Starting phenix.real_space_refine on Fri Sep 27 08:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jxc_9893/09_2024/6jxc_9893.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 41 5.16 5 C 9560 2.51 5 N 2758 2.21 5 O 2911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15270 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 15270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2345, 15270 Classifications: {'peptide': 2345} Incomplete info: {'truncation_to_alanine': 1110} Link IDs: {'PTRANS': 64, 'TRANS': 2280} Chain breaks: 28 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 4011 Unresolved non-hydrogen angles: 5149 Unresolved non-hydrogen dihedrals: 3355 Unresolved non-hydrogen chiralities: 389 Planarities with less than four sites: {'GLN:plan1': 42, 'ARG:plan': 45, 'TYR:plan': 57, 'ASN:plan1': 78, 'TRP:plan': 15, 'HIS:plan': 21, 'PHE:plan': 69, 'GLU:plan': 76, 'ASP:plan': 56} Unresolved non-hydrogen planarities: 2152 Time building chain proxies: 9.71, per 1000 atoms: 0.64 Number of scatterers: 15270 At special positions: 0 Unit cell: (152.55, 98.55, 199.8, 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 41 16.00 O 2911 8.00 N 2758 7.00 C 9560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 3.8 seconds 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 1 sheets defined 69.5% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 53 through 67 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 110 through 124 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.885A pdb=" N THR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.614A pdb=" N ASN A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.649A pdb=" N PHE A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.523A pdb=" N LYS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 521 through 534 Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 597 through 603 removed outlier: 3.625A pdb=" N LEU A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 641 Processing helix chain 'A' and resid 668 through 682 Processing helix chain 'A' and resid 708 through 721 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.865A pdb=" N ASN A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 865 through 884 Processing helix chain 'A' and resid 895 through 910 Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 945 through 963 Processing helix chain 'A' and resid 967 through 979 removed outlier: 3.903A pdb=" N ARG A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 995 Processing helix chain 'A' and resid 1003 through 1014 Processing helix chain 'A' and resid 1023 through 1034 Processing helix chain 'A' and resid 1041 through 1052 Proline residue: A1049 - end of helix Processing helix chain 'A' and resid 1056 through 1069 Processing helix chain 'A' and resid 1072 through 1076 Processing helix chain 'A' and resid 1079 through 1089 removed outlier: 4.349A pdb=" N GLN A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1096 Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1135 through 1147 Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1151 through 1161 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1172 through 1181 Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1183 through 1193 Processing helix chain 'A' and resid 1199 through 1207 removed outlier: 5.926A pdb=" N TYR A1204 " --> pdb=" O THR A1201 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS A1205 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A1207 " --> pdb=" O TYR A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1217 removed outlier: 3.570A pdb=" N MET A1212 " --> pdb=" O TYR A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1234 removed outlier: 3.843A pdb=" N LEU A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1250 Processing helix chain 'A' and resid 1256 through 1261 Processing helix chain 'A' and resid 1263 through 1269 Processing helix chain 'A' and resid 1271 through 1277 removed outlier: 3.516A pdb=" N ALA A1275 " --> pdb=" O GLN A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1298 Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1305 through 1319 removed outlier: 3.830A pdb=" N ARG A1309 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1327 Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.507A pdb=" N ILE A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1361 Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 4.423A pdb=" N LYS A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1397 Processing helix chain 'A' and resid 1398 through 1401 Processing helix chain 'A' and resid 1406 through 1418 Processing helix chain 'A' and resid 1441 through 1451 Processing helix chain 'A' and resid 1465 through 1473 Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1493 through 1499 Processing helix chain 'A' and resid 1516 through 1523 Processing helix chain 'A' and resid 1530 through 1542 Processing helix chain 'A' and resid 1549 through 1567 removed outlier: 4.294A pdb=" N PHE A1553 " --> pdb=" O THR A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 Processing helix chain 'A' and resid 1583 through 1589 removed outlier: 3.941A pdb=" N LYS A1587 " --> pdb=" O GLU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1598 through 1606 Processing helix chain 'A' and resid 1610 through 1617 removed outlier: 3.529A pdb=" N ASP A1614 " --> pdb=" O SER A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1639 removed outlier: 4.163A pdb=" N LEU A1634 " --> pdb=" O ALA A1631 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A1636 " --> pdb=" O SER A1633 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN A1637 " --> pdb=" O LEU A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1641 through 1653 Proline residue: A1650 - end of helix Processing helix chain 'A' and resid 1654 through 1656 No H-bonds generated for 'chain 'A' and resid 1654 through 1656' Processing helix chain 'A' and resid 1659 through 1667 Processing helix chain 'A' and resid 1668 through 1670 No H-bonds generated for 'chain 'A' and resid 1668 through 1670' Processing helix chain 'A' and resid 1675 through 1685 removed outlier: 3.603A pdb=" N LEU A1679 " --> pdb=" O PRO A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1698 removed outlier: 4.140A pdb=" N SER A1698 " --> pdb=" O VAL A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1721 Processing helix chain 'A' and resid 1728 through 1733 Processing helix chain 'A' and resid 1739 through 1746 Processing helix chain 'A' and resid 1750 through 1757 Processing helix chain 'A' and resid 1766 through 1774 Processing helix chain 'A' and resid 1780 through 1784 Processing helix chain 'A' and resid 1794 through 1799 Processing helix chain 'A' and resid 1805 through 1819 Processing helix chain 'A' and resid 1827 through 1837 Processing helix chain 'A' and resid 1856 through 1863 Processing helix chain 'A' and resid 1877 through 1887 Processing helix chain 'A' and resid 1894 through 1913 Processing helix chain 'A' and resid 1917 through 1933 removed outlier: 4.341A pdb=" N LYS A1931 " --> pdb=" O ILE A1927 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A1932 " --> pdb=" O GLU A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1957 Processing helix chain 'A' and resid 1965 through 1983 Processing helix chain 'A' and resid 1989 through 2013 removed outlier: 3.544A pdb=" N TYR A1993 " --> pdb=" O LYS A1989 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2028 removed outlier: 5.217A pdb=" N ARG A2020 " --> pdb=" O GLN A2016 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A2026 " --> pdb=" O ALA A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2030 No H-bonds generated for 'chain 'A' and resid 2029 through 2030' Processing helix chain 'A' and resid 2031 through 2035 Processing helix chain 'A' and resid 2038 through 2059 removed outlier: 5.241A pdb=" N GLN A2044 " --> pdb=" O SER A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2063 through 2079 Processing helix chain 'A' and resid 2088 through 2094 Processing helix chain 'A' and resid 2101 through 2113 Processing helix chain 'A' and resid 2123 through 2128 Processing helix chain 'A' and resid 2137 through 2158 Processing helix chain 'A' and resid 2159 through 2164 Processing helix chain 'A' and resid 2164 through 2182 removed outlier: 4.026A pdb=" N LYS A2177 " --> pdb=" O LYS A2173 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A2180 " --> pdb=" O LEU A2176 " (cutoff:3.500A) Processing helix chain 'A' and resid 2197 through 2239 removed outlier: 4.081A pdb=" N ARG A2202 " --> pdb=" O ARG A2198 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A2203 " --> pdb=" O HIS A2199 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A2204 " --> pdb=" O TYR A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2242 through 2257 removed outlier: 4.912A pdb=" N ASP A2248 " --> pdb=" O ASN A2244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A2257 " --> pdb=" O LEU A2253 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2271 removed outlier: 4.868A pdb=" N LEU A2266 " --> pdb=" O LYS A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2274 No H-bonds generated for 'chain 'A' and resid 2272 through 2274' Processing helix chain 'A' and resid 2279 through 2282 Processing helix chain 'A' and resid 2283 through 2288 Processing helix chain 'A' and resid 2297 through 2312 Processing helix chain 'A' and resid 2312 through 2328 removed outlier: 3.688A pdb=" N SER A2316 " --> pdb=" O LEU A2312 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A2318 " --> pdb=" O TYR A2314 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER A2319 " --> pdb=" O ASP A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2355 removed outlier: 3.888A pdb=" N ARG A2355 " --> pdb=" O GLN A2351 " (cutoff:3.500A) Processing helix chain 'A' and resid 2359 through 2379 Proline residue: A2365 - end of helix Processing helix chain 'A' and resid 2397 through 2405 removed outlier: 4.102A pdb=" N LEU A2403 " --> pdb=" O TRP A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2431 Processing helix chain 'A' and resid 2471 through 2486 removed outlier: 4.023A pdb=" N MET A2477 " --> pdb=" O GLN A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2494 through 2498 Processing helix chain 'A' and resid 2524 through 2533 Processing helix chain 'A' and resid 2539 through 2549 removed outlier: 3.601A pdb=" N ALA A2543 " --> pdb=" O THR A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2550 through 2552 No H-bonds generated for 'chain 'A' and resid 2550 through 2552' Processing helix chain 'A' and resid 2556 through 2561 Processing helix chain 'A' and resid 2561 through 2566 Processing helix chain 'A' and resid 2573 through 2579 removed outlier: 4.051A pdb=" N PHE A2577 " --> pdb=" O LEU A2573 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2609 removed outlier: 3.580A pdb=" N SER A2601 " --> pdb=" O GLY A2597 " (cutoff:3.500A) Processing helix chain 'A' and resid 2655 through 2660 Processing helix chain 'A' and resid 2667 through 2684 Processing helix chain 'A' and resid 2684 through 2695 Processing helix chain 'A' and resid 2708 through 2713 Processing helix chain 'A' and resid 2737 through 2752 removed outlier: 3.908A pdb=" N VAL A2748 " --> pdb=" O ALA A2744 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A2749 " --> pdb=" O LEU A2745 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A2750 " --> pdb=" O LYS A2746 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2772 Processing helix chain 'A' and resid 2772 through 2777 Processing sheet with id=AA1, first strand: chain 'A' and resid 2618 through 2620 1010 hydrogen bonds defined for protein. 2913 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: 7.50 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2741 1.30 - 1.43: 3724 1.43 - 1.56: 8853 1.56 - 1.70: 53 1.70 - 1.83: 66 Bond restraints: 15437 Sorted by residual: bond pdb=" CA LYS A2278 " pdb=" C LYS A2278 " ideal model delta sigma weight residual 1.533 1.487 0.046 5.60e-03 3.19e+04 6.82e+01 bond pdb=" CB HIS A1530 " pdb=" CG HIS A1530 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB HIS A1973 " pdb=" CG HIS A1973 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.44e+01 bond pdb=" CB HIS A1965 " pdb=" CG HIS A1965 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.44e+01 bond pdb=" CB HIS A2629 " pdb=" CG HIS A2629 " ideal model delta sigma weight residual 1.497 1.417 0.080 1.40e-02 5.10e+03 3.23e+01 ... (remaining 15432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 18635 2.51 - 5.02: 2075 5.02 - 7.54: 310 7.54 - 10.05: 51 10.05 - 12.56: 8 Bond angle restraints: 21079 Sorted by residual: angle pdb=" N SER A1369 " pdb=" CA SER A1369 " pdb=" C SER A1369 " ideal model delta sigma weight residual 114.62 102.90 11.72 1.14e+00 7.69e-01 1.06e+02 angle pdb=" N GLU A1986 " pdb=" CA GLU A1986 " pdb=" C GLU A1986 " ideal model delta sigma weight residual 111.36 101.85 9.51 1.09e+00 8.42e-01 7.62e+01 angle pdb=" N LEU A1724 " pdb=" CA LEU A1724 " pdb=" C LEU A1724 " ideal model delta sigma weight residual 113.88 103.29 10.59 1.23e+00 6.61e-01 7.41e+01 angle pdb=" C ILE A2644 " pdb=" N PRO A2645 " pdb=" CA PRO A2645 " ideal model delta sigma weight residual 120.03 127.83 -7.80 9.90e-01 1.02e+00 6.21e+01 angle pdb=" N PRO A 287 " pdb=" CA PRO A 287 " pdb=" CB PRO A 287 " ideal model delta sigma weight residual 103.33 111.87 -8.54 1.10e+00 8.26e-01 6.03e+01 ... (remaining 21074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9091 18.00 - 36.00: 135 36.00 - 54.00: 33 54.00 - 72.00: 16 72.00 - 90.00: 5 Dihedral angle restraints: 9280 sinusoidal: 2391 harmonic: 6889 Sorted by residual: dihedral pdb=" C SER A1369 " pdb=" N SER A1369 " pdb=" CA SER A1369 " pdb=" CB SER A1369 " ideal model delta harmonic sigma weight residual -122.60 -111.91 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" N PHE A1747 " pdb=" C PHE A1747 " pdb=" CA PHE A1747 " pdb=" CB PHE A1747 " ideal model delta harmonic sigma weight residual 122.80 133.01 -10.21 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" C ASN A2468 " pdb=" N ASN A2468 " pdb=" CA ASN A2468 " pdb=" CB ASN A2468 " ideal model delta harmonic sigma weight residual -122.60 -132.10 9.50 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 9277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2098 0.101 - 0.202: 415 0.202 - 0.303: 82 0.303 - 0.404: 8 0.404 - 0.505: 3 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CA PHE A1747 " pdb=" N PHE A1747 " pdb=" C PHE A1747 " pdb=" CB PHE A1747 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CA MET A1757 " pdb=" N MET A1757 " pdb=" C MET A1757 " pdb=" CB MET A1757 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA ASN A2264 " pdb=" N ASN A2264 " pdb=" C ASN A2264 " pdb=" CB ASN A2264 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 2603 not shown) Planarity restraints: 2786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2226 " -0.061 2.00e-02 2.50e+03 2.98e-02 2.23e+01 pdb=" CG TRP A2226 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A2226 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A2226 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP A2226 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A2226 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A2226 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2226 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2226 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A2226 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2248 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ASP A2248 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP A2248 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A2249 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2312 " -0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A2313 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A2313 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A2313 " -0.048 5.00e-02 4.00e+02 ... (remaining 2783 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3627 2.76 - 3.29: 17332 3.29 - 3.83: 23858 3.83 - 4.36: 29123 4.36 - 4.90: 43045 Nonbonded interactions: 116985 Sorted by model distance: nonbonded pdb=" CB LYS A2505 " pdb=" OE2 GLU A2517 " model vdw 2.221 3.440 nonbonded pdb=" OH TYR A2504 " pdb=" CA ILE A2630 " model vdw 2.258 3.470 nonbonded pdb=" OE2 GLU A2740 " pdb=" NH2 ARG A2743 " model vdw 2.304 3.120 nonbonded pdb=" OD2 ASP A2243 " pdb=" NZ LYS A2278 " model vdw 2.309 3.120 nonbonded pdb=" OG SER A1465 " pdb=" OE1 GLN A1500 " model vdw 2.319 3.040 ... (remaining 116980 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.180 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 45.330 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 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 : 0.018 0.127 15437 Z= 1.189 Angle : 1.707 12.559 21079 Z= 1.181 Chirality : 0.086 0.505 2606 Planarity : 0.010 0.095 2786 Dihedral : 8.992 89.996 4752 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 3.02 % Allowed : 9.27 % Favored : 87.71 % Rotamer: Outliers : 0.38 % Allowed : 0.57 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2287 helix: -0.04 (0.12), residues: 1476 sheet: -1.40 (1.28), residues: 12 loop : -2.33 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.007 TRP A2226 HIS 0.012 0.003 HIS A1973 PHE 0.044 0.004 PHE A2481 TYR 0.047 0.006 TYR A2063 ARG 0.012 0.001 ARG A1453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 429 time to evaluate : 1.765 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: A 1685 ILE cc_start: 0.7818 (pt) cc_final: 0.7118 (tp) REVERT: A 1811 ASN cc_start: 0.8493 (m-40) cc_final: 0.8278 (m-40) REVERT: A 1836 ASP cc_start: 0.8709 (m-30) cc_final: 0.8407 (t0) REVERT: A 1888 LEU cc_start: 0.8066 (tp) cc_final: 0.7831 (tt) REVERT: A 2010 ILE cc_start: 0.9496 (pt) cc_final: 0.8343 (pt) REVERT: A 2320 VAL cc_start: 0.7850 (t) cc_final: 0.7619 (t) REVERT: A 2539 THR cc_start: 0.7336 (p) cc_final: 0.6799 (p) REVERT: A 2586 ASP cc_start: 0.7495 (m-30) cc_final: 0.7180 (m-30) REVERT: A 2672 SER cc_start: 0.9400 (m) cc_final: 0.8937 (t) REVERT: A 2689 CYS cc_start: 0.6196 (t) cc_final: 0.5350 (t) outliers start: 4 outliers final: 2 residues processed: 432 average time/residue: 0.2906 time to fit residues: 179.4158 Evaluate side-chains 254 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 252 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1384 ASN ** A1476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1733 GLN A1737 GLN A1887 ASN ** A1973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN A2521 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15437 Z= 0.237 Angle : 0.782 9.746 21079 Z= 0.429 Chirality : 0.042 0.228 2606 Planarity : 0.005 0.056 2786 Dihedral : 5.696 38.708 2408 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 1.79 % Allowed : 10.14 % Favored : 88.06 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2287 helix: 1.04 (0.13), residues: 1474 sheet: -1.66 (1.21), residues: 12 loop : -3.05 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2226 HIS 0.006 0.001 HIS A1525 PHE 0.037 0.002 PHE A1929 TYR 0.024 0.002 TYR A1411 ARG 0.007 0.001 ARG A2071 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 ILE cc_start: 0.7526 (pt) cc_final: 0.6866 (tp) REVERT: A 1774 CYS cc_start: 0.6370 (m) cc_final: 0.6041 (m) REVERT: A 1827 LYS cc_start: 0.6873 (mptt) cc_final: 0.6540 (mttp) REVERT: A 2019 LEU cc_start: 0.9007 (mt) cc_final: 0.8721 (pp) REVERT: A 2478 GLU cc_start: 0.8375 (tp30) cc_final: 0.8097 (tm-30) REVERT: A 2540 PHE cc_start: 0.5940 (p90) cc_final: 0.5707 (p90) REVERT: A 2583 ASP cc_start: 0.6503 (p0) cc_final: 0.5966 (p0) REVERT: A 2586 ASP cc_start: 0.7088 (m-30) cc_final: 0.6848 (m-30) REVERT: A 2672 SER cc_start: 0.9074 (m) cc_final: 0.8501 (t) REVERT: A 2774 SER cc_start: 0.8687 (t) cc_final: 0.8426 (t) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.2799 time to fit residues: 136.0880 Evaluate side-chains 233 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 176 optimal weight: 50.0000 chunk 144 optimal weight: 6.9990 chunk 58 optimal weight: 50.0000 chunk 212 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1384 ASN A1788 HIS A1973 HIS A2012 ASN A2135 HIS A2154 GLN A2244 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15437 Z= 0.343 Angle : 0.803 7.581 21079 Z= 0.443 Chirality : 0.044 0.209 2606 Planarity : 0.005 0.052 2786 Dihedral : 5.702 37.621 2408 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 1.71 % Allowed : 12.16 % Favored : 86.14 % Rotamer: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2287 helix: 1.16 (0.13), residues: 1471 sheet: -1.88 (1.28), residues: 12 loop : -3.42 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A2277 HIS 0.012 0.002 HIS A1912 PHE 0.027 0.002 PHE A1808 TYR 0.017 0.002 TYR A2606 ARG 0.008 0.001 ARG A1684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1381 LEU cc_start: 0.8158 (mt) cc_final: 0.7956 (mt) REVERT: A 1950 MET cc_start: 0.8257 (mtm) cc_final: 0.8050 (mtm) REVERT: A 2113 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7265 (mtp85) REVERT: A 2156 LEU cc_start: 0.7160 (mp) cc_final: 0.6885 (mt) REVERT: A 2478 GLU cc_start: 0.8556 (tp30) cc_final: 0.8333 (tm-30) REVERT: A 2502 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7199 (mmp-170) REVERT: A 2540 PHE cc_start: 0.7116 (p90) cc_final: 0.5906 (p90) REVERT: A 2583 ASP cc_start: 0.6768 (p0) cc_final: 0.6355 (p0) REVERT: A 2586 ASP cc_start: 0.7152 (m-30) cc_final: 0.6908 (m-30) REVERT: A 2672 SER cc_start: 0.9158 (m) cc_final: 0.8600 (t) outliers start: 1 outliers final: 1 residues processed: 278 average time/residue: 0.2573 time to fit residues: 108.1170 Evaluate side-chains 205 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1759 ASN A1912 HIS A1973 HIS A2244 ASN A2397 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15437 Z= 0.192 Angle : 0.679 9.670 21079 Z= 0.368 Chirality : 0.041 0.244 2606 Planarity : 0.004 0.055 2786 Dihedral : 5.351 35.648 2408 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 1.75 % Allowed : 10.76 % Favored : 87.49 % Rotamer: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 2287 helix: 1.51 (0.14), residues: 1471 sheet: -1.59 (1.30), residues: 12 loop : -3.39 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2108 HIS 0.007 0.001 HIS A1912 PHE 0.017 0.001 PHE A1894 TYR 0.018 0.001 TYR A1533 ARG 0.013 0.001 ARG A2544 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1774 CYS cc_start: 0.6718 (m) cc_final: 0.5975 (m) REVERT: A 1798 ASN cc_start: 0.8377 (m110) cc_final: 0.8045 (m-40) REVERT: A 2156 LEU cc_start: 0.6837 (mp) cc_final: 0.6583 (mp) REVERT: A 2482 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 2502 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7064 (mmp-170) REVERT: A 2540 PHE cc_start: 0.6396 (p90) cc_final: 0.5827 (p90) REVERT: A 2583 ASP cc_start: 0.6550 (p0) cc_final: 0.6125 (p0) REVERT: A 2586 ASP cc_start: 0.7118 (m-30) cc_final: 0.6666 (m-30) REVERT: A 2672 SER cc_start: 0.9101 (m) cc_final: 0.8603 (t) REVERT: A 2749 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.2589 time to fit residues: 107.4963 Evaluate side-chains 209 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1392 GLN A1759 ASN A1912 HIS A2135 HIS A2244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15437 Z= 0.305 Angle : 0.739 12.305 21079 Z= 0.400 Chirality : 0.043 0.310 2606 Planarity : 0.004 0.060 2786 Dihedral : 5.504 35.883 2408 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 1.71 % Allowed : 12.59 % Favored : 85.70 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2287 helix: 1.27 (0.14), residues: 1497 sheet: -1.54 (1.53), residues: 12 loop : -3.75 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A2399 HIS 0.007 0.002 HIS A2227 PHE 0.031 0.002 PHE A1808 TYR 0.015 0.002 TYR A2594 ARG 0.012 0.001 ARG A2544 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1774 CYS cc_start: 0.6693 (m) cc_final: 0.6099 (m) REVERT: A 2113 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7311 (mtp85) REVERT: A 2156 LEU cc_start: 0.7145 (mp) cc_final: 0.6784 (mp) REVERT: A 2482 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8176 (tm-30) REVERT: A 2502 ARG cc_start: 0.7718 (mmp80) cc_final: 0.7098 (mmp-170) REVERT: A 2672 SER cc_start: 0.9172 (m) cc_final: 0.8612 (t) REVERT: A 2688 MET cc_start: 0.7641 (mmt) cc_final: 0.7205 (mmm) REVERT: A 2749 GLU cc_start: 0.7262 (tm-30) cc_final: 0.7036 (tm-30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2481 time to fit residues: 100.1689 Evaluate side-chains 206 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 50.0000 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 132 optimal weight: 0.0010 chunk 55 optimal weight: 30.0000 chunk 226 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 18 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1372 ASN A1392 GLN A2055 ASN A2135 HIS A2244 ASN ** A2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 15437 Z= 0.485 Angle : 0.911 10.852 21079 Z= 0.494 Chirality : 0.048 0.242 2606 Planarity : 0.005 0.064 2786 Dihedral : 6.451 37.540 2408 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 1.88 % Allowed : 13.60 % Favored : 84.52 % Rotamer: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2287 helix: 0.53 (0.13), residues: 1465 sheet: -1.51 (1.64), residues: 12 loop : -4.07 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A2399 HIS 0.011 0.003 HIS A2629 PHE 0.057 0.003 PHE A1808 TYR 0.034 0.002 TYR A2242 ARG 0.007 0.001 ARG A2544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1414 ASP cc_start: 0.8169 (p0) cc_final: 0.7583 (p0) REVERT: A 1484 LYS cc_start: 0.8110 (tppt) cc_final: 0.7387 (ptpp) REVERT: A 1685 ILE cc_start: 0.8019 (pt) cc_final: 0.7689 (pt) REVERT: A 1774 CYS cc_start: 0.6693 (m) cc_final: 0.6410 (m) REVERT: A 1795 ASN cc_start: 0.8162 (p0) cc_final: 0.7908 (p0) REVERT: A 1950 MET cc_start: 0.8079 (mtm) cc_final: 0.7837 (mtm) REVERT: A 1976 MET cc_start: 0.7753 (mtp) cc_final: 0.7430 (mtp) REVERT: A 2072 ASP cc_start: 0.7209 (m-30) cc_final: 0.6993 (m-30) REVERT: A 2113 ARG cc_start: 0.7774 (mtm180) cc_final: 0.7347 (mtp180) REVERT: A 2502 ARG cc_start: 0.7941 (mmp80) cc_final: 0.7124 (mmp-170) REVERT: A 2539 THR cc_start: 0.7587 (p) cc_final: 0.7376 (p) REVERT: A 2672 SER cc_start: 0.9275 (m) cc_final: 0.8723 (t) REVERT: A 2688 MET cc_start: 0.8145 (mmt) cc_final: 0.7888 (mmm) REVERT: A 2749 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 2750 GLU cc_start: 0.7860 (tp30) cc_final: 0.7616 (tp30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2662 time to fit residues: 89.4879 Evaluate side-chains 187 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 126 optimal weight: 0.0270 chunk 225 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1392 GLN A1694 HIS A1887 ASN A2244 ASN A2614 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15437 Z= 0.197 Angle : 0.715 12.209 21079 Z= 0.378 Chirality : 0.041 0.222 2606 Planarity : 0.004 0.063 2786 Dihedral : 5.493 36.127 2408 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.59 % Favored : 86.58 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2287 helix: 1.22 (0.14), residues: 1486 sheet: -1.19 (1.70), residues: 12 loop : -3.87 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1681 HIS 0.005 0.001 HIS A1525 PHE 0.023 0.002 PHE A1553 TYR 0.016 0.001 TYR A1673 ARG 0.005 0.001 ARG A2020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1714 MET cc_start: 0.7593 (tmm) cc_final: 0.7345 (tmm) REVERT: A 1795 ASN cc_start: 0.7620 (p0) cc_final: 0.7406 (p0) REVERT: A 1975 LEU cc_start: 0.9203 (tp) cc_final: 0.8724 (tp) REVERT: A 2113 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7428 (mtp180) REVERT: A 2262 LYS cc_start: 0.8152 (mptt) cc_final: 0.7777 (mmtm) REVERT: A 2502 ARG cc_start: 0.7536 (mmp80) cc_final: 0.6957 (mmp-170) REVERT: A 2672 SER cc_start: 0.9082 (m) cc_final: 0.8442 (t) REVERT: A 2689 CYS cc_start: 0.7552 (p) cc_final: 0.6934 (t) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2643 time to fit residues: 114.8024 Evaluate side-chains 206 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 67 optimal weight: 50.0000 chunk 44 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 50.0000 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15437 Z= 0.248 Angle : 0.718 9.793 21079 Z= 0.384 Chirality : 0.043 0.369 2606 Planarity : 0.004 0.067 2786 Dihedral : 5.372 37.031 2408 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 1.84 % Allowed : 13.21 % Favored : 84.96 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.19), residues: 2287 helix: 1.31 (0.14), residues: 1490 sheet: -1.95 (1.49), residues: 12 loop : -3.94 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A2108 HIS 0.017 0.002 HIS A2712 PHE 0.022 0.002 PHE A1808 TYR 0.018 0.001 TYR A1411 ARG 0.006 0.001 ARG A2544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1795 ASN cc_start: 0.7688 (p0) cc_final: 0.7440 (p0) REVERT: A 1976 MET cc_start: 0.7503 (mtp) cc_final: 0.7200 (mtp) REVERT: A 2113 ARG cc_start: 0.7559 (mtm180) cc_final: 0.7317 (mtp180) REVERT: A 2156 LEU cc_start: 0.7162 (mp) cc_final: 0.6956 (mt) REVERT: A 2262 LYS cc_start: 0.8119 (mptt) cc_final: 0.7797 (mmtm) REVERT: A 2412 THR cc_start: 0.7324 (p) cc_final: 0.7123 (p) REVERT: A 2476 ILE cc_start: 0.8745 (mm) cc_final: 0.8544 (mm) REVERT: A 2502 ARG cc_start: 0.7687 (mmp80) cc_final: 0.6988 (mmp-170) REVERT: A 2672 SER cc_start: 0.9093 (m) cc_final: 0.8587 (t) REVERT: A 2674 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7068 (mt-10) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2422 time to fit residues: 92.2632 Evaluate side-chains 192 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 40.0000 chunk 189 optimal weight: 0.0770 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 HIS A2244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15437 Z= 0.186 Angle : 0.697 9.613 21079 Z= 0.366 Chirality : 0.042 0.295 2606 Planarity : 0.004 0.064 2786 Dihedral : 5.096 35.506 2408 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.50 % Favored : 86.66 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2287 helix: 1.53 (0.14), residues: 1496 sheet: -1.98 (1.50), residues: 12 loop : -3.84 (0.20), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A2783 HIS 0.013 0.001 HIS A2712 PHE 0.020 0.001 PHE A2051 TYR 0.020 0.001 TYR A1533 ARG 0.004 0.001 ARG A2544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1441 ASP cc_start: 0.6697 (p0) cc_final: 0.6027 (t0) REVERT: A 1755 MET cc_start: 0.7737 (ttm) cc_final: 0.7483 (tpp) REVERT: A 1976 MET cc_start: 0.7466 (mtp) cc_final: 0.7133 (mtp) REVERT: A 2156 LEU cc_start: 0.6826 (mp) cc_final: 0.6591 (mt) REVERT: A 2207 TYR cc_start: 0.6130 (t80) cc_final: 0.5926 (t80) REVERT: A 2320 VAL cc_start: 0.8018 (t) cc_final: 0.7755 (t) REVERT: A 2325 LEU cc_start: 0.7372 (tp) cc_final: 0.7159 (tp) REVERT: A 2672 SER cc_start: 0.8981 (m) cc_final: 0.8374 (t) REVERT: A 2688 MET cc_start: 0.7986 (mmt) cc_final: 0.7753 (mmm) REVERT: A 2689 CYS cc_start: 0.7573 (p) cc_final: 0.6799 (t) REVERT: A 2760 GLU cc_start: 0.7954 (mp0) cc_final: 0.7719 (mp0) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2386 time to fit residues: 101.0278 Evaluate side-chains 195 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.0270 chunk 135 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 233 optimal weight: 0.0030 chunk 214 optimal weight: 0.8980 chunk 185 optimal weight: 0.0050 chunk 19 optimal weight: 50.0000 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2244 ASN A2712 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15437 Z= 0.184 Angle : 0.683 9.465 21079 Z= 0.359 Chirality : 0.041 0.277 2606 Planarity : 0.004 0.070 2786 Dihedral : 4.876 34.066 2408 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 1.84 % Allowed : 12.02 % Favored : 86.14 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 2287 helix: 1.70 (0.14), residues: 1500 sheet: -1.93 (1.56), residues: 12 loop : -3.94 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A2783 HIS 0.011 0.002 HIS A2712 PHE 0.021 0.001 PHE A2051 TYR 0.027 0.001 TYR A1561 ARG 0.005 0.000 ARG A1684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4574 Ramachandran restraints generated. 2287 Oldfield, 0 Emsley, 2287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1441 ASP cc_start: 0.6523 (p0) cc_final: 0.5937 (t0) REVERT: A 1976 MET cc_start: 0.7458 (mtp) cc_final: 0.7109 (mtp) REVERT: A 2217 LEU cc_start: 0.6832 (pp) cc_final: 0.6533 (pp) REVERT: A 2672 SER cc_start: 0.9066 (m) cc_final: 0.8476 (t) REVERT: A 2688 MET cc_start: 0.7907 (mmt) cc_final: 0.7703 (mmm) REVERT: A 2689 CYS cc_start: 0.7611 (p) cc_final: 0.6796 (t) REVERT: A 2760 GLU cc_start: 0.8168 (mp0) cc_final: 0.7271 (mp0) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2392 time to fit residues: 98.6163 Evaluate side-chains 196 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 0.0070 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 190 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 34 optimal weight: 40.0000 chunk 163 optimal weight: 0.9980 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2244 ASN A2629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.123163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106676 restraints weight = 62601.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108344 restraints weight = 39562.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109482 restraints weight = 27916.360| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15437 Z= 0.182 Angle : 0.669 9.568 21079 Z= 0.353 Chirality : 0.040 0.298 2606 Planarity : 0.004 0.068 2786 Dihedral : 4.799 34.502 2408 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 1.79 % Allowed : 11.59 % Favored : 86.62 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2287 helix: 1.82 (0.14), residues: 1497 sheet: -1.90 (1.61), residues: 12 loop : -3.90 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1919 HIS 0.008 0.001 HIS A1530 PHE 0.024 0.001 PHE A2518 TYR 0.020 0.001 TYR A1819 ARG 0.006 0.001 ARG A2502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.86 seconds wall clock time: 56 minutes 33.35 seconds (3393.35 seconds total)