Starting phenix.real_space_refine on Sat Aug 23 23:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_9893.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_9893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_9893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_9893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jxc_9893/08_2025/6jxc_9893.map" } resolution = 4.1 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= 0.011 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 76, 'ASN:plan1': 78, 'PHE:plan': 69, 'ARG:plan': 45, 'ASP:plan': 56, 'HIS:plan': 21, 'TYR:plan': 57, 'GLN:plan1': 42, 'TRP:plan': 15} Unresolved non-hydrogen planarities: 2152 Time building chain proxies: 3.02, per 1000 atoms: 0.20 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: 1.07 Conformation dependent library (CDL) restraints added in 646.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.98 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: 2.51 Time building geometry restraints manager: 1.38 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.200 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- 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= 1.084 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 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: -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 ARG 0.012 0.001 ARG A1453 TYR 0.047 0.006 TYR A2063 PHE 0.044 0.004 PHE A2481 TRP 0.061 0.007 TRP A2226 HIS 0.012 0.003 HIS A1973 Details of bonding type rmsd covalent geometry : bond 0.01775 (15437) covalent geometry : angle 1.70665 (21079) hydrogen bonds : bond 0.18047 ( 1010) hydrogen bonds : angle 6.59726 ( 2913) *********************** 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 to be fit. rotamer outliers: 4 poor density : 429 time to evaluate : 0.407 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: 0.1057 time to fit residues: 65.7391 Evaluate side-chains 254 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.0970 overall best weight: 3.5784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1737 GLN A1759 ASN A1887 ASN A1973 HIS A2521 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.105876 restraints weight = 62062.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.107855 restraints weight = 42046.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.110033 restraints weight = 26906.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110102 restraints weight = 19361.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.110136 restraints weight = 16436.316| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15437 Z= 0.220 Angle : 0.817 9.244 21079 Z= 0.449 Chirality : 0.044 0.235 2606 Planarity : 0.005 0.058 2786 Dihedral : 5.929 40.266 2408 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 1.97 % Allowed : 10.23 % Favored : 87.80 % Rotamer: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.04 % 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: -0.62 (0.18), residues: 2287 helix: 0.97 (0.13), residues: 1489 sheet: -1.72 (1.14), residues: 12 loop : -3.26 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2020 TYR 0.020 0.002 TYR A1411 PHE 0.035 0.002 PHE A1929 TRP 0.019 0.002 TRP A2226 HIS 0.006 0.002 HIS A1912 Details of bonding type rmsd covalent geometry : bond 0.00453 (15437) covalent geometry : angle 0.81743 (21079) hydrogen bonds : bond 0.05959 ( 1010) hydrogen bonds : angle 5.14335 ( 2913) *********************** 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 310 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1685 ILE cc_start: 0.8476 (pt) cc_final: 0.7972 (tp) REVERT: A 1798 ASN cc_start: 0.7832 (m-40) cc_final: 0.7455 (m110) REVERT: A 1806 LYS cc_start: 0.8563 (mttt) cc_final: 0.8235 (ttpt) REVERT: A 1827 LYS cc_start: 0.6202 (mptt) cc_final: 0.6000 (mttp) REVERT: A 1929 PHE cc_start: 0.8274 (m-80) cc_final: 0.7898 (m-80) REVERT: A 2019 LEU cc_start: 0.9197 (mt) cc_final: 0.8596 (pp) REVERT: A 2325 LEU cc_start: 0.9050 (tp) cc_final: 0.8800 (tp) REVERT: A 2478 GLU cc_start: 0.8435 (tp30) cc_final: 0.8042 (tm-30) REVERT: A 2505 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7807 (mppt) REVERT: A 2517 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5791 (mm-30) REVERT: A 2540 PHE cc_start: 0.7921 (p90) cc_final: 0.6853 (p90) REVERT: A 2583 ASP cc_start: 0.7249 (p0) cc_final: 0.6370 (p0) REVERT: A 2586 ASP cc_start: 0.6866 (m-30) cc_final: 0.6206 (m-30) REVERT: A 2672 SER cc_start: 0.9467 (m) cc_final: 0.8791 (t) REVERT: A 2750 GLU cc_start: 0.7872 (tp30) cc_final: 0.7567 (tp30) REVERT: A 2774 SER cc_start: 0.9111 (t) cc_final: 0.8789 (t) outliers start: 1 outliers final: 1 residues processed: 310 average time/residue: 0.1041 time to fit residues: 47.7227 Evaluate side-chains 230 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 45 optimal weight: 0.4980 chunk 217 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1759 ASN A1973 HIS A2244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108104 restraints weight = 62055.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.110038 restraints weight = 38730.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.111365 restraints weight = 26827.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.112300 restraints weight = 20052.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.112885 restraints weight = 16040.974| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15437 Z= 0.148 Angle : 0.703 9.944 21079 Z= 0.381 Chirality : 0.040 0.223 2606 Planarity : 0.004 0.051 2786 Dihedral : 5.257 37.228 2408 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 1.71 % Allowed : 11.15 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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: -0.19 (0.18), residues: 2287 helix: 1.43 (0.14), residues: 1470 sheet: -1.82 (1.16), residues: 12 loop : -3.26 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1684 TYR 0.019 0.001 TYR A1533 PHE 0.030 0.002 PHE A1929 TRP 0.021 0.002 TRP A2696 HIS 0.011 0.001 HIS A1912 Details of bonding type rmsd covalent geometry : bond 0.00299 (15437) covalent geometry : angle 0.70316 (21079) hydrogen bonds : bond 0.04742 ( 1010) hydrogen bonds : angle 4.56826 ( 2913) *********************** 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 298 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1487 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7914 (mtmt) REVERT: A 1681 TRP cc_start: 0.6774 (t60) cc_final: 0.6258 (t60) REVERT: A 1685 ILE cc_start: 0.8283 (pt) cc_final: 0.7817 (tp) REVERT: A 1714 MET cc_start: 0.7605 (tmm) cc_final: 0.6574 (tmm) REVERT: A 1774 CYS cc_start: 0.7002 (m) cc_final: 0.6242 (m) REVERT: A 1794 LEU cc_start: 0.7859 (tp) cc_final: 0.7406 (tp) REVERT: A 1798 ASN cc_start: 0.7868 (m-40) cc_final: 0.7623 (m110) REVERT: A 1806 LYS cc_start: 0.8630 (mttt) cc_final: 0.8364 (ttpt) REVERT: A 2019 LEU cc_start: 0.9123 (mt) cc_final: 0.8450 (pp) REVERT: A 2062 GLU cc_start: 0.7179 (tt0) cc_final: 0.6795 (tp30) REVERT: A 2113 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.6762 (mtp85) REVERT: A 2263 ILE cc_start: 0.8848 (mp) cc_final: 0.8645 (mm) REVERT: A 2277 TRP cc_start: 0.5197 (m-90) cc_final: 0.4829 (m-90) REVERT: A 2325 LEU cc_start: 0.8921 (tp) cc_final: 0.8667 (tp) REVERT: A 2478 GLU cc_start: 0.8579 (tp30) cc_final: 0.8262 (tm-30) REVERT: A 2502 ARG cc_start: 0.7789 (mmp80) cc_final: 0.7071 (mmp-170) REVERT: A 2505 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7538 (mppt) REVERT: A 2540 PHE cc_start: 0.7988 (p90) cc_final: 0.6077 (p90) REVERT: A 2583 ASP cc_start: 0.7109 (p0) cc_final: 0.6061 (p0) REVERT: A 2672 SER cc_start: 0.9445 (m) cc_final: 0.8779 (t) REVERT: A 2688 MET cc_start: 0.8090 (mmt) cc_final: 0.7632 (mmt) REVERT: A 2751 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8513 (mmtp) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1067 time to fit residues: 48.2599 Evaluate side-chains 224 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1528 GLN A1769 GLN A1973 HIS A2244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.108876 restraints weight = 61713.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110745 restraints weight = 38034.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.112045 restraints weight = 26358.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.112975 restraints weight = 19763.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.113537 restraints weight = 15848.611| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 15437 Z= 0.135 Angle : 0.662 14.743 21079 Z= 0.356 Chirality : 0.040 0.208 2606 Planarity : 0.004 0.064 2786 Dihedral : 5.080 35.744 2408 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 1.79 % Allowed : 10.54 % Favored : 87.67 % Rotamer: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % 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: 0.00 (0.19), residues: 2287 helix: 1.59 (0.14), residues: 1486 sheet: -1.32 (1.32), residues: 12 loop : -3.33 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A2544 TYR 0.034 0.001 TYR A1546 PHE 0.026 0.001 PHE A1929 TRP 0.017 0.001 TRP A2696 HIS 0.008 0.001 HIS A1912 Details of bonding type rmsd covalent geometry : bond 0.00276 (15437) covalent geometry : angle 0.66238 (21079) hydrogen bonds : bond 0.04206 ( 1010) hydrogen bonds : angle 4.33332 ( 2913) *********************** 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 289 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.478 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 1295 LEU cc_start: 0.9314 (tp) cc_final: 0.8987 (tp) REVERT: A 1401 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7849 (mmm160) REVERT: A 1440 ASP cc_start: 0.7734 (m-30) cc_final: 0.6744 (p0) REVERT: A 1681 TRP cc_start: 0.6883 (t60) cc_final: 0.6101 (t60) REVERT: A 1714 MET cc_start: 0.7584 (tmm) cc_final: 0.6177 (tmm) REVERT: A 1794 LEU cc_start: 0.7974 (tp) cc_final: 0.7442 (tp) REVERT: A 1798 ASN cc_start: 0.7878 (m-40) cc_final: 0.7592 (m110) REVERT: A 1806 LYS cc_start: 0.8632 (mttt) cc_final: 0.8371 (ttpt) REVERT: A 2113 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.7178 (mtp180) REVERT: A 2325 LEU cc_start: 0.8853 (tp) cc_final: 0.8483 (tp) REVERT: A 2502 ARG cc_start: 0.7737 (mmp80) cc_final: 0.6989 (mmp-170) REVERT: A 2516 ILE cc_start: 0.6430 (pt) cc_final: 0.5992 (pt) REVERT: A 2540 PHE cc_start: 0.7921 (p90) cc_final: 0.6197 (p90) REVERT: A 2672 SER cc_start: 0.9398 (m) cc_final: 0.8758 (t) outliers start: 1 outliers final: 0 residues processed: 289 average time/residue: 0.1147 time to fit residues: 49.7627 Evaluate side-chains 218 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 200 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 1 optimal weight: 50.0000 chunk 90 optimal weight: 0.0470 chunk 214 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1733 GLN A1769 GLN A1860 ASN A1973 HIS A2244 ASN A2397 GLN A2712 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.127794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.112296 restraints weight = 62919.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.113305 restraints weight = 43854.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.113705 restraints weight = 33971.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.114351 restraints weight = 28595.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.114441 restraints weight = 25244.510| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15437 Z= 0.128 Angle : 0.636 10.346 21079 Z= 0.340 Chirality : 0.039 0.197 2606 Planarity : 0.004 0.064 2786 Dihedral : 4.900 35.260 2408 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 1.75 % Allowed : 10.67 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % 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 (0.19), residues: 2287 helix: 1.68 (0.14), residues: 1496 sheet: -1.19 (1.38), residues: 12 loop : -3.46 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A2544 TYR 0.016 0.001 TYR A1546 PHE 0.019 0.001 PHE A1929 TRP 0.017 0.001 TRP A2058 HIS 0.012 0.001 HIS A2712 Details of bonding type rmsd covalent geometry : bond 0.00242 (15437) covalent geometry : angle 0.63574 (21079) hydrogen bonds : bond 0.03842 ( 1010) hydrogen bonds : angle 4.12073 ( 2913) *********************** 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 288 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.562 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 1401 ARG cc_start: 0.8257 (mmt180) cc_final: 0.7872 (mmm160) REVERT: A 1440 ASP cc_start: 0.7711 (m-30) cc_final: 0.6681 (p0) REVERT: A 1487 LYS cc_start: 0.8348 (mtpt) cc_final: 0.7822 (mtmt) REVERT: A 1681 TRP cc_start: 0.7054 (t60) cc_final: 0.6208 (t60) REVERT: A 1685 ILE cc_start: 0.8347 (pt) cc_final: 0.7794 (tp) REVERT: A 1714 MET cc_start: 0.7573 (tmm) cc_final: 0.6544 (tmm) REVERT: A 1794 LEU cc_start: 0.7926 (tp) cc_final: 0.7310 (tp) REVERT: A 1798 ASN cc_start: 0.7598 (m-40) cc_final: 0.7118 (m110) REVERT: A 2285 GLN cc_start: 0.8029 (mp10) cc_final: 0.7788 (mt0) REVERT: A 2325 LEU cc_start: 0.8901 (tp) cc_final: 0.8671 (tp) REVERT: A 2326 TYR cc_start: 0.7448 (t80) cc_final: 0.7240 (t80) REVERT: A 2476 ILE cc_start: 0.8840 (mm) cc_final: 0.8628 (tp) REVERT: A 2502 ARG cc_start: 0.7540 (mmp80) cc_final: 0.6979 (mmp-170) REVERT: A 2540 PHE cc_start: 0.7984 (p90) cc_final: 0.7594 (p90) REVERT: A 2583 ASP cc_start: 0.7213 (p0) cc_final: 0.6878 (p0) REVERT: A 2672 SER cc_start: 0.9421 (m) cc_final: 0.8782 (t) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1032 time to fit residues: 45.7412 Evaluate side-chains 222 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 60 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 196 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 233 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1788 HIS A1973 HIS A2135 HIS A2244 ASN A2397 GLN A2414 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.116297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.099614 restraints weight = 63619.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100998 restraints weight = 42107.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102014 restraints weight = 30730.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.102715 restraints weight = 24113.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103086 restraints weight = 20118.936| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 15437 Z= 0.360 Angle : 0.916 10.634 21079 Z= 0.501 Chirality : 0.048 0.223 2606 Planarity : 0.006 0.064 2786 Dihedral : 6.128 36.729 2408 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 1.84 % Allowed : 12.59 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.13 % 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: -1.17 (0.18), residues: 2287 helix: 0.72 (0.13), residues: 1486 sheet: -0.99 (2.03), residues: 12 loop : -3.89 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1721 TYR 0.029 0.003 TYR A1546 PHE 0.060 0.003 PHE A1808 TRP 0.017 0.003 TRP A2108 HIS 0.010 0.003 HIS A2227 Details of bonding type rmsd covalent geometry : bond 0.00752 (15437) covalent geometry : angle 0.91582 (21079) hydrogen bonds : bond 0.06266 ( 1010) hydrogen bonds : angle 5.44426 ( 2913) *********************** 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 235 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.405 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 1297 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8567 (mmtm) REVERT: A 1714 MET cc_start: 0.7758 (tmm) cc_final: 0.7463 (tmm) REVERT: A 1806 LYS cc_start: 0.8400 (mttt) cc_final: 0.8111 (ttpp) REVERT: A 1821 THR cc_start: 0.8403 (p) cc_final: 0.8107 (t) REVERT: A 1976 MET cc_start: 0.8097 (mtp) cc_final: 0.7878 (mtp) REVERT: A 2219 LEU cc_start: 0.8289 (tp) cc_final: 0.7994 (tp) REVERT: A 2325 LEU cc_start: 0.9097 (tp) cc_final: 0.8857 (tp) REVERT: A 2326 TYR cc_start: 0.8092 (t80) cc_final: 0.7807 (t80) REVERT: A 2502 ARG cc_start: 0.7898 (mmp80) cc_final: 0.7136 (mmp-170) REVERT: A 2539 THR cc_start: 0.8302 (p) cc_final: 0.8090 (p) REVERT: A 2540 PHE cc_start: 0.8342 (p90) cc_final: 0.7999 (p90) REVERT: A 2583 ASP cc_start: 0.8022 (p0) cc_final: 0.7493 (p0) REVERT: A 2672 SER cc_start: 0.9517 (m) cc_final: 0.9083 (t) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1054 time to fit residues: 37.7977 Evaluate side-chains 192 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 223 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 196 optimal weight: 50.0000 chunk 73 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1798 ASN A1973 HIS A2055 ASN A2154 GLN A2244 ASN A2397 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.120803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103555 restraints weight = 61741.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105315 restraints weight = 38205.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106568 restraints weight = 26578.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107455 restraints weight = 20038.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107976 restraints weight = 16181.472| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5681 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= 0.153 Angle : 0.690 10.580 21079 Z= 0.370 Chirality : 0.041 0.310 2606 Planarity : 0.004 0.070 2786 Dihedral : 5.428 35.098 2408 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 1.79 % Allowed : 11.50 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.09 % 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: -0.47 (0.19), residues: 2287 helix: 1.30 (0.14), residues: 1508 sheet: -1.25 (1.68), residues: 12 loop : -3.82 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1721 TYR 0.032 0.002 TYR A1411 PHE 0.019 0.001 PHE A1929 TRP 0.016 0.002 TRP A2058 HIS 0.005 0.001 HIS A1912 Details of bonding type rmsd covalent geometry : bond 0.00317 (15437) covalent geometry : angle 0.69043 (21079) hydrogen bonds : bond 0.04522 ( 1010) hydrogen bonds : angle 4.54540 ( 2913) *********************** 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 268 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1795 ASN cc_start: 0.8605 (p0) cc_final: 0.8304 (p0) REVERT: A 1806 LYS cc_start: 0.8477 (mttt) cc_final: 0.8233 (ttpt) REVERT: A 1821 THR cc_start: 0.8356 (p) cc_final: 0.8089 (t) REVERT: A 1932 ILE cc_start: 0.8893 (tt) cc_final: 0.8685 (tt) REVERT: A 2219 LEU cc_start: 0.8284 (tp) cc_final: 0.8022 (tp) REVERT: A 2325 LEU cc_start: 0.8923 (tp) cc_final: 0.8662 (tp) REVERT: A 2326 TYR cc_start: 0.7683 (t80) cc_final: 0.7452 (t80) REVERT: A 2414 ASN cc_start: 0.8582 (m-40) cc_final: 0.8341 (m-40) REVERT: A 2488 LEU cc_start: 0.9317 (mm) cc_final: 0.8834 (mt) REVERT: A 2502 ARG cc_start: 0.7792 (mmp80) cc_final: 0.7108 (mmp-170) REVERT: A 2583 ASP cc_start: 0.7619 (p0) cc_final: 0.7217 (p0) REVERT: A 2672 SER cc_start: 0.9477 (m) cc_final: 0.8818 (t) REVERT: A 2740 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7867 (mm-30) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.0977 time to fit residues: 40.5569 Evaluate side-chains 201 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 106 optimal weight: 0.0060 chunk 148 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 220 optimal weight: 0.9980 chunk 185 optimal weight: 0.0270 chunk 1 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 231 optimal weight: 0.0570 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1694 HIS ** A1987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106446 restraints weight = 62478.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108247 restraints weight = 38776.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109496 restraints weight = 27054.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110421 restraints weight = 20406.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.111042 restraints weight = 16338.317| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15437 Z= 0.133 Angle : 0.658 10.546 21079 Z= 0.348 Chirality : 0.040 0.209 2606 Planarity : 0.004 0.066 2786 Dihedral : 5.010 34.702 2408 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 1.79 % Allowed : 11.59 % Favored : 86.62 % 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 : 0.04 % 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 (0.19), residues: 2287 helix: 1.68 (0.14), residues: 1504 sheet: -1.33 (1.50), residues: 12 loop : -3.82 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2544 TYR 0.017 0.001 TYR A1546 PHE 0.026 0.001 PHE A1929 TRP 0.014 0.002 TRP A2696 HIS 0.005 0.001 HIS A1525 Details of bonding type rmsd covalent geometry : bond 0.00270 (15437) covalent geometry : angle 0.65765 (21079) hydrogen bonds : bond 0.03873 ( 1010) hydrogen bonds : angle 4.13231 ( 2913) *********************** 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 275 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1484 LYS cc_start: 0.7604 (tppt) cc_final: 0.6287 (ptpp) REVERT: A 1732 LEU cc_start: 0.8720 (tp) cc_final: 0.8492 (tp) REVERT: A 1738 ILE cc_start: 0.9025 (mp) cc_final: 0.8756 (mp) REVERT: A 1806 LYS cc_start: 0.8378 (mttt) cc_final: 0.8028 (ttpp) REVERT: A 1821 THR cc_start: 0.8284 (p) cc_final: 0.8059 (t) REVERT: A 2219 LEU cc_start: 0.8364 (tp) cc_final: 0.8161 (tp) REVERT: A 2325 LEU cc_start: 0.8710 (tp) cc_final: 0.8481 (tp) REVERT: A 2464 MET cc_start: 0.7441 (tpp) cc_final: 0.7218 (mmm) REVERT: A 2502 ARG cc_start: 0.7531 (mmp80) cc_final: 0.6999 (mmp-170) REVERT: A 2583 ASP cc_start: 0.7399 (p0) cc_final: 0.7141 (p0) REVERT: A 2672 SER cc_start: 0.9495 (m) cc_final: 0.8879 (t) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1018 time to fit residues: 43.5426 Evaluate side-chains 207 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 227 optimal weight: 0.1980 chunk 48 optimal weight: 40.0000 chunk 229 optimal weight: 8.9990 chunk 193 optimal weight: 0.0070 overall best weight: 1.6500 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.122673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105828 restraints weight = 62032.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107530 restraints weight = 39561.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.108690 restraints weight = 27958.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109301 restraints weight = 21530.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.110047 restraints weight = 18073.039| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15437 Z= 0.137 Angle : 0.661 11.338 21079 Z= 0.351 Chirality : 0.041 0.201 2606 Planarity : 0.004 0.071 2786 Dihedral : 4.908 33.709 2408 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 1.79 % Allowed : 11.72 % Favored : 86.49 % 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 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: -0.02 (0.19), residues: 2287 helix: 1.73 (0.14), residues: 1509 sheet: -1.54 (1.55), residues: 12 loop : -3.85 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2544 TYR 0.027 0.001 TYR A1411 PHE 0.023 0.002 PHE A1553 TRP 0.028 0.002 TRP A2399 HIS 0.005 0.001 HIS A1525 Details of bonding type rmsd covalent geometry : bond 0.00290 (15437) covalent geometry : angle 0.66067 (21079) hydrogen bonds : bond 0.03883 ( 1010) hydrogen bonds : angle 4.13407 ( 2913) *********************** 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 257 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1484 LYS cc_start: 0.7606 (tppt) cc_final: 0.6307 (ptpp) REVERT: A 1732 LEU cc_start: 0.8764 (tp) cc_final: 0.8548 (tp) REVERT: A 1806 LYS cc_start: 0.8409 (mttt) cc_final: 0.8038 (ttpp) REVERT: A 2072 ASP cc_start: 0.7714 (m-30) cc_final: 0.7496 (m-30) REVERT: A 2219 LEU cc_start: 0.8419 (tp) cc_final: 0.8194 (tp) REVERT: A 2325 LEU cc_start: 0.8506 (tp) cc_final: 0.8289 (tp) REVERT: A 2464 MET cc_start: 0.7525 (tpp) cc_final: 0.7265 (mmm) REVERT: A 2477 MET cc_start: 0.7766 (mmm) cc_final: 0.7469 (tpp) REVERT: A 2488 LEU cc_start: 0.9190 (mm) cc_final: 0.8799 (mt) REVERT: A 2502 ARG cc_start: 0.7734 (mmp80) cc_final: 0.7117 (mmp-170) REVERT: A 2511 PRO cc_start: 0.7207 (Cg_endo) cc_final: 0.6995 (Cg_exo) REVERT: A 2539 THR cc_start: 0.7855 (p) cc_final: 0.7569 (p) REVERT: A 2583 ASP cc_start: 0.7624 (p0) cc_final: 0.7256 (p0) REVERT: A 2672 SER cc_start: 0.9497 (m) cc_final: 0.8887 (t) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.0915 time to fit residues: 36.9200 Evaluate side-chains 197 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 15 optimal weight: 50.0000 chunk 223 optimal weight: 0.5980 chunk 175 optimal weight: 40.0000 chunk 165 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 27 optimal weight: 40.0000 chunk 150 optimal weight: 4.9990 overall best weight: 6.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1973 HIS A2135 HIS A2244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.115458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099331 restraints weight = 64086.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.100710 restraints weight = 42447.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101692 restraints weight = 30954.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.102391 restraints weight = 24512.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.102723 restraints weight = 20456.443| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 15437 Z= 0.328 Angle : 0.901 11.845 21079 Z= 0.488 Chirality : 0.048 0.272 2606 Planarity : 0.005 0.066 2786 Dihedral : 6.137 39.439 2408 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 1.88 % Allowed : 13.64 % Favored : 84.48 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % 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: -1.16 (0.18), residues: 2287 helix: 0.78 (0.14), residues: 1488 sheet: -1.04 (2.07), residues: 12 loop : -4.01 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A2472 TYR 0.046 0.003 TYR A2242 PHE 0.054 0.003 PHE A1808 TRP 0.032 0.003 TRP A2783 HIS 0.010 0.002 HIS A2629 Details of bonding type rmsd covalent geometry : bond 0.00699 (15437) covalent geometry : angle 0.90125 (21079) hydrogen bonds : bond 0.05875 ( 1010) hydrogen bonds : angle 5.27841 ( 2913) ********************** 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 228 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1681 TRP cc_start: 0.7734 (t60) cc_final: 0.7384 (t60) REVERT: A 1685 ILE cc_start: 0.8523 (pt) cc_final: 0.8120 (pt) REVERT: A 1714 MET cc_start: 0.7901 (tmm) cc_final: 0.7530 (tmm) REVERT: A 1732 LEU cc_start: 0.8904 (tp) cc_final: 0.8663 (tp) REVERT: A 1806 LYS cc_start: 0.8537 (mttt) cc_final: 0.8201 (ttpp) REVERT: A 1879 LYS cc_start: 0.9165 (ttpt) cc_final: 0.8725 (tttt) REVERT: A 1976 MET cc_start: 0.8133 (mtp) cc_final: 0.7765 (mtp) REVERT: A 2072 ASP cc_start: 0.7870 (m-30) cc_final: 0.7532 (m-30) REVERT: A 2221 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8534 (ttmm) REVERT: A 2262 LYS cc_start: 0.8464 (mptt) cc_final: 0.8121 (mmtm) REVERT: A 2325 LEU cc_start: 0.8952 (tp) cc_final: 0.8732 (tp) REVERT: A 2477 MET cc_start: 0.7918 (mmm) cc_final: 0.7649 (tpp) REVERT: A 2539 THR cc_start: 0.7961 (p) cc_final: 0.7667 (p) REVERT: A 2583 ASP cc_start: 0.8001 (p0) cc_final: 0.7372 (p0) REVERT: A 2672 SER cc_start: 0.9568 (m) cc_final: 0.9143 (t) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1042 time to fit residues: 36.2829 Evaluate side-chains 181 residues out of total 2156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 156 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 167 optimal weight: 0.0000 chunk 66 optimal weight: 30.0000 chunk 211 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1282 HIS A1887 ASN A1973 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.118835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.102193 restraints weight = 62070.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.103819 restraints weight = 39353.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.104943 restraints weight = 27902.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.105642 restraints weight = 21455.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106241 restraints weight = 17809.142| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15437 Z= 0.176 Angle : 0.732 11.370 21079 Z= 0.391 Chirality : 0.043 0.232 2606 Planarity : 0.004 0.074 2786 Dihedral : 5.619 37.689 2408 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 1.88 % Allowed : 12.20 % Favored : 85.92 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.04 % 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: -0.69 (0.19), residues: 2287 helix: 1.21 (0.14), residues: 1486 sheet: -1.50 (1.69), residues: 12 loop : -3.96 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1721 TYR 0.039 0.002 TYR A1819 PHE 0.023 0.002 PHE A1929 TRP 0.021 0.002 TRP A2783 HIS 0.006 0.002 HIS A2629 Details of bonding type rmsd covalent geometry : bond 0.00384 (15437) covalent geometry : angle 0.73182 (21079) hydrogen bonds : bond 0.04539 ( 1010) hydrogen bonds : angle 4.59253 ( 2913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.19 seconds wall clock time: 40 minutes 29.85 seconds (2429.85 seconds total)