Starting phenix.real_space_refine on Sun Aug 24 20:41:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.cif Found real_map, /net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.map" model { file = "/net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9euw_19988/08_2025/9euw_19988.cif" } resolution = 2.8 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= -0.007 sd= 1.109 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 76 5.16 5 C 14119 2.51 5 N 3874 2.21 5 O 4269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s 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: 22338 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2803, 22338 Classifications: {'peptide': 2803} Link IDs: {'PCIS': 1, 'PTRANS': 115, 'TRANS': 2686} Chain breaks: 5 Time building chain proxies: 4.14, per 1000 atoms: 0.19 Number of scatterers: 22338 At special positions: 0 Unit cell: (180.686, 192.038, 112.574, 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 76 16.00 O 4269 8.00 N 3874 7.00 C 14119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A3182 " - pdb=" SG CYS A3205 " distance=2.03 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: 1.14 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 30 sheets defined 43.1% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.673A pdb=" N ASP A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.071A pdb=" N ASP A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.826A pdb=" N PHE A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.557A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 422 through 452 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 472 through 502 removed outlier: 3.663A pdb=" N GLN A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 removed outlier: 4.190A pdb=" N SER A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.566A pdb=" N MET A 530 " --> pdb=" O TYR A 526 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 531 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.940A pdb=" N ARG A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.669A pdb=" N ASP A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.701A pdb=" N GLU A 607 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 630 removed outlier: 3.659A pdb=" N LYS A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 6.165A pdb=" N ASP A 634 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 636 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 695 removed outlier: 3.611A pdb=" N ASP A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 718 through 733 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.652A pdb=" N GLY A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 776 Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 837 through 841 removed outlier: 3.910A pdb=" N THR A 840 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 864 through 877 removed outlier: 5.813A pdb=" N LYS A 873 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 888 Processing helix chain 'A' and resid 892 through 909 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 952 through 966 removed outlier: 3.905A pdb=" N ASN A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 Processing helix chain 'A' and resid 1120 through 1139 removed outlier: 3.719A pdb=" N PHE A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1167 Processing helix chain 'A' and resid 1172 through 1184 Processing helix chain 'A' and resid 1200 through 1209 removed outlier: 3.569A pdb=" N GLU A1209 " --> pdb=" O ASN A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1229 removed outlier: 4.359A pdb=" N SER A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Proline residue: A1221 - end of helix Processing helix chain 'A' and resid 1237 through 1246 Processing helix chain 'A' and resid 1248 through 1252 Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.894A pdb=" N GLY A1293 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1294 " --> pdb=" O PRO A1290 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A1311 " --> pdb=" O VAL A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1324 Processing helix chain 'A' and resid 1326 through 1332 Processing helix chain 'A' and resid 1333 through 1347 Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.301A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A1376 " --> pdb=" O LEU A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1387 Processing helix chain 'A' and resid 1388 through 1391 removed outlier: 3.561A pdb=" N GLY A1391 " --> pdb=" O GLN A1388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1391' Processing helix chain 'A' and resid 1441 through 1460 removed outlier: 4.229A pdb=" N PHE A1445 " --> pdb=" O SER A1441 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A1446 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A1449 " --> pdb=" O PHE A1445 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A1452 " --> pdb=" O HIS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.969A pdb=" N THR A1490 " --> pdb=" O LEU A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1515 Processing helix chain 'A' and resid 1521 through 1548 removed outlier: 3.891A pdb=" N THR A1547 " --> pdb=" O ASN A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1568 Processing helix chain 'A' and resid 1606 through 1621 removed outlier: 3.573A pdb=" N ALA A1610 " --> pdb=" O SER A1606 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A1621 " --> pdb=" O MET A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1628 Processing helix chain 'A' and resid 1634 through 1639 Processing helix chain 'A' and resid 1647 through 1654 removed outlier: 3.772A pdb=" N ASN A1651 " --> pdb=" O ASP A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 removed outlier: 3.680A pdb=" N ASN A1675 " --> pdb=" O ASP A1671 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A1676 " --> pdb=" O ARG A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1689 through 1695 Processing helix chain 'A' and resid 1712 through 1714 No H-bonds generated for 'chain 'A' and resid 1712 through 1714' Processing helix chain 'A' and resid 1719 through 1730 Processing helix chain 'A' and resid 1733 through 1748 Processing helix chain 'A' and resid 1757 through 1761 Processing helix chain 'A' and resid 1765 through 1767 No H-bonds generated for 'chain 'A' and resid 1765 through 1767' Processing helix chain 'A' and resid 1768 through 1799 removed outlier: 3.623A pdb=" N GLY A1788 " --> pdb=" O GLN A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1857 removed outlier: 4.045A pdb=" N VAL A1844 " --> pdb=" O VAL A1840 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A1846 " --> pdb=" O GLU A1842 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A1847 " --> pdb=" O VAL A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1883 Processing helix chain 'A' and resid 1898 through 1920 Processing helix chain 'A' and resid 1928 through 1944 removed outlier: 3.527A pdb=" N ALA A1932 " --> pdb=" O ARG A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1961 removed outlier: 3.571A pdb=" N GLY A1949 " --> pdb=" O GLY A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1982 removed outlier: 4.996A pdb=" N GLN A1979 " --> pdb=" O ASN A1975 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A1980 " --> pdb=" O SER A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2003 removed outlier: 3.763A pdb=" N THR A1989 " --> pdb=" O SER A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2006 No H-bonds generated for 'chain 'A' and resid 2004 through 2006' Processing helix chain 'A' and resid 2029 through 2037 removed outlier: 3.845A pdb=" N ASN A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2059 removed outlier: 4.289A pdb=" N HIS A2059 " --> pdb=" O ASP A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2111 through 2120 Processing helix chain 'A' and resid 2127 through 2131 Processing helix chain 'A' and resid 2222 through 2232 Processing helix chain 'A' and resid 2379 through 2381 No H-bonds generated for 'chain 'A' and resid 2379 through 2381' Processing helix chain 'A' and resid 2406 through 2413 removed outlier: 4.595A pdb=" N ASN A2411 " --> pdb=" O ALA A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2444 through 2452 Processing helix chain 'A' and resid 2458 through 2469 Processing helix chain 'A' and resid 2610 through 2617 removed outlier: 3.632A pdb=" N ARG A2615 " --> pdb=" O GLY A2611 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A2616 " --> pdb=" O ASP A2612 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A2617 " --> pdb=" O VAL A2613 " (cutoff:3.500A) Processing helix chain 'A' and resid 2742 through 2749 removed outlier: 3.999A pdb=" N GLN A2749 " --> pdb=" O GLN A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2778 through 2787 removed outlier: 3.975A pdb=" N LYS A2782 " --> pdb=" O THR A2778 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2838 removed outlier: 3.585A pdb=" N GLU A2834 " --> pdb=" O ARG A2830 " (cutoff:3.500A) Processing helix chain 'A' and resid 2839 through 2844 removed outlier: 4.225A pdb=" N GLY A2843 " --> pdb=" O PRO A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2845 through 2848 removed outlier: 3.675A pdb=" N PHE A2848 " --> pdb=" O THR A2845 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2845 through 2848' Processing helix chain 'A' and resid 2850 through 2856 removed outlier: 5.176A pdb=" N ASN A2855 " --> pdb=" O ALA A2852 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2884 Processing helix chain 'A' and resid 2982 through 2986 removed outlier: 3.770A pdb=" N TYR A2986 " --> pdb=" O TRP A2983 " (cutoff:3.500A) Processing helix chain 'A' and resid 3056 through 3070 Processing helix chain 'A' and resid 3072 through 3087 removed outlier: 3.764A pdb=" N VAL A3087 " --> pdb=" O MET A3083 " (cutoff:3.500A) Processing helix chain 'A' and resid 3097 through 3102 removed outlier: 4.579A pdb=" N HIS A3101 " --> pdb=" O GLU A3097 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A3102 " --> pdb=" O LEU A3098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3097 through 3102' Processing helix chain 'A' and resid 3192 through 3195 Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 510 removed outlier: 6.357A pdb=" N ILE A 316 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TRP A 348 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 318 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE A 319 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 652 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795 removed outlier: 4.266A pdb=" N LYS A 794 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 935 through 936 Processing sheet with id=AA6, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 3.793A pdb=" N GLY A1188 " --> pdb=" O SER A1282 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A1269 " --> pdb=" O THR A1276 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN A1278 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N GLY A1267 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA8, first strand: chain 'A' and resid 1464 through 1466 removed outlier: 4.370A pdb=" N ASN A1464 " --> pdb=" O ASP A1603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1679 through 1682 Processing sheet with id=AB1, first strand: chain 'A' and resid 1702 through 1703 Processing sheet with id=AB2, first strand: chain 'A' and resid 1814 through 1815 removed outlier: 3.538A pdb=" N VAL A1838 " --> pdb=" O PHE A1823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.693A pdb=" N LEU A2070 " --> pdb=" O ILE A2156 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A2155 " --> pdb=" O LEU A2213 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A2210 " --> pdb=" O ALA A2247 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLN A2249 " --> pdb=" O THR A2210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A2212 " --> pdb=" O GLN A2249 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A2246 " --> pdb=" O THR A2268 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER A2270 " --> pdb=" O LEU A2246 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A2248 " --> pdb=" O SER A2270 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A2269 " --> pdb=" O VAL A2314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2139 through 2140 removed outlier: 10.778A pdb=" N TYR A2163 " --> pdb=" O GLY A2094 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER A2096 " --> pdb=" O TYR A2163 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA A2165 " --> pdb=" O SER A2096 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A2098 " --> pdb=" O ALA A2165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2139 through 2140 removed outlier: 6.524A pdb=" N LEU A2091 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A2083 " --> pdb=" O LEU A2091 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS A2093 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET A2081 " --> pdb=" O HIS A2093 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY A2079 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR A2202 " --> pdb=" O GLY A2079 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET A2081 " --> pdb=" O THR A2202 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A2204 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A2083 " --> pdb=" O ILE A2204 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A2254 " --> pdb=" O THR A2304 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A2306 " --> pdb=" O GLY A2254 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR A2256 " --> pdb=" O THR A2306 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLU A2299 " --> pdb=" O THR A2295 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A2295 " --> pdb=" O GLU A2299 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A2293 " --> pdb=" O PRO A2301 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2168 through 2172 Processing sheet with id=AB7, first strand: chain 'A' and resid 2280 through 2283 removed outlier: 7.170A pdb=" N LEU A2280 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE A2324 " --> pdb=" O LEU A2280 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A2282 " --> pdb=" O ILE A2324 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP A2321 " --> pdb=" O THR A2340 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE A2342 " --> pdb=" O ASP A2321 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A2323 " --> pdb=" O ILE A2342 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN A2403 " --> pdb=" O LEU A2360 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU A2362 " --> pdb=" O GLN A2403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2330 through 2333 removed outlier: 6.280A pdb=" N ASN A2330 " --> pdb=" O ARG A2349 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE A2351 " --> pdb=" O ASN A2330 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE A2332 " --> pdb=" O ILE A2351 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A2346 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLU A2372 " --> pdb=" O GLY A2346 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN A2348 " --> pdb=" O GLU A2372 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE A2374 " --> pdb=" O ASN A2348 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR A2350 " --> pdb=" O PHE A2374 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE A2417 " --> pdb=" O ALA A2429 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A2426 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A2435 " --> pdb=" O ARG A2432 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N SER A2472 " --> pdb=" O ILE A2436 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A2438 " --> pdb=" O SER A2472 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR A2474 " --> pdb=" O LEU A2438 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE A2440 " --> pdb=" O THR A2474 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A2476 " --> pdb=" O ILE A2440 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A2442 " --> pdb=" O GLU A2476 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A2478 " --> pdb=" O LEU A2442 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A2486 " --> pdb=" O PHE A2479 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A2485 " --> pdb=" O GLN A2498 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A2498 " --> pdb=" O GLN A2485 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR A2516 " --> pdb=" O GLN A2540 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A2542 " --> pdb=" O THR A2516 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A2518 " --> pdb=" O ILE A2542 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A2539 " --> pdb=" O THR A2586 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N SER A2588 " --> pdb=" O THR A2539 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A2541 " --> pdb=" O SER A2588 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A2563 " --> pdb=" O ILE A2626 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A2624 " --> pdb=" O GLY A2565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2383 through 2384 removed outlier: 4.752A pdb=" N ILE A2393 " --> pdb=" O LYS A2384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2505 through 2508 removed outlier: 6.700A pdb=" N TYR A2526 " --> pdb=" O ASP A2554 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A2553 " --> pdb=" O ALA A2601 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLN A2603 " --> pdb=" O ILE A2553 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP A2606 " --> pdb=" O ILE A2602 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2637 through 2640 removed outlier: 6.527A pdb=" N ARG A2637 " --> pdb=" O CYS A2663 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU A2665 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A2639 " --> pdb=" O GLU A2665 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A2711 " --> pdb=" O ALA A2686 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA A2686 " --> pdb=" O TYR A2711 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A2713 " --> pdb=" O LYS A2684 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2649 through 2651 removed outlier: 6.322A pdb=" N LEU A2721 " --> pdb=" O LEU A2679 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A2704 " --> pdb=" O LYS A2672 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2731 through 2733 Processing sheet with id=AC5, first strand: chain 'A' and resid 2737 through 2741 removed outlier: 7.086A pdb=" N GLY A2737 " --> pdb=" O SER A2762 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE A2764 " --> pdb=" O GLY A2737 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET A2739 " --> pdb=" O ILE A2764 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 2858 through 2860 Processing sheet with id=AC7, first strand: chain 'A' and resid 2909 through 2912 removed outlier: 6.778A pdb=" N MET A2909 " --> pdb=" O ILE A2973 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER A2975 " --> pdb=" O MET A2909 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A2911 " --> pdb=" O SER A2975 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2935 through 2938 removed outlier: 6.449A pdb=" N ARG A2935 " --> pdb=" O SER A2989 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A2991 " --> pdb=" O ARG A2935 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A2937 " --> pdb=" O LEU A2991 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A2993 " --> pdb=" O LYS A2937 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU A2988 " --> pdb=" O VAL A3008 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A3008 " --> pdb=" O LEU A2988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A3035 " --> pdb=" O MET A3013 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2947 through 2950 Processing sheet with id=AD1, first strand: chain 'A' and resid 3106 through 3110 removed outlier: 6.266A pdb=" N GLN A3152 " --> pdb=" O ILE A3198 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL A3200 " --> pdb=" O GLN A3152 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR A3154 " --> pdb=" O VAL A3200 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR A3199 " --> pdb=" O VAL A3188 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL A3188 " --> pdb=" O TYR A3199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A3201 " --> pdb=" O THR A3186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3123 through 3125 Processing sheet with id=AD3, first strand: chain 'A' and resid 3132 through 3135 1002 hydrogen bonds defined for protein. 2826 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: 6.78 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7308 1.34 - 1.45: 2921 1.45 - 1.57: 12407 1.57 - 1.69: 1 1.69 - 1.81: 138 Bond restraints: 22775 Sorted by residual: bond pdb=" CA ASN A 951 " pdb=" CB ASN A 951 " ideal model delta sigma weight residual 1.530 1.597 -0.066 1.50e-02 4.44e+03 1.96e+01 bond pdb=" N VAL A2647 " pdb=" CA VAL A2647 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.30e-03 1.16e+04 1.70e+01 bond pdb=" N ASN A1812 " pdb=" CA ASN A1812 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.18e-02 7.18e+03 8.65e+00 bond pdb=" N VAL A1810 " pdb=" CA VAL A1810 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.54e+00 bond pdb=" N LYS A2190 " pdb=" CA LYS A2190 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.33e+00 ... (remaining 22770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 30360 1.96 - 3.92: 439 3.92 - 5.88: 47 5.88 - 7.84: 12 7.84 - 9.79: 3 Bond angle restraints: 30861 Sorted by residual: angle pdb=" C ARG A2188 " pdb=" CA ARG A2188 " pdb=" CB ARG A2188 " ideal model delta sigma weight residual 116.54 110.51 6.03 1.15e+00 7.56e-01 2.75e+01 angle pdb=" N VAL A2647 " pdb=" CA VAL A2647 " pdb=" C VAL A2647 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" CA SER A1809 " pdb=" C SER A1809 " pdb=" O SER A1809 " ideal model delta sigma weight residual 122.27 117.91 4.36 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N LEU A2641 " pdb=" CA LEU A2641 " pdb=" C LEU A2641 " ideal model delta sigma weight residual 113.20 108.65 4.55 1.21e+00 6.83e-01 1.41e+01 angle pdb=" CB GLU A1678 " pdb=" CG GLU A1678 " pdb=" CD GLU A1678 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.70e+00 3.46e-01 1.22e+01 ... (remaining 30856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 11768 17.67 - 35.33: 1502 35.33 - 53.00: 426 53.00 - 70.67: 98 70.67 - 88.34: 31 Dihedral angle restraints: 13825 sinusoidal: 5660 harmonic: 8165 Sorted by residual: dihedral pdb=" CA MET A 574 " pdb=" C MET A 574 " pdb=" N GLN A 575 " pdb=" CA GLN A 575 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA MET A2825 " pdb=" C MET A2825 " pdb=" N ASP A2826 " pdb=" CA ASP A2826 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER A2088 " pdb=" C SER A2088 " pdb=" N PRO A2089 " pdb=" CA PRO A2089 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2635 0.043 - 0.086: 606 0.086 - 0.129: 239 0.129 - 0.172: 13 0.172 - 0.215: 3 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CA ILE A1813 " pdb=" N ILE A1813 " pdb=" C ILE A1813 " pdb=" CB ILE A1813 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA VAL A 773 " pdb=" N VAL A 773 " pdb=" C VAL A 773 " pdb=" CB VAL A 773 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA VAL A2647 " pdb=" N VAL A2647 " pdb=" C VAL A2647 " pdb=" CB VAL A2647 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 3493 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A2755 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A2756 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A2756 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A2756 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A2692 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO A2693 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A2693 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A2693 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1802 " 0.213 9.50e-02 1.11e+02 9.54e-02 5.58e+00 pdb=" NE ARG A1802 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A1802 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1802 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A1802 " 0.008 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1767 2.74 - 3.28: 22016 3.28 - 3.82: 37213 3.82 - 4.36: 44162 4.36 - 4.90: 76877 Nonbonded interactions: 182035 Sorted by model distance: nonbonded pdb=" O ASP A 615 " pdb=" ND2 ASN A 619 " model vdw 2.198 3.120 nonbonded pdb=" OG SER A1401 " pdb=" OD2 ASP A1416 " model vdw 2.199 3.040 nonbonded pdb=" N GLU A1842 " pdb=" OE1 GLU A1842 " model vdw 2.210 3.120 nonbonded pdb=" N GLU A1965 " pdb=" OE1 GLU A1965 " model vdw 2.213 3.120 nonbonded pdb=" OG1 THR A3215 " pdb=" OD1 ASN A3217 " model vdw 2.214 3.040 ... (remaining 182030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22776 Z= 0.186 Angle : 0.558 9.795 30863 Z= 0.314 Chirality : 0.042 0.215 3496 Planarity : 0.005 0.110 3983 Dihedral : 17.400 88.337 8560 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.69 % Allowed : 25.50 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2791 helix: 2.15 (0.16), residues: 1068 sheet: -0.46 (0.23), residues: 590 loop : -0.51 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2418 TYR 0.017 0.001 TYR A1296 PHE 0.012 0.001 PHE A 962 TRP 0.014 0.001 TRP A2046 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00343 (22775) covalent geometry : angle 0.55807 (30861) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.99403 ( 2) hydrogen bonds : bond 0.15274 ( 1000) hydrogen bonds : angle 5.96325 ( 2826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1648 MET cc_start: 0.8304 (mtm) cc_final: 0.8088 (ptp) REVERT: A 1796 HIS cc_start: 0.7969 (t70) cc_final: 0.7732 (t-90) REVERT: A 1822 ARG cc_start: 0.7067 (mtp85) cc_final: 0.5947 (tmt170) REVERT: A 2908 ILE cc_start: 0.9064 (mp) cc_final: 0.8843 (mm) outliers start: 67 outliers final: 55 residues processed: 252 average time/residue: 0.4610 time to fit residues: 135.6193 Evaluate side-chains 235 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 860 PHE Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1143 SER Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1235 SER Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1328 SER Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1623 THR Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 2002 SER Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2153 ASP Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2367 ASN Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2708 SER Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2781 LEU Chi-restraints excluded: chain A residue 2796 SER Chi-restraints excluded: chain A residue 2910 THR Chi-restraints excluded: chain A residue 2912 THR Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2915 THR Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2968 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3024 ASP Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3165 ILE Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 478 ASN A 577 ASN A 656 HIS A 872 GLN ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 GLN ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2879 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091339 restraints weight = 36879.468| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.22 r_work: 0.3065 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22776 Z= 0.117 Angle : 0.498 7.559 30863 Z= 0.261 Chirality : 0.041 0.157 3496 Planarity : 0.004 0.068 3983 Dihedral : 5.461 64.107 3139 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.37 % Allowed : 23.90 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2791 helix: 2.17 (0.16), residues: 1082 sheet: -0.42 (0.22), residues: 587 loop : -0.41 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2418 TYR 0.012 0.001 TYR A2121 PHE 0.010 0.001 PHE A 359 TRP 0.011 0.001 TRP A2046 HIS 0.006 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00250 (22775) covalent geometry : angle 0.49812 (30861) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.32774 ( 2) hydrogen bonds : bond 0.04185 ( 1000) hydrogen bonds : angle 4.57667 ( 2826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 201 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7377 (mttt) cc_final: 0.6979 (mmtp) REVERT: A 560 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: A 703 SER cc_start: 0.7699 (t) cc_final: 0.7128 (p) REVERT: A 994 MET cc_start: 0.5792 (pp-130) cc_final: 0.4724 (ptt) REVERT: A 1700 ASP cc_start: 0.7923 (p0) cc_final: 0.7652 (p0) REVERT: A 1702 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7446 (mtm-85) REVERT: A 1988 GLU cc_start: 0.8253 (mp0) cc_final: 0.7569 (mp0) REVERT: A 2051 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7917 (tptp) REVERT: A 2524 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 2799 VAL cc_start: 0.9134 (t) cc_final: 0.8902 (m) REVERT: A 2818 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8439 (mtt90) outliers start: 84 outliers final: 39 residues processed: 267 average time/residue: 0.4861 time to fit residues: 150.3004 Evaluate side-chains 226 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1822 ARG Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 2051 LYS Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2524 SER Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2739 MET Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2796 SER Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 277 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 HIS ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN A2099 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2371 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2879 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.087847 restraints weight = 37188.611| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.17 r_work: 0.3010 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22776 Z= 0.249 Angle : 0.566 7.436 30863 Z= 0.294 Chirality : 0.044 0.158 3496 Planarity : 0.005 0.056 3983 Dihedral : 4.854 57.405 3085 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.34 % Allowed : 23.17 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.16), residues: 2791 helix: 2.11 (0.16), residues: 1070 sheet: -0.59 (0.22), residues: 595 loop : -0.48 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2418 TYR 0.019 0.002 TYR A 555 PHE 0.016 0.002 PHE A2479 TRP 0.012 0.001 TRP A3113 HIS 0.009 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00590 (22775) covalent geometry : angle 0.56613 (30861) SS BOND : bond 0.00097 ( 1) SS BOND : angle 1.59307 ( 2) hydrogen bonds : bond 0.04767 ( 1000) hydrogen bonds : angle 4.52651 ( 2826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 186 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7367 (mttt) cc_final: 0.6938 (mmtp) REVERT: A 560 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: A 623 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8891 (tmmt) REVERT: A 853 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8438 (mmtt) REVERT: A 994 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.4813 (ptt) REVERT: A 1412 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8463 (pp) REVERT: A 1700 ASP cc_start: 0.7896 (p0) cc_final: 0.7680 (p0) REVERT: A 1702 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7488 (mtm-85) REVERT: A 1912 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: A 1988 GLU cc_start: 0.8289 (mp0) cc_final: 0.7603 (mp0) REVERT: A 2524 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 2525 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7916 (ttt90) REVERT: A 2648 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7851 (mmp) REVERT: A 2807 GLN cc_start: 0.9029 (mt0) cc_final: 0.8565 (pt0) REVERT: A 2818 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8394 (mtt90) outliers start: 108 outliers final: 43 residues processed: 270 average time/residue: 0.5232 time to fit residues: 163.5832 Evaluate side-chains 233 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1689 VAL Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2302 VAL Chi-restraints excluded: chain A residue 2349 ARG Chi-restraints excluded: chain A residue 2524 SER Chi-restraints excluded: chain A residue 2525 ARG Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2697 VAL Chi-restraints excluded: chain A residue 2739 MET Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2781 LEU Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2915 THR Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 133 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 0.0060 chunk 151 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2570 ASN A2879 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.090839 restraints weight = 36845.344| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.95 r_work: 0.3073 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22776 Z= 0.116 Angle : 0.489 8.464 30863 Z= 0.253 Chirality : 0.041 0.194 3496 Planarity : 0.004 0.055 3983 Dihedral : 4.530 56.261 3079 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.25 % Allowed : 24.30 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2791 helix: 2.24 (0.16), residues: 1070 sheet: -0.57 (0.22), residues: 593 loop : -0.41 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2877 TYR 0.014 0.001 TYR A3046 PHE 0.011 0.001 PHE A 962 TRP 0.014 0.001 TRP A2746 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00263 (22775) covalent geometry : angle 0.48853 (30861) SS BOND : bond 0.00104 ( 1) SS BOND : angle 1.36835 ( 2) hydrogen bonds : bond 0.03747 ( 1000) hydrogen bonds : angle 4.24387 ( 2826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7361 (mttt) cc_final: 0.6927 (mmtp) REVERT: A 560 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8326 (mmt) REVERT: A 611 ASN cc_start: 0.8887 (m-40) cc_final: 0.8541 (m-40) REVERT: A 612 GLU cc_start: 0.8636 (mp0) cc_final: 0.8230 (pm20) REVERT: A 623 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8902 (ptmt) REVERT: A 994 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.4774 (ptt) REVERT: A 1412 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8504 (pp) REVERT: A 1664 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7383 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7815 (pp20) cc_final: 0.7507 (pp20) REVERT: A 1700 ASP cc_start: 0.7895 (p0) cc_final: 0.7667 (p0) REVERT: A 1702 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8233 (t70) cc_final: 0.7798 (t70) REVERT: A 1848 GLN cc_start: 0.8435 (tp40) cc_final: 0.8213 (tp-100) REVERT: A 1857 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7473 (tt) REVERT: A 1912 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 1988 GLU cc_start: 0.8322 (mp0) cc_final: 0.7619 (mp0) REVERT: A 2648 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7765 (mmp) REVERT: A 2818 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (mtt90) REVERT: A 2908 ILE cc_start: 0.8987 (mp) cc_final: 0.8776 (mm) REVERT: A 3020 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.4529 (t80) outliers start: 81 outliers final: 35 residues processed: 264 average time/residue: 0.4901 time to fit residues: 149.8247 Evaluate side-chains 236 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1857 LEU Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2739 MET Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3111 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 211 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A1317 GLN ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN A2099 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2879 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087627 restraints weight = 37011.818| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.15 r_work: 0.3014 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22776 Z= 0.243 Angle : 0.565 9.634 30863 Z= 0.291 Chirality : 0.044 0.187 3496 Planarity : 0.004 0.055 3983 Dihedral : 4.655 54.438 3074 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.82 % Allowed : 23.94 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2791 helix: 2.16 (0.16), residues: 1064 sheet: -0.76 (0.22), residues: 603 loop : -0.46 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2418 TYR 0.019 0.002 TYR A 555 PHE 0.015 0.002 PHE A2479 TRP 0.012 0.001 TRP A3113 HIS 0.010 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00575 (22775) covalent geometry : angle 0.56450 (30861) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.59318 ( 2) hydrogen bonds : bond 0.04576 ( 1000) hydrogen bonds : angle 4.37237 ( 2826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 189 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7393 (mttt) cc_final: 0.6916 (mmtm) REVERT: A 470 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8780 (tttp) REVERT: A 560 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8389 (mmt) REVERT: A 623 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8908 (ptmt) REVERT: A 853 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8455 (mmtt) REVERT: A 994 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.4852 (ptt) REVERT: A 1317 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: A 1412 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8494 (pp) REVERT: A 1664 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7411 (ttp-170) REVERT: A 1700 ASP cc_start: 0.7882 (p0) cc_final: 0.7667 (p0) REVERT: A 1702 ARG cc_start: 0.7892 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8232 (t70) cc_final: 0.7831 (t70) REVERT: A 1912 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: A 1944 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 1988 GLU cc_start: 0.8338 (mp0) cc_final: 0.7632 (mp0) REVERT: A 2303 MET cc_start: 0.8484 (mtp) cc_final: 0.8082 (mtm) REVERT: A 2524 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8754 (m) REVERT: A 2648 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8024 (mmp) REVERT: A 2786 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8313 (t70) REVERT: A 2818 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8378 (mtt90) REVERT: A 3020 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.4405 (t80) outliers start: 95 outliers final: 58 residues processed: 263 average time/residue: 0.4667 time to fit residues: 143.5579 Evaluate side-chains 251 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1317 GLN Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1578 THR Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1715 SER Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2349 ARG Chi-restraints excluded: chain A residue 2524 SER Chi-restraints excluded: chain A residue 2617 LEU Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2739 MET Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2784 MET Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2878 ILE Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2915 THR Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 169 optimal weight: 0.9980 chunk 130 optimal weight: 0.0070 chunk 120 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 981 HIS A1212 ASN ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS A1901 GLN A1916 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2758 ASN A2879 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.090478 restraints weight = 37038.485| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.96 r_work: 0.3067 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22776 Z= 0.116 Angle : 0.510 10.049 30863 Z= 0.262 Chirality : 0.041 0.168 3496 Planarity : 0.004 0.056 3983 Dihedral : 4.469 53.377 3074 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.25 % Allowed : 24.62 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.16), residues: 2791 helix: 2.23 (0.16), residues: 1065 sheet: -0.67 (0.22), residues: 596 loop : -0.45 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2418 TYR 0.015 0.001 TYR A1296 PHE 0.011 0.001 PHE A 962 TRP 0.016 0.001 TRP A2746 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00263 (22775) covalent geometry : angle 0.50950 (30861) SS BOND : bond 0.00109 ( 1) SS BOND : angle 1.46614 ( 2) hydrogen bonds : bond 0.03742 ( 1000) hydrogen bonds : angle 4.19013 ( 2826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 199 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7342 (mttt) cc_final: 0.6862 (mptp) REVERT: A 560 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8385 (mmt) REVERT: A 612 GLU cc_start: 0.8657 (mp0) cc_final: 0.8345 (pm20) REVERT: A 623 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8902 (ptmt) REVERT: A 948 HIS cc_start: 0.8433 (m90) cc_final: 0.8138 (m-70) REVERT: A 994 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.4903 (ptt) REVERT: A 1321 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: A 1412 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8490 (pp) REVERT: A 1664 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7339 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7777 (pp20) cc_final: 0.7527 (pp20) REVERT: A 1791 ASP cc_start: 0.8237 (t70) cc_final: 0.7855 (t70) REVERT: A 1848 GLN cc_start: 0.8444 (tp40) cc_final: 0.8198 (tp-100) REVERT: A 1912 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: A 1988 GLU cc_start: 0.8356 (mp0) cc_final: 0.7678 (mp0) REVERT: A 2786 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8309 (t70) REVERT: A 2799 VAL cc_start: 0.9192 (t) cc_final: 0.8934 (m) REVERT: A 2807 GLN cc_start: 0.9047 (mt0) cc_final: 0.8604 (pt0) REVERT: A 2818 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8355 (mtt90) REVERT: A 2908 ILE cc_start: 0.8996 (mp) cc_final: 0.8786 (mm) REVERT: A 3020 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4491 (t80) REVERT: A 3101 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7982 (m170) outliers start: 81 outliers final: 45 residues processed: 256 average time/residue: 0.5129 time to fit residues: 152.6567 Evaluate side-chains 245 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1715 SER Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2119 VAL Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2739 MET Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2818 ARG Chi-restraints excluded: chain A residue 2913 VAL Chi-restraints excluded: chain A residue 2915 THR Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 24 optimal weight: 0.6980 chunk 220 optimal weight: 0.0040 chunk 141 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 222 optimal weight: 0.0170 chunk 21 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 chunk 256 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 700 ASN A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 HIS ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2879 GLN A3140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091855 restraints weight = 36661.992| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.22 r_work: 0.3070 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22776 Z= 0.102 Angle : 0.501 10.285 30863 Z= 0.255 Chirality : 0.041 0.189 3496 Planarity : 0.004 0.067 3983 Dihedral : 4.250 51.629 3073 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.69 % Allowed : 25.18 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 2791 helix: 2.35 (0.16), residues: 1065 sheet: -0.58 (0.22), residues: 593 loop : -0.39 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2418 TYR 0.010 0.001 TYR A 555 PHE 0.010 0.001 PHE A 962 TRP 0.015 0.001 TRP A2746 HIS 0.005 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00228 (22775) covalent geometry : angle 0.50111 (30861) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.27684 ( 2) hydrogen bonds : bond 0.03381 ( 1000) hydrogen bonds : angle 4.05191 ( 2826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 208 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7337 (mttt) cc_final: 0.6837 (mmtm) REVERT: A 470 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8809 (tttp) REVERT: A 560 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (mmt) REVERT: A 623 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8907 (ptmt) REVERT: A 948 HIS cc_start: 0.8407 (m90) cc_final: 0.8046 (m-70) REVERT: A 994 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.4915 (ptt) REVERT: A 1412 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8503 (pp) REVERT: A 1664 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7887 (pp20) cc_final: 0.7605 (pp20) REVERT: A 1700 ASP cc_start: 0.8059 (p0) cc_final: 0.7708 (p0) REVERT: A 1791 ASP cc_start: 0.8218 (t70) cc_final: 0.7816 (t70) REVERT: A 1848 GLN cc_start: 0.8416 (tp40) cc_final: 0.8174 (tp-100) REVERT: A 1912 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: A 1988 GLU cc_start: 0.8379 (mp0) cc_final: 0.7697 (mp0) REVERT: A 2786 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8303 (t70) REVERT: A 2795 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7373 (ptm160) REVERT: A 2799 VAL cc_start: 0.9220 (t) cc_final: 0.9013 (m) REVERT: A 2807 GLN cc_start: 0.9055 (mt0) cc_final: 0.8602 (pt0) REVERT: A 2825 MET cc_start: -0.0151 (ptp) cc_final: -0.0613 (ptp) REVERT: A 3020 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.4501 (t80) outliers start: 67 outliers final: 34 residues processed: 256 average time/residue: 0.5385 time to fit residues: 159.7117 Evaluate side-chains 234 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1715 SER Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1965 GLU Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 238 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 171 optimal weight: 0.4980 chunk 220 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 700 ASN A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN A2099 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2879 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090931 restraints weight = 36713.191| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.21 r_work: 0.3062 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22776 Z= 0.130 Angle : 0.510 11.317 30863 Z= 0.260 Chirality : 0.041 0.185 3496 Planarity : 0.004 0.073 3983 Dihedral : 4.050 48.104 3067 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.53 % Allowed : 25.58 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.16), residues: 2791 helix: 2.35 (0.16), residues: 1064 sheet: -0.59 (0.22), residues: 597 loop : -0.38 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2418 TYR 0.017 0.001 TYR A1296 PHE 0.011 0.001 PHE A 359 TRP 0.014 0.001 TRP A2746 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00303 (22775) covalent geometry : angle 0.50949 (30861) SS BOND : bond 0.00124 ( 1) SS BOND : angle 1.27638 ( 2) hydrogen bonds : bond 0.03565 ( 1000) hydrogen bonds : angle 4.05443 ( 2826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 200 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7363 (mttt) cc_final: 0.6861 (mmtm) REVERT: A 470 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8792 (tttp) REVERT: A 560 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8401 (mmt) REVERT: A 612 GLU cc_start: 0.8674 (mp0) cc_final: 0.8337 (pm20) REVERT: A 623 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8909 (ptmt) REVERT: A 948 HIS cc_start: 0.8434 (m90) cc_final: 0.8105 (m-70) REVERT: A 994 MET cc_start: 0.5934 (OUTLIER) cc_final: 0.4926 (ptt) REVERT: A 1317 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 1412 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8482 (pp) REVERT: A 1664 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7337 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7948 (pp20) cc_final: 0.7664 (pp20) REVERT: A 1700 ASP cc_start: 0.8042 (p0) cc_final: 0.7807 (p0) REVERT: A 1702 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7511 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8222 (t70) cc_final: 0.7826 (t70) REVERT: A 1897 MET cc_start: 0.8355 (tpt) cc_final: 0.8136 (tpp) REVERT: A 1912 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: A 1942 THR cc_start: 0.8709 (t) cc_final: 0.8424 (p) REVERT: A 1988 GLU cc_start: 0.8382 (mp0) cc_final: 0.7677 (mp0) REVERT: A 2786 HIS cc_start: 0.8724 (OUTLIER) cc_final: 0.8301 (t70) REVERT: A 2795 ARG cc_start: 0.7667 (ptm160) cc_final: 0.7385 (ptm160) REVERT: A 2799 VAL cc_start: 0.9150 (t) cc_final: 0.8922 (m) REVERT: A 2807 GLN cc_start: 0.9066 (mt0) cc_final: 0.8618 (pt0) REVERT: A 2825 MET cc_start: -0.0286 (ptp) cc_final: -0.0731 (ptp) REVERT: A 3020 TYR cc_start: 0.5204 (OUTLIER) cc_final: 0.4498 (t80) outliers start: 63 outliers final: 35 residues processed: 247 average time/residue: 0.4782 time to fit residues: 138.1809 Evaluate side-chains 237 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1715 SER Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1912 GLN Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2088 SER Chi-restraints excluded: chain A residue 2629 SER Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3099 LEU Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 128 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 119 optimal weight: 0.0970 chunk 193 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A2106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2758 ASN A2879 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.091902 restraints weight = 36714.593| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.20 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22776 Z= 0.111 Angle : 0.509 11.433 30863 Z= 0.258 Chirality : 0.041 0.182 3496 Planarity : 0.004 0.060 3983 Dihedral : 3.978 47.241 3067 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.33 % Allowed : 25.82 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.16), residues: 2791 helix: 2.37 (0.16), residues: 1065 sheet: -0.49 (0.22), residues: 590 loop : -0.38 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2418 TYR 0.011 0.001 TYR A 555 PHE 0.010 0.001 PHE A 962 TRP 0.015 0.001 TRP A2746 HIS 0.006 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00257 (22775) covalent geometry : angle 0.50894 (30861) SS BOND : bond 0.00099 ( 1) SS BOND : angle 1.27750 ( 2) hydrogen bonds : bond 0.03409 ( 1000) hydrogen bonds : angle 3.98998 ( 2826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7484 (mttt) cc_final: 0.7028 (mmtp) REVERT: A 470 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8778 (tttp) REVERT: A 560 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8384 (mmt) REVERT: A 611 ASN cc_start: 0.8729 (m-40) cc_final: 0.8509 (m110) REVERT: A 612 GLU cc_start: 0.8671 (mp0) cc_final: 0.8350 (pm20) REVERT: A 623 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8905 (ptmt) REVERT: A 703 SER cc_start: 0.7638 (t) cc_final: 0.7067 (p) REVERT: A 907 MET cc_start: 0.8437 (mtp) cc_final: 0.8234 (mtm) REVERT: A 948 HIS cc_start: 0.8442 (m90) cc_final: 0.8093 (m-70) REVERT: A 994 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.4933 (ptt) REVERT: A 1317 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6860 (tm-30) REVERT: A 1412 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8502 (pp) REVERT: A 1664 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7322 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7993 (pp20) cc_final: 0.7726 (pp20) REVERT: A 1700 ASP cc_start: 0.8110 (p0) cc_final: 0.7866 (p0) REVERT: A 1702 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7540 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8213 (t70) cc_final: 0.7813 (t70) REVERT: A 1848 GLN cc_start: 0.8421 (tp40) cc_final: 0.8186 (tp-100) REVERT: A 1942 THR cc_start: 0.8708 (t) cc_final: 0.8423 (p) REVERT: A 1988 GLU cc_start: 0.8423 (mp0) cc_final: 0.7710 (mp0) REVERT: A 2786 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.8320 (t70) REVERT: A 2795 ARG cc_start: 0.7629 (ptm160) cc_final: 0.7346 (ptm160) REVERT: A 2799 VAL cc_start: 0.9202 (t) cc_final: 0.8988 (m) REVERT: A 2807 GLN cc_start: 0.9064 (mt0) cc_final: 0.8613 (pt0) REVERT: A 2825 MET cc_start: -0.0523 (ptp) cc_final: -0.0847 (ptp) REVERT: A 2879 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7019 (mt0) REVERT: A 3020 TYR cc_start: 0.5200 (OUTLIER) cc_final: 0.4484 (t80) outliers start: 58 outliers final: 32 residues processed: 251 average time/residue: 0.5085 time to fit residues: 148.4922 Evaluate side-chains 240 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 177 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN A2099 ASN A2106 HIS ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.123813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091102 restraints weight = 36920.177| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.20 r_work: 0.3066 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22776 Z= 0.131 Angle : 0.526 12.073 30863 Z= 0.266 Chirality : 0.042 0.207 3496 Planarity : 0.004 0.067 3983 Dihedral : 3.994 47.787 3066 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.85 % Allowed : 26.39 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2791 helix: 2.34 (0.16), residues: 1066 sheet: -0.51 (0.22), residues: 593 loop : -0.36 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2418 TYR 0.012 0.001 TYR A2121 PHE 0.032 0.001 PHE A2627 TRP 0.016 0.001 TRP A2746 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00306 (22775) covalent geometry : angle 0.52621 (30861) SS BOND : bond 0.00125 ( 1) SS BOND : angle 1.30062 ( 2) hydrogen bonds : bond 0.03544 ( 1000) hydrogen bonds : angle 4.01604 ( 2826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5582 Ramachandran restraints generated. 2791 Oldfield, 0 Emsley, 2791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 261 LYS cc_start: 0.7491 (mttt) cc_final: 0.7035 (mmtp) REVERT: A 470 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8779 (tttp) REVERT: A 611 ASN cc_start: 0.8753 (m-40) cc_final: 0.8526 (m110) REVERT: A 612 GLU cc_start: 0.8671 (mp0) cc_final: 0.8350 (pm20) REVERT: A 623 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8909 (ptmt) REVERT: A 703 SER cc_start: 0.7639 (t) cc_final: 0.7084 (p) REVERT: A 948 HIS cc_start: 0.8441 (m90) cc_final: 0.8100 (m-70) REVERT: A 994 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.4951 (ptt) REVERT: A 1317 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 1412 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 1664 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7324 (ttp-170) REVERT: A 1678 GLU cc_start: 0.7996 (pp20) cc_final: 0.7747 (pp20) REVERT: A 1702 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8220 (t70) cc_final: 0.7825 (t70) REVERT: A 1848 GLN cc_start: 0.8434 (tp40) cc_final: 0.8197 (tp-100) REVERT: A 1942 THR cc_start: 0.8722 (t) cc_final: 0.8436 (p) REVERT: A 1988 GLU cc_start: 0.8428 (mp0) cc_final: 0.7708 (mp0) REVERT: A 2562 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8582 (tm) REVERT: A 2786 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8332 (t70) REVERT: A 2795 ARG cc_start: 0.7636 (ptm160) cc_final: 0.7358 (ptm160) REVERT: A 2799 VAL cc_start: 0.9174 (t) cc_final: 0.8957 (m) REVERT: A 2807 GLN cc_start: 0.9070 (mt0) cc_final: 0.8622 (pt0) REVERT: A 2825 MET cc_start: -0.0433 (ptp) cc_final: -0.0823 (ptp) REVERT: A 2879 GLN cc_start: 0.7398 (mm-40) cc_final: 0.6957 (mt0) REVERT: A 3020 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.4454 (t80) outliers start: 46 outliers final: 33 residues processed: 227 average time/residue: 0.5132 time to fit residues: 135.6678 Evaluate side-chains 233 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1664 ARG Chi-restraints excluded: chain A residue 1670 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1944 THR Chi-restraints excluded: chain A residue 1990 MET Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2221 LEU Chi-restraints excluded: chain A residue 2562 LEU Chi-restraints excluded: chain A residue 2644 LEU Chi-restraints excluded: chain A residue 2757 ASP Chi-restraints excluded: chain A residue 2772 THR Chi-restraints excluded: chain A residue 2786 HIS Chi-restraints excluded: chain A residue 2798 SER Chi-restraints excluded: chain A residue 2920 LEU Chi-restraints excluded: chain A residue 2947 THR Chi-restraints excluded: chain A residue 2952 THR Chi-restraints excluded: chain A residue 2963 VAL Chi-restraints excluded: chain A residue 2984 GLU Chi-restraints excluded: chain A residue 2994 ILE Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3020 TYR Chi-restraints excluded: chain A residue 3108 SER Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3205 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 28 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 200 optimal weight: 0.0010 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1796 HIS ** A1901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1916 ASN ** A2500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.123801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091051 restraints weight = 36866.480| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.23 r_work: 0.3065 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.180 22776 Z= 0.162 Angle : 0.678 59.162 30863 Z= 0.380 Chirality : 0.041 0.227 3496 Planarity : 0.004 0.066 3983 Dihedral : 4.000 47.800 3066 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.13 % Allowed : 26.14 % Favored : 71.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.16), residues: 2791 helix: 2.34 (0.16), residues: 1066 sheet: -0.51 (0.22), residues: 593 loop : -0.36 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A2418 TYR 0.013 0.001 TYR A2121 PHE 0.026 0.001 PHE A2627 TRP 0.016 0.001 TRP A2746 HIS 0.007 0.001 HIS A1182 Details of bonding type rmsd covalent geometry : bond 0.00369 (22775) covalent geometry : angle 0.67778 (30861) SS BOND : bond 0.00120 ( 1) SS BOND : angle 1.29280 ( 2) hydrogen bonds : bond 0.03555 ( 1000) hydrogen bonds : angle 4.00975 ( 2826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6345.50 seconds wall clock time: 108 minutes 56.90 seconds (6536.90 seconds total)