start: 0.8357 (m170) cc_final: 0.8141 (m-70) REVERT: A 2144 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7760 (mp) REVERT: A 2179 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7270 (tpp80) REVERT: A 2240 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7612 (mtp85) REVERT: A 2292 MET cc_start: 0.8198 (mmm) cc_final: 0.7922 (tpp) REVERT: A 2303 MET cc_start: 0.7642 (mmt) cc_final: 0.7416 (mmt) REVERT: A 2412 HIS cc_start: 0.7775 (m170) cc_final: 0.7545 (m170) REVERT: A 2448 TRP cc_start: 0.9103 (t-100) cc_final: 0.8597 (t60) REVERT: A 2449 GLN cc_start: 0.8530 (tp40) cc_final: 0.7920 (mm110) REVERT: A 2480 GLN cc_start: 0.8751 (tp40) cc_final: 0.8418 (tt0) REVERT: A 2498 GLN cc_start: 0.8327 (tp40) cc_final: 0.8072 (tp40) REVERT: A 2503 TYR cc_start: 0.9231 (m-80) cc_final: 0.8440 (m-80) REVERT: A 2525 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8252 (ttt-90) REVERT: A 2535 GLN cc_start: 0.8752 (pm20) cc_final: 0.8318 (pm20) REVERT: A 2646 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8295 (pt0) REVERT: A 2702 LEU cc_start: 0.9138 (mp) cc_final: 0.8865 (mp) REVERT: A 2709 ARG cc_start: 0.8716 (mtp180) cc_final: 0.8451 (mtp180) REVERT: A 2731 LEU cc_start: 0.7674 (tp) cc_final: 0.7447 (tt) REVERT: A 2750 GLU cc_start: 0.8456 (pp20) cc_final: 0.7760 (pp20) REVERT: A 2777 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7475 (mmmt) REVERT: A 2789 MET cc_start: 0.8030 (mmm) cc_final: 0.7822 (mmt) REVERT: A 2800 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8019 (ttm-80) REVERT: A 2818 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7062 (tpp80) REVERT: A 2825 MET cc_start: 0.7904 (mmm) cc_final: 0.7556 (ttt) REVERT: A 2860 GLN cc_start: 0.7307 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 2941 MET cc_start: 0.8519 (mpp) cc_final: 0.8030 (mpp) REVERT: A 2944 LYS cc_start: 0.8748 (mttp) cc_final: 0.8298 (mttp) REVERT: A 2993 GLU cc_start: 0.7982 (tt0) cc_final: 0.7399 (tp30) REVERT: A 3013 MET cc_start: 0.8249 (mmp) cc_final: 0.7849 (mmm) REVERT: A 3014 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7871 (mm110) REVERT: A 3062 MET cc_start: 0.8967 (mmm) cc_final: 0.8321 (mmm) REVERT: A 3074 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 3084 ASP cc_start: 0.8953 (t0) cc_final: 0.8614 (t0) REVERT: A 3122 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 3151 TYR cc_start: 0.8377 (m-80) cc_final: 0.7626 (m-80) REVERT: A 3189 ASP cc_start: 0.8689 (t0) cc_final: 0.8165 (t0) REVERT: A 3193 TYR cc_start: 0.8697 (t80) cc_final: 0.7189 (t80) outliers start: 51 outliers final: 39 residues processed: 544 average time/residue: 0.1763 time to fit residues: 148.3027 Evaluate side-chains 540 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 497 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1192 GLU Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2091 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2863 ASP Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3079 ASP Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 2 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 169 optimal weight: 40.0000 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106684 restraints weight = 36692.984| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.52 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23719 Z= 0.153 Angle : 0.632 12.290 32138 Z= 0.314 Chirality : 0.044 0.288 3628 Planarity : 0.004 0.044 4151 Dihedral : 3.995 24.905 3171 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.81 % Allowed : 19.04 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 2903 helix: 1.65 (0.16), residues: 1138 sheet: -0.24 (0.23), residues: 539 loop : -1.53 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3007 TYR 0.015 0.001 TYR A1592 PHE 0.035 0.001 PHE A2278 TRP 0.013 0.001 TRP A3063 HIS 0.007 0.001 HIS A2950 Details of bonding type rmsd covalent geometry : bond 0.00360 (23718) covalent geometry : angle 0.63237 (32136) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.03723 ( 2) hydrogen bonds : bond 0.03620 ( 1049) hydrogen bonds : angle 4.33316 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5806 Ramachandran restraints generated. 2903 Oldfield, 0 Emsley, 2903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 504 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8544 (tp30) cc_final: 0.8165 (tp30) REVERT: A 252 MET cc_start: 0.8981 (mtt) cc_final: 0.8740 (mtt) REVERT: A 305 TYR cc_start: 0.3720 (t80) cc_final: 0.3366 (t80) REVERT: A 324 SER cc_start: 0.9126 (m) cc_final: 0.8797 (p) REVERT: A 441 GLN cc_start: 0.9291 (tp40) cc_final: 0.9077 (tp-100) REVERT: A 604 ASN cc_start: 0.8113 (t0) cc_final: 0.7496 (t0) REVERT: A 642 THR cc_start: 0.9027 (m) cc_final: 0.8654 (t) REVERT: A 696 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8072 (ttm-80) REVERT: A 951 ASN cc_start: 0.8199 (t0) cc_final: 0.7818 (p0) REVERT: A 953 ASN cc_start: 0.8683 (t0) cc_final: 0.7998 (t0) REVERT: A 1087 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7720 (pp) REVERT: A 1120 PHE cc_start: 0.7426 (m-80) cc_final: 0.6979 (m-80) REVERT: A 1122 LYS cc_start: 0.9327 (tppt) cc_final: 0.9081 (tppt) REVERT: A 1335 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 1373 LEU cc_start: 0.9281 (tp) cc_final: 0.9072 (tp) REVERT: A 1491 GLU cc_start: 0.8548 (pm20) cc_final: 0.8228 (pm20) REVERT: A 1671 ASP cc_start: 0.8667 (m-30) cc_final: 0.8356 (t0) REVERT: A 1863 MET cc_start: 0.5136 (tpt) cc_final: 0.4917 (tpp) REVERT: A 1918 PHE cc_start: 0.8881 (t80) cc_final: 0.8513 (m-80) REVERT: A 2070 LEU cc_start: 0.8984 (pp) cc_final: 0.8559 (mm) REVERT: A 2084 ASP cc_start: 0.7376 (t0) cc_final: 0.6530 (p0) REVERT: A 2144 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7839 (mp) REVERT: A 2179 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7372 (tpp80) REVERT: A 2292 MET cc_start: 0.8183 (mmm) cc_final: 0.7957 (tpp) REVERT: A 2303 MET cc_start: 0.7787 (mmt) cc_final: 0.7504 (mmt) REVERT: A 2412 HIS cc_start: 0.7864 (m170) cc_final: 0.7659 (m170) REVERT: A 2449 GLN cc_start: 0.8525 (tp40) cc_final: 0.7973 (mm110) REVERT: A 2471 TRP cc_start: 0.8683 (m100) cc_final: 0.8007 (m100) REVERT: A 2480 GLN cc_start: 0.8753 (tp40) cc_final: 0.8435 (tt0) REVERT: A 2498 GLN cc_start: 0.8356 (tp40) cc_final: 0.8141 (tp40) REVERT: A 2503 TYR cc_start: 0.9250 (m-80) cc_final: 0.8437 (m-80) REVERT: A 2525 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8306 (ttt-90) REVERT: A 2535 GLN cc_start: 0.8818 (pm20) cc_final: 0.8420 (pm20) REVERT: A 2646 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8277 (pt0) REVERT: A 2702 LEU cc_start: 0.9104 (mp) cc_final: 0.8779 (mp) REVERT: A 2709 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8379 (mtp180) REVERT: A 2715 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8277 (mt-10) REVERT: A 2744 ARG cc_start: 0.7962 (ptt90) cc_final: 0.7665 (ptt180) REVERT: A 2750 GLU cc_start: 0.8520 (pp20) cc_final: 0.7889 (pp20) REVERT: A 2777 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7560 (mmmt) REVERT: A 2800 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8166 (ttm-80) REVERT: A 2807 GLN cc_start: 0.7224 (pp30) cc_final: 0.6910 (pp30) REVERT: A 2818 ARG cc_start: 0.7852 (mmt-90) cc_final: 0.7116 (tpp80) REVERT: A 2825 MET cc_start: 0.7944 (mmm) cc_final: 0.7546 (ttt) REVERT: A 2860 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 2941 MET cc_start: 0.8604 (mpp) cc_final: 0.8090 (mpp) REVERT: A 2944 LYS cc_start: 0.8707 (mttp) cc_final: 0.8227 (mttp) REVERT: A 2993 GLU cc_start: 0.7978 (tt0) cc_final: 0.7467 (tp30) REVERT: A 3014 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7898 (mm110) REVERT: A 3062 MET cc_start: 0.8995 (mmm) cc_final: 0.8350 (mmm) REVERT: A 3074 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.7918 (t) REVERT: A 3084 ASP cc_start: 0.8910 (t0) cc_final: 0.8628 (t0) REVERT: A 3122 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7822 (p) REVERT: A 3151 TYR cc_start: 0.8428 (m-80) cc_final: 0.7788 (m-80) REVERT: A 3189 ASP cc_start: 0.8706 (t0) cc_final: 0.8232 (t0) REVERT: A 3193 TYR cc_start: 0.8762 (t80) cc_final: 0.7306 (t80) outliers start: 47 outliers final: 41 residues processed: 525 average time/residue: 0.1769 time to fit residues: 143.8689 Evaluate side-chains 539 residues out of total 2594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 494 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1420 SER Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1621 THR Chi-restraints excluded: chain A residue 1668 THR Chi-restraints excluded: chain A residue 1700 ASP Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1780 THR Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2091 LEU Chi-restraints excluded: chain A residue 2144 ILE Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2425 MET Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2536 ILE Chi-restraints excluded: chain A residue 2607 THR Chi-restraints excluded: chain A residue 2670 VAL Chi-restraints excluded: chain A residue 2674 VAL Chi-restraints excluded: chain A residue 2753 ILE Chi-restraints excluded: chain A residue 2763 LEU Chi-restraints excluded: chain A residue 2797 LEU Chi-restraints excluded: chain A residue 2812 SER Chi-restraints excluded: chain A residue 2863 ASP Chi-restraints excluded: chain A residue 2959 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3074 SER Chi-restraints excluded: chain A residue 3079 ASP Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3122 THR Chi-restraints excluded: chain A residue 3138 THR Chi-restraints excluded: chain A residue 3141 ASN Chi-restraints excluded: chain A residue 3176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 287 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 HIS A1514 ASN ** A1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2133 HIS ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106442 restraints weight = 36284.489| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.49 r_work: 0.3122 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23719 Z= 0.153 Angle : 0.648 13.640 32138 Z= 0.320 Chirality : 0.044 0.293 3628 Planarity : 0.004 0.044 4151 Dihedral : 4.070 25.699 3171 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.85 % Allowed : 19.16 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2903 helix: 1.60 (0.15), residues: 1141 sheet: -0.24 (0.23), residues: 538 loop : -1.58 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1729 TYR 0.024 0.001 TYR A1073 PHE 0.031 0.001 PHE A2278 TRP 0.014 0.001 TRP A3063 HIS 0.009 0.001 HIS A2950 Details of bonding type rmsd covalent geometry : bond 0.00359 (23718) covalent geometry : angle 0.64842 (32136) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.94424 ( 2) hydrogen bonds : bond 0.03679 ( 1049) hydrogen bonds : angle 4.35422 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7657.55 seconds wall clock time: 131 minutes 44.15 seconds (7904.15 seconds total)