Starting phenix.real_space_refine on Sun Aug 24 22:26:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhh_53169/08_2025/9qhh_53169.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.866 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 4270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 22339 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 22339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2803, 22339 Classifications: {'peptide': 2803} Link IDs: {'PTRANS': 116, 'TRANS': 2686} Chain breaks: 5 Time building chain proxies: 4.83, per 1000 atoms: 0.22 Number of scatterers: 22339 At special positions: 0 Unit cell: (179.74, 189.2, 111.628, 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 4270 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 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: 92 helices and 30 sheets defined 42.3% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.558A 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 325 through 340 removed outlier: 4.398A pdb=" N TYR A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.551A pdb=" N ALA A 353 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 354' Processing helix chain 'A' and resid 355 through 379 removed outlier: 3.952A pdb=" N VAL A 362 " --> pdb=" O LYS A 358 " (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: 3.760A pdb=" N LYS A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 500 " --> pdb=" O ASP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.846A pdb=" N SER A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.647A pdb=" N THR A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 removed outlier: 3.990A pdb=" N ARG A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.592A pdb=" N GLN A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.520A pdb=" N LEU A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 614 through 629 Processing helix chain 'A' and resid 630 through 631 No H-bonds generated for 'chain 'A' and resid 630 through 631' Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.860A pdb=" N ILE A 636 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 700 removed outlier: 3.521A pdb=" N ASP A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.739A pdb=" N GLY A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 removed outlier: 4.309A pdb=" N GLU A 777 " --> pdb=" O LEU A 774 " (cutoff:3.500A) 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: 3.919A 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: 5.932A pdb=" N LYS A 873 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 4.940A 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: 4.013A pdb=" N ASN A 966 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 3.611A pdb=" N GLU A 980 " --> pdb=" O SER A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1139 removed outlier: 3.610A pdb=" N PHE A1139 " --> pdb=" O ILE A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1153 No H-bonds generated for 'chain 'A' and resid 1151 through 1153' 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 1208 Processing helix chain 'A' and resid 1212 through 1229 removed outlier: 4.179A pdb=" N SER A1217 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 4.913A 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 1312 removed outlier: 3.677A pdb=" N GLY A1293 " --> pdb=" O ASN A1289 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A1311 " --> pdb=" O VAL A1307 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A1312 " --> pdb=" O ARG A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1323 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 1375 removed outlier: 4.351A pdb=" N LEU A1370 " --> pdb=" O ALA A1366 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1375 " --> pdb=" O SER A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1388 removed outlier: 3.822A pdb=" N GLN A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1442 through 1460 removed outlier: 4.031A pdb=" N TYR A1446 " --> pdb=" O TRP A1442 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLN A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ARG A1452 " --> pdb=" O HIS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1479 Processing helix chain 'A' and resid 1480 through 1490 removed outlier: 3.947A 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: 3.855A pdb=" N SER A1526 " --> pdb=" O LYS A1522 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A1527 " --> pdb=" O ASP A1523 " (cutoff:3.500A) removed outlier: 3.521A 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 1620 Processing helix chain 'A' and resid 1621 through 1629 Processing helix chain 'A' and resid 1634 through 1639 Processing helix chain 'A' and resid 1646 through 1654 removed outlier: 4.243A pdb=" N TRP A1650 " --> pdb=" O SER A1646 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A1651 " --> pdb=" O ASP A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1676 removed outlier: 3.595A pdb=" N ASN A1675 " --> pdb=" O ASP A1671 " (cutoff:3.500A) removed outlier: 3.889A 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 1719 through 1730 Processing helix chain 'A' and resid 1733 through 1747 Processing helix chain 'A' and resid 1757 through 1761 Processing helix chain 'A' and resid 1769 through 1799 removed outlier: 4.034A pdb=" N GLY A1788 " --> pdb=" O GLN A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1857 removed outlier: 3.977A pdb=" N VAL A1844 " --> pdb=" O VAL A1840 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A1846 " --> pdb=" O GLU A1842 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A1847 " --> pdb=" O VAL A1843 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1885 Processing helix chain 'A' and resid 1898 through 1920 Processing helix chain 'A' and resid 1928 through 1945 Processing helix chain 'A' and resid 1945 through 1961 removed outlier: 3.616A pdb=" N GLY A1949 " --> pdb=" O GLY A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1964 through 1977 Processing helix chain 'A' and resid 1977 through 1982 Processing helix chain 'A' and resid 1985 through 2004 removed outlier: 3.613A pdb=" N THR A1989 " --> pdb=" O SER A1985 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A2004 " --> pdb=" O SER A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2038 removed outlier: 4.064A pdb=" N ARG A2038 " --> pdb=" O ARG A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2041 through 2059 removed outlier: 4.246A 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 2383 Processing helix chain 'A' and resid 2407 through 2412 removed outlier: 4.469A pdb=" N ASN A2411 " --> pdb=" O ALA A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2452 Processing helix chain 'A' and resid 2458 through 2470 Processing helix chain 'A' and resid 2610 through 2617 removed outlier: 3.502A pdb=" N ILE A2616 " --> pdb=" O ASP A2612 " (cutoff:3.500A) Processing helix chain 'A' and resid 2742 through 2748 Processing helix chain 'A' and resid 2780 through 2788 Processing helix chain 'A' and resid 2831 through 2844 Proline residue: A2839 - end of helix removed outlier: 3.623A pdb=" N ILE A2842 " --> pdb=" O ARG A2838 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A2843 " --> pdb=" O PRO A2839 " (cutoff:3.500A) Processing helix chain 'A' and resid 2845 through 2849 Processing helix chain 'A' and resid 2850 through 2854 Processing helix chain 'A' and resid 2868 through 2884 Processing helix chain 'A' and resid 3056 through 3070 removed outlier: 3.670A pdb=" N SER A3070 " --> pdb=" O GLN A3066 " (cutoff:3.500A) Processing helix chain 'A' and resid 3072 through 3086 Processing helix chain 'A' and resid 3097 through 3102 removed outlier: 3.755A pdb=" N HIS A3101 " --> pdb=" O GLU A3097 " (cutoff:3.500A) 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: 6.220A pdb=" N TYR A 345 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS A 509 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 347 " --> pdb=" O LYS A 509 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 316 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP A 348 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A 318 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A 319 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 652 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 651 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA4, first strand: chain 'A' and resid 935 through 936 Processing sheet with id=AA5, first strand: chain 'A' and resid 1145 through 1149 removed outlier: 6.462A pdb=" N ILE A 971 " --> pdb=" O ALA A1146 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A1148 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE A 973 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A1188 " --> pdb=" O SER A1282 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A1269 " --> pdb=" O THR A1276 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLN A1278 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N GLY A1267 " --> pdb=" O GLN A1278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1196 through 1197 Processing sheet with id=AA7, first strand: chain 'A' and resid 1464 through 1466 removed outlier: 4.199A pdb=" N ASN A1464 " --> pdb=" O ASP A1603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1679 through 1682 Processing sheet with id=AA9, first strand: chain 'A' and resid 1697 through 1698 removed outlier: 3.549A pdb=" N ARG A1717 " --> pdb=" O THR A1698 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1810 through 1812 removed outlier: 6.224A pdb=" N GLN A1826 " --> pdb=" O GLU A1811 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1815 through 1817 removed outlier: 6.522A pdb=" N ARG A1822 " --> pdb=" O ALA A1816 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.676A pdb=" N THR A2210 " --> pdb=" O ALA A2247 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLN A2249 " --> pdb=" O THR A2210 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A2212 " --> pdb=" O GLN A2249 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A2246 " --> pdb=" O THR A2268 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER A2270 " --> pdb=" O LEU A2246 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A2248 " --> pdb=" O SER A2270 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A2269 " --> pdb=" O VAL A2314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2091 through 2095 removed outlier: 6.403A pdb=" N LEU A2091 " --> pdb=" O LEU A2083 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A2083 " --> pdb=" O LEU A2091 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS A2093 " --> pdb=" O MET A2081 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET A2081 " --> pdb=" O HIS A2093 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLN A2200 " --> pdb=" O GLY A2079 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A2081 " --> pdb=" O GLN A2200 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU A2299 " --> pdb=" O THR A2295 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR A2295 " --> pdb=" O GLU A2299 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A2293 " --> pdb=" O PRO A2301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2098 through 2100 removed outlier: 6.759A pdb=" N PHE A2098 " --> pdb=" O ALA A2165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A2162 " --> pdb=" O LEU A2197 " (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: 6.877A pdb=" N LEU A2280 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A2324 " --> pdb=" O LEU A2280 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A2282 " --> pdb=" O ILE A2324 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A2339 " --> pdb=" O THR A2361 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N THR A2363 " --> pdb=" O GLY A2339 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A2360 " --> pdb=" O ASN A2401 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN A2403 " --> pdb=" O LEU A2360 " (cutoff:3.500A) removed outlier: 5.917A 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: 6.878A pdb=" N GLY A2346 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU A2372 " --> pdb=" O GLY A2346 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN A2348 " --> pdb=" O GLU A2372 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE A2374 " --> pdb=" O ASN A2348 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A2350 " --> pdb=" O PHE A2374 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE A2417 " --> pdb=" O ALA A2429 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR A2426 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A2435 " --> pdb=" O ARG A2432 " (cutoff:3.500A) removed outlier: 12.552A pdb=" N THR A2474 " --> pdb=" O GLY A2435 " (cutoff:3.500A) removed outlier: 12.252A pdb=" N GLN A2437 " --> pdb=" O THR A2474 " (cutoff:3.500A) removed outlier: 12.443A pdb=" N GLU A2476 " --> pdb=" O GLN A2437 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N ALA A2439 " --> pdb=" O GLU A2476 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N ARG A2478 " --> pdb=" O ALA A2439 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER A2441 " --> pdb=" O ARG A2478 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLN A2480 " --> pdb=" O SER A2441 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS A2443 " --> pdb=" O GLN A2480 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A2486 " --> pdb=" O PHE A2479 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY A2565 " --> pdb=" O GLY A2625 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY A2625 " --> pdb=" O GLY A2565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2505 through 2508 removed outlier: 6.286A pdb=" N PHE A2506 " --> pdb=" O ILE A2527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 2552 through 2554 removed outlier: 6.645A pdb=" N ILE A2553 " --> pdb=" O ALA A2601 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A2603 " --> pdb=" O ILE A2553 " (cutoff:3.500A) removed outlier: 6.580A 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: 6.983A pdb=" N ARG A2637 " --> pdb=" O CYS A2663 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU A2665 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A2639 " --> pdb=" O GLU A2665 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A2685 " --> pdb=" O ILE A2713 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A2715 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A2683 " --> pdb=" O GLU A2715 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2649 through 2651 removed outlier: 3.792A pdb=" N SER A2680 " --> pdb=" O LEU A2721 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2702 through 2704 removed outlier: 4.099A pdb=" N LYS A2673 " --> pdb=" O HIS A2727 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A2727 " --> pdb=" O LYS A2673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A2675 " --> pdb=" O LYS A2725 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A2725 " --> pdb=" O GLU A2675 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2731 through 2733 removed outlier: 6.293A pdb=" N ILE A2752 " --> pdb=" O THR A2816 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2738 through 2741 Processing sheet with id=AC7, first strand: chain 'A' and resid 2858 through 2860 Processing sheet with id=AC8, first strand: chain 'A' and resid 2909 through 2912 removed outlier: 6.491A pdb=" N MET A2909 " --> pdb=" O ILE A2973 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER A2975 " --> pdb=" O MET A2909 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A2911 " --> pdb=" O SER A2975 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A2950 " --> pdb=" O GLN A2958 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2935 through 2938 removed outlier: 6.249A pdb=" N ARG A2935 " --> pdb=" O SER A2989 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A2991 " --> pdb=" O ARG A2935 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A2937 " --> pdb=" O LEU A2991 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLU A2993 " --> pdb=" O LYS A2937 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A2988 " --> pdb=" O VAL A3008 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL A3008 " --> pdb=" O LEU A2988 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 3104 through 3110 Processing sheet with id=AD2, first strand: chain 'A' and resid 3122 through 3125 removed outlier: 4.567A pdb=" N THR A3122 " --> pdb=" O VAL A3185 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A3185 " --> pdb=" O THR A3122 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 3132 through 3135 1019 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.77 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4964 1.33 - 1.45: 4873 1.45 - 1.57: 12801 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 22776 Sorted by residual: bond pdb=" N ILE A2704 " pdb=" CA ILE A2704 " ideal model delta sigma weight residual 1.457 1.494 -0.036 9.00e-03 1.23e+04 1.63e+01 bond pdb=" N ILE A1419 " pdb=" CA ILE A1419 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.30e-03 1.16e+04 1.50e+01 bond pdb=" N VAL A2341 " pdb=" CA VAL A2341 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N ILE A 779 " pdb=" CA ILE A 779 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.20e-02 6.94e+03 1.23e+01 bond pdb=" N LEU A3044 " pdb=" CA LEU A3044 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.23e+01 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 30277 2.64 - 5.29: 517 5.29 - 7.93: 57 7.93 - 10.57: 10 10.57 - 13.22: 1 Bond angle restraints: 30862 Sorted by residual: angle pdb=" N ALA A2945 " pdb=" CA ALA A2945 " pdb=" C ALA A2945 " ideal model delta sigma weight residual 112.87 99.65 13.22 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N GLN A2787 " pdb=" CA GLN A2787 " pdb=" C GLN A2787 " ideal model delta sigma weight residual 111.71 101.81 9.90 1.15e+00 7.56e-01 7.41e+01 angle pdb=" N LEU A2781 " pdb=" CA LEU A2781 " pdb=" C LEU A2781 " ideal model delta sigma weight residual 111.28 104.12 7.16 1.09e+00 8.42e-01 4.32e+01 angle pdb=" N ASP A1524 " pdb=" CA ASP A1524 " pdb=" C ASP A1524 " ideal model delta sigma weight residual 114.56 106.94 7.62 1.27e+00 6.20e-01 3.60e+01 angle pdb=" N ILE A1419 " pdb=" CA ILE A1419 " pdb=" C ILE A1419 " ideal model delta sigma weight residual 113.20 107.78 5.42 9.60e-01 1.09e+00 3.19e+01 ... (remaining 30857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11825 17.93 - 35.87: 1540 35.87 - 53.80: 346 53.80 - 71.73: 81 71.73 - 89.67: 34 Dihedral angle restraints: 13826 sinusoidal: 5661 harmonic: 8165 Sorted by residual: dihedral pdb=" CB CYS A3182 " pdb=" SG CYS A3182 " pdb=" SG CYS A3205 " pdb=" CB CYS A3205 " ideal model delta sinusoidal sigma weight residual 93.00 48.99 44.01 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA ARG A2818 " pdb=" C ARG A2818 " pdb=" N ASP A2819 " pdb=" CA ASP A2819 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET A2967 " pdb=" C MET A2967 " pdb=" N VAL A2968 " pdb=" CA VAL A2968 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 13823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2650 0.052 - 0.104: 651 0.104 - 0.156: 161 0.156 - 0.208: 25 0.208 - 0.260: 9 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CA THR A2947 " pdb=" N THR A2947 " pdb=" C THR A2947 " pdb=" CB THR A2947 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE A 854 " pdb=" CA ILE A 854 " pdb=" CG1 ILE A 854 " pdb=" CG2 ILE A 854 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ALA A2945 " pdb=" N ALA A2945 " pdb=" C ALA A2945 " pdb=" CB ALA A2945 " both_signs ideal model delta sigma weight residual False 2.48 2.73 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3493 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1800 " 0.058 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A1801 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A1801 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A1801 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 354 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C PHE A 354 " 0.052 2.00e-02 2.50e+03 pdb=" O PHE A 354 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 355 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A2949 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C TYR A2949 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR A2949 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS A2950 " -0.017 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 473 2.67 - 3.23: 22001 3.23 - 3.79: 35281 3.79 - 4.34: 47876 4.34 - 4.90: 78231 Nonbonded interactions: 183862 Sorted by model distance: nonbonded pdb=" OD1 ASP A1700 " pdb=" N GLY A1701 " model vdw 2.114 3.120 nonbonded pdb=" O LEU A3098 " pdb=" OG1 THR A3102 " model vdw 2.195 3.040 nonbonded pdb=" ND2 ASN A2267 " pdb=" O GLY A2309 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN A3142 " pdb=" OG SER A3145 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLN A2646 " pdb=" N MET A2648 " model vdw 2.209 3.120 ... (remaining 183857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.730 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.006 0.054 22777 Z= 0.293 Angle : 0.810 13.215 30864 Z= 0.468 Chirality : 0.051 0.260 3496 Planarity : 0.006 0.103 3983 Dihedral : 17.215 89.666 8561 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.65 % Favored : 96.17 % Rotamer: Outliers : 0.84 % Allowed : 26.98 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.16), residues: 2791 helix: 1.04 (0.16), residues: 1013 sheet: -0.31 (0.23), residues: 561 loop : -0.86 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A2791 TYR 0.037 0.002 TYR A2497 PHE 0.034 0.003 PHE A 984 TRP 0.020 0.002 TRP A2046 HIS 0.012 0.002 HIS A2786 Details of bonding type rmsd covalent geometry : bond 0.00562 (22776) covalent geometry : angle 0.80982 (30862) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.00141 ( 2) hydrogen bonds : bond 0.14848 ( 1019) hydrogen bonds : angle 6.48294 ( 2871) *********************** 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 354 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 333 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.6962 (mmm) cc_final: 0.6678 (mmm) REVERT: A 1129 HIS cc_start: 0.7100 (m-70) cc_final: 0.6890 (m-70) REVERT: A 1850 LEU cc_start: 0.8114 (tm) cc_final: 0.7862 (tm) REVERT: A 2962 GLN cc_start: 0.1663 (OUTLIER) cc_final: 0.0505 (pp30) outliers start: 21 outliers final: 9 residues processed: 348 average time/residue: 0.1936 time to fit residues: 99.9050 Evaluate side-chains 254 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1434 HIS Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2433 GLU Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2632 THR Chi-restraints excluded: chain A residue 2783 LEU Chi-restraints excluded: chain A residue 2785 CYS Chi-restraints excluded: chain A residue 2853 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 3046 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 404 GLN A 480 GLN A 486 ASN A 923 GLN A1315 ASN ** A1502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1510 HIS A1514 ASN ** A1747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1795 GLN A1979 GLN A2123 ASN A2457 ASN A2580 GLN ** A2786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3067 GLN A3101 HIS A3140 GLN ** A3168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.150080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.112397 restraints weight = 49509.213| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.84 r_work: 0.3553 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22777 Z= 0.138 Angle : 0.605 10.364 30864 Z= 0.310 Chirality : 0.043 0.174 3496 Planarity : 0.005 0.074 3983 Dihedral : 5.011 71.407 3075 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 3.41 % Allowed : 24.05 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.16), residues: 2791 helix: 1.49 (0.16), residues: 1053 sheet: -0.38 (0.23), residues: 553 loop : -0.70 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2769 TYR 0.020 0.002 TYR A2949 PHE 0.019 0.002 PHE A2506 TRP 0.013 0.001 TRP A2046 HIS 0.007 0.001 HIS A2549 Details of bonding type rmsd covalent geometry : bond 0.00309 (22776) covalent geometry : angle 0.60450 (30862) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.28024 ( 2) hydrogen bonds : bond 0.04175 ( 1019) hydrogen bonds : angle 5.00525 ( 2871) *********************** 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 351 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 266 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8918 (pp) REVERT: A 388 ASN cc_start: 0.8041 (m110) cc_final: 0.7687 (m-40) REVERT: A 590 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7460 (tpp80) REVERT: A 594 ASP cc_start: 0.8404 (t0) cc_final: 0.8170 (t0) REVERT: A 630 LYS cc_start: 0.8921 (pptt) cc_final: 0.8672 (pptt) REVERT: A 695 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7630 (mtp-110) REVERT: A 778 PHE cc_start: 0.7845 (m-80) cc_final: 0.7324 (m-80) REVERT: A 1129 HIS cc_start: 0.7766 (m-70) cc_final: 0.7507 (m-70) REVERT: A 1257 LEU cc_start: 0.8889 (tp) cc_final: 0.8495 (mt) REVERT: A 1330 CYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8118 (p) REVERT: A 1456 MET cc_start: 0.8836 (tpp) cc_final: 0.8611 (tpp) REVERT: A 1568 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 1685 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 1853 MET cc_start: 0.8583 (ttt) cc_final: 0.8183 (ptm) REVERT: A 1910 MET cc_start: 0.8472 (mtp) cc_final: 0.8244 (mtp) REVERT: A 1928 ARG cc_start: 0.8401 (ptt90) cc_final: 0.8119 (ptt90) REVERT: A 1986 TYR cc_start: 0.6999 (t80) cc_final: 0.6425 (t80) REVERT: A 2055 ASP cc_start: 0.8434 (m-30) cc_final: 0.8170 (m-30) REVERT: A 2529 MET cc_start: 0.9154 (pmm) cc_final: 0.8652 (pmm) REVERT: A 2646 GLN cc_start: 0.8418 (tp-100) cc_final: 0.7735 (mm-40) REVERT: A 2675 GLU cc_start: -0.2775 (OUTLIER) cc_final: -0.3784 (mp0) REVERT: A 2789 MET cc_start: 0.3624 (mtt) cc_final: 0.2860 (mtt) REVERT: A 2962 GLN cc_start: 0.2869 (OUTLIER) cc_final: 0.1721 (pp30) REVERT: A 3157 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7830 (tp) outliers start: 85 outliers final: 35 residues processed: 324 average time/residue: 0.1661 time to fit residues: 82.5837 Evaluate side-chains 273 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2570 ASN Chi-restraints excluded: chain A residue 2584 GLN Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2675 GLU Chi-restraints excluded: chain A residue 2785 CYS Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 3032 PHE Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3157 ILE Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 101 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 chunk 257 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 ASN A1514 ASN A1666 GLN ** A1747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1979 GLN A2399 ASN A2457 ASN ** A2786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3101 HIS ** A3168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.146810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.109995 restraints weight = 48988.280| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.85 r_work: 0.3511 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22777 Z= 0.155 Angle : 0.568 10.138 30864 Z= 0.293 Chirality : 0.043 0.173 3496 Planarity : 0.004 0.064 3983 Dihedral : 4.507 72.998 3061 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 3.69 % Allowed : 23.28 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.16), residues: 2791 helix: 1.61 (0.16), residues: 1052 sheet: -0.37 (0.23), residues: 551 loop : -0.67 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A2671 TYR 0.019 0.002 TYR A2949 PHE 0.015 0.002 PHE A 984 TRP 0.022 0.001 TRP A2623 HIS 0.017 0.001 HIS A3101 Details of bonding type rmsd covalent geometry : bond 0.00344 (22776) covalent geometry : angle 0.56781 (30862) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.86303 ( 2) hydrogen bonds : bond 0.03883 ( 1019) hydrogen bonds : angle 4.81733 ( 2871) *********************** 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 343 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 251 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 302 LYS cc_start: 0.8626 (tptt) cc_final: 0.7402 (tptt) REVERT: A 306 TYR cc_start: 0.7604 (m-80) cc_final: 0.6643 (m-80) REVERT: A 330 SER cc_start: 0.9293 (t) cc_final: 0.8865 (p) REVERT: A 388 ASN cc_start: 0.7989 (m110) cc_final: 0.7758 (m-40) REVERT: A 437 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7612 (mtp) REVERT: A 557 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: A 594 ASP cc_start: 0.8363 (t0) cc_final: 0.8154 (t0) REVERT: A 619 ASN cc_start: 0.8950 (t0) cc_final: 0.8486 (m110) REVERT: A 630 LYS cc_start: 0.8977 (pptt) cc_final: 0.8669 (pptt) REVERT: A 693 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: A 695 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7718 (mtp-110) REVERT: A 778 PHE cc_start: 0.7772 (m-80) cc_final: 0.7360 (m-80) REVERT: A 870 ASP cc_start: 0.9029 (m-30) cc_final: 0.8716 (t0) REVERT: A 871 LEU cc_start: 0.8750 (mt) cc_final: 0.8499 (mt) REVERT: A 1129 HIS cc_start: 0.7713 (m-70) cc_final: 0.7467 (m-70) REVERT: A 1181 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.6882 (mp) REVERT: A 1257 LEU cc_start: 0.8986 (tp) cc_final: 0.8571 (mt) REVERT: A 1555 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7172 (p) REVERT: A 1568 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7819 (mm-30) REVERT: A 1640 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7228 (mm110) REVERT: A 1648 MET cc_start: 0.8547 (ptm) cc_final: 0.7861 (ptp) REVERT: A 1685 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9028 (tp) REVERT: A 1853 MET cc_start: 0.8589 (ttt) cc_final: 0.8138 (ptm) REVERT: A 1910 MET cc_start: 0.8516 (mtp) cc_final: 0.8280 (mtp) REVERT: A 1928 ARG cc_start: 0.8398 (ptt90) cc_final: 0.8034 (ptt90) REVERT: A 1965 GLU cc_start: 0.8008 (tp30) cc_final: 0.7541 (tp30) REVERT: A 1986 TYR cc_start: 0.7026 (t80) cc_final: 0.6732 (t80) REVERT: A 2123 ASN cc_start: 0.8234 (t0) cc_final: 0.7513 (t0) REVERT: A 2529 MET cc_start: 0.8995 (pmm) cc_final: 0.8500 (pmm) REVERT: A 2675 GLU cc_start: -0.2647 (OUTLIER) cc_final: -0.3718 (mp0) REVERT: A 2714 PHE cc_start: 0.4687 (m-80) cc_final: 0.4176 (m-80) REVERT: A 2962 GLN cc_start: 0.3354 (OUTLIER) cc_final: 0.1619 (pp30) REVERT: A 3061 MET cc_start: 0.8656 (ppp) cc_final: 0.8444 (ppp) REVERT: A 3123 ILE cc_start: 0.4430 (OUTLIER) cc_final: 0.3895 (mt) outliers start: 92 outliers final: 52 residues processed: 320 average time/residue: 0.1565 time to fit residues: 77.7630 Evaluate side-chains 293 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1535 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1555 THR Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2303 MET Chi-restraints excluded: chain A residue 2399 ASN Chi-restraints excluded: chain A residue 2484 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2584 GLN Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2671 ARG Chi-restraints excluded: chain A residue 2675 GLU Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2785 CYS Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 3006 LEU Chi-restraints excluded: chain A residue 3013 MET Chi-restraints excluded: chain A residue 3032 PHE Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 242 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 251 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1194 ASN A1315 ASN ** A1747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2457 ASN ** A2786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.146400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109292 restraints weight = 49735.801| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.79 r_work: 0.3503 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22777 Z= 0.133 Angle : 0.550 11.770 30864 Z= 0.281 Chirality : 0.042 0.160 3496 Planarity : 0.004 0.060 3983 Dihedral : 4.429 72.225 3061 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 3.77 % Allowed : 23.08 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.16), residues: 2791 helix: 1.73 (0.16), residues: 1061 sheet: -0.38 (0.23), residues: 549 loop : -0.68 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.015 0.001 TYR A2949 PHE 0.017 0.001 PHE A 570 TRP 0.016 0.001 TRP A2746 HIS 0.004 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00302 (22776) covalent geometry : angle 0.55003 (30862) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.71454 ( 2) hydrogen bonds : bond 0.03636 ( 1019) hydrogen bonds : angle 4.66967 ( 2871) *********************** 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 336 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 242 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8947 (pp) REVERT: A 305 TYR cc_start: 0.8663 (t80) cc_final: 0.8402 (t80) REVERT: A 306 TYR cc_start: 0.8210 (m-80) cc_final: 0.7196 (m-80) REVERT: A 330 SER cc_start: 0.9335 (t) cc_final: 0.8946 (p) REVERT: A 388 ASN cc_start: 0.8052 (m110) cc_final: 0.7781 (m110) REVERT: A 437 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: A 557 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7543 (m-30) REVERT: A 594 ASP cc_start: 0.8367 (t0) cc_final: 0.8160 (t0) REVERT: A 619 ASN cc_start: 0.8931 (t0) cc_final: 0.8468 (m110) REVERT: A 693 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: A 695 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7656 (mtp-110) REVERT: A 870 ASP cc_start: 0.9045 (m-30) cc_final: 0.8695 (t0) REVERT: A 871 LEU cc_start: 0.8715 (mt) cc_final: 0.8489 (mt) REVERT: A 1129 HIS cc_start: 0.7688 (m-70) cc_final: 0.7457 (m-70) REVERT: A 1181 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6799 (mp) REVERT: A 1257 LEU cc_start: 0.8949 (tp) cc_final: 0.8522 (mt) REVERT: A 1330 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 1555 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7202 (p) REVERT: A 1568 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 1640 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7075 (mm110) REVERT: A 1685 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9064 (tp) REVERT: A 1853 MET cc_start: 0.8541 (ttt) cc_final: 0.7629 (ptm) REVERT: A 1863 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.5527 (pmm) REVERT: A 1897 MET cc_start: 0.7880 (tpt) cc_final: 0.7653 (tpt) REVERT: A 1910 MET cc_start: 0.8491 (mtp) cc_final: 0.8258 (mtp) REVERT: A 1928 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8145 (ptt90) REVERT: A 1965 GLU cc_start: 0.8004 (tp30) cc_final: 0.7546 (tp30) REVERT: A 1986 TYR cc_start: 0.6989 (t80) cc_final: 0.6333 (t80) REVERT: A 2123 ASN cc_start: 0.8293 (t0) cc_final: 0.7933 (t0) REVERT: A 2425 MET cc_start: 0.8004 (mtt) cc_final: 0.7664 (mtp) REVERT: A 2529 MET cc_start: 0.8965 (pmm) cc_final: 0.8495 (pmm) REVERT: A 2675 GLU cc_start: -0.2747 (OUTLIER) cc_final: -0.3982 (mp0) REVERT: A 2786 HIS cc_start: 0.7727 (t70) cc_final: 0.7506 (t-170) REVERT: A 2962 GLN cc_start: 0.3372 (OUTLIER) cc_final: 0.1559 (pp30) REVERT: A 3123 ILE cc_start: 0.4346 (OUTLIER) cc_final: 0.3911 (mt) outliers start: 94 outliers final: 57 residues processed: 310 average time/residue: 0.1350 time to fit residues: 65.7865 Evaluate side-chains 296 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1535 ILE Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1555 THR Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2044 THR Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2484 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2570 ASN Chi-restraints excluded: chain A residue 2584 GLN Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2675 GLU Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2861 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 3006 LEU Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3063 TRP Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3123 ILE Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3204 THR Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 262 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 240 optimal weight: 0.7980 chunk 117 optimal weight: 0.0980 chunk 222 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 972 ASN A2164 GLN A2412 HIS A2457 ASN ** A2786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2860 GLN ** A3168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.147207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110578 restraints weight = 48490.601| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.85 r_work: 0.3525 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22777 Z= 0.105 Angle : 0.535 12.002 30864 Z= 0.272 Chirality : 0.041 0.171 3496 Planarity : 0.004 0.060 3983 Dihedral : 4.295 70.928 3060 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 3.17 % Allowed : 23.85 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.16), residues: 2791 helix: 1.93 (0.16), residues: 1053 sheet: -0.36 (0.23), residues: 552 loop : -0.60 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2038 TYR 0.019 0.001 TYR A1407 PHE 0.015 0.001 PHE A1139 TRP 0.015 0.001 TRP A2746 HIS 0.005 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00232 (22776) covalent geometry : angle 0.53499 (30862) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.53644 ( 2) hydrogen bonds : bond 0.03393 ( 1019) hydrogen bonds : angle 4.48370 ( 2871) *********************** 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 311 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 TYR cc_start: 0.8668 (t80) cc_final: 0.8412 (t80) REVERT: A 330 SER cc_start: 0.9318 (t) cc_final: 0.8830 (p) REVERT: A 437 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7521 (mtp) REVERT: A 557 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: A 619 ASN cc_start: 0.8886 (t0) cc_final: 0.8473 (m110) REVERT: A 630 LYS cc_start: 0.9064 (pptt) cc_final: 0.8643 (ptpp) REVERT: A 693 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 695 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7674 (mtp-110) REVERT: A 870 ASP cc_start: 0.8974 (m-30) cc_final: 0.8640 (t0) REVERT: A 871 LEU cc_start: 0.8645 (mt) cc_final: 0.8389 (mt) REVERT: A 957 MET cc_start: 0.8958 (tpp) cc_final: 0.8707 (tpp) REVERT: A 1129 HIS cc_start: 0.7653 (m-70) cc_final: 0.7421 (m-70) REVERT: A 1257 LEU cc_start: 0.8891 (tp) cc_final: 0.8472 (mt) REVERT: A 1330 CYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8133 (p) REVERT: A 1568 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7671 (pp20) REVERT: A 1685 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9086 (tp) REVERT: A 1700 ASP cc_start: 0.8082 (t70) cc_final: 0.7625 (t0) REVERT: A 1702 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8490 (m-30) cc_final: 0.8198 (m-30) REVERT: A 1853 MET cc_start: 0.8499 (ttt) cc_final: 0.7641 (ptm) REVERT: A 1863 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5455 (pmm) REVERT: A 1897 MET cc_start: 0.7898 (tpt) cc_final: 0.7671 (tpt) REVERT: A 1910 MET cc_start: 0.8504 (mtp) cc_final: 0.8280 (mtp) REVERT: A 1928 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (ptt90) REVERT: A 2055 ASP cc_start: 0.8402 (m-30) cc_final: 0.8058 (m-30) REVERT: A 2123 ASN cc_start: 0.8281 (t0) cc_final: 0.7921 (t0) REVERT: A 2425 MET cc_start: 0.8006 (mtt) cc_final: 0.7670 (mtp) REVERT: A 2529 MET cc_start: 0.8943 (pmm) cc_final: 0.8540 (pmm) REVERT: A 2628 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7403 (mtm180) REVERT: A 2789 MET cc_start: 0.3450 (mtt) cc_final: 0.2884 (ttm) REVERT: A 2962 GLN cc_start: 0.3016 (OUTLIER) cc_final: 0.1277 (pp30) REVERT: A 3061 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7978 (ppp) outliers start: 79 outliers final: 53 residues processed: 286 average time/residue: 0.1726 time to fit residues: 76.9377 Evaluate side-chains 288 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1465 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2036 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2556 LEU Chi-restraints excluded: chain A residue 2584 GLN Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2814 ARG Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 3017 THR Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3061 MET Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 56 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 197 optimal weight: 0.0060 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 ASN A2164 GLN A2412 HIS ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS A2748 GLN A2787 GLN A2996 GLN ** A3168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.137304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101965 restraints weight = 49708.851| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.75 r_work: 0.3386 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22777 Z= 0.283 Angle : 0.725 11.069 30864 Z= 0.373 Chirality : 0.048 0.229 3496 Planarity : 0.006 0.087 3983 Dihedral : 5.017 80.366 3060 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 4.18 % Allowed : 23.73 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2791 helix: 1.35 (0.15), residues: 1062 sheet: -0.80 (0.23), residues: 526 loop : -0.88 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2671 TYR 0.022 0.003 TYR A2121 PHE 0.020 0.003 PHE A1613 TRP 0.033 0.003 TRP A3117 HIS 0.009 0.002 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00651 (22776) covalent geometry : angle 0.72524 (30862) SS BOND : bond 0.00304 ( 1) SS BOND : angle 0.67747 ( 2) hydrogen bonds : bond 0.04925 ( 1019) hydrogen bonds : angle 5.08409 ( 2871) *********************** 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 349 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 245 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 388 ASN cc_start: 0.8093 (m110) cc_final: 0.7784 (m110) REVERT: A 470 LYS cc_start: 0.8532 (tppt) cc_final: 0.8214 (tppt) REVERT: A 557 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 584 GLU cc_start: 0.8652 (pm20) cc_final: 0.8272 (pm20) REVERT: A 619 ASN cc_start: 0.8893 (t0) cc_final: 0.8480 (m110) REVERT: A 630 LYS cc_start: 0.9055 (pptt) cc_final: 0.8672 (ptpp) REVERT: A 693 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: A 812 ASN cc_start: 0.8852 (t0) cc_final: 0.8600 (t0) REVERT: A 870 ASP cc_start: 0.9045 (m-30) cc_final: 0.8741 (t0) REVERT: A 1129 HIS cc_start: 0.7739 (m-70) cc_final: 0.7524 (m-70) REVERT: A 1330 CYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 1341 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 1685 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9193 (tp) REVERT: A 1791 ASP cc_start: 0.8589 (m-30) cc_final: 0.8230 (m-30) REVERT: A 1863 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.5862 (pmm) REVERT: A 1897 MET cc_start: 0.8038 (tpt) cc_final: 0.7776 (tpt) REVERT: A 1928 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (ptt90) REVERT: A 1965 GLU cc_start: 0.8145 (tp30) cc_final: 0.7692 (tp30) REVERT: A 2123 ASN cc_start: 0.8363 (t0) cc_final: 0.8034 (t0) REVERT: A 2425 MET cc_start: 0.8114 (mtt) cc_final: 0.7888 (mtp) REVERT: A 2529 MET cc_start: 0.8882 (pmm) cc_final: 0.8550 (pmm) REVERT: A 2538 PRO cc_start: 0.6725 (Cg_exo) cc_final: 0.5839 (Cg_endo) REVERT: A 2714 PHE cc_start: 0.5954 (m-80) cc_final: 0.5751 (m-80) REVERT: A 2789 MET cc_start: 0.4172 (mtt) cc_final: 0.3739 (ttm) REVERT: A 2986 TYR cc_start: 0.5423 (OUTLIER) cc_final: 0.5148 (t80) REVERT: A 3061 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (ppp) outliers start: 104 outliers final: 72 residues processed: 318 average time/residue: 0.1737 time to fit residues: 85.6103 Evaluate side-chains 309 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 898 GLU Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 985 ILE Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1341 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1532 TYR Chi-restraints excluded: chain A residue 1535 ILE Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1555 THR Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1850 LEU Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2032 ILE Chi-restraints excluded: chain A residue 2036 VAL Chi-restraints excluded: chain A residue 2044 THR Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2484 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2570 ASN Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2805 ARG Chi-restraints excluded: chain A residue 2853 TYR Chi-restraints excluded: chain A residue 2861 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 2973 ILE Chi-restraints excluded: chain A residue 2986 TYR Chi-restraints excluded: chain A residue 3032 PHE Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3061 MET Chi-restraints excluded: chain A residue 3063 TRP Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3126 THR Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3204 THR Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 3 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 256 optimal weight: 0.4980 chunk 246 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1834 HIS A1979 GLN A2164 GLN A2412 HIS A2457 ASN ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2748 GLN ** A2787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2996 GLN A3223 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.142472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.107475 restraints weight = 49817.545| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.59 r_work: 0.3533 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22777 Z= 0.136 Angle : 0.589 9.594 30864 Z= 0.299 Chirality : 0.043 0.169 3496 Planarity : 0.004 0.059 3983 Dihedral : 4.653 73.799 3060 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 25.09 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2791 helix: 1.72 (0.16), residues: 1052 sheet: -0.71 (0.23), residues: 537 loop : -0.75 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2814 TYR 0.013 0.001 TYR A2949 PHE 0.018 0.001 PHE A2506 TRP 0.014 0.001 TRP A2046 HIS 0.007 0.001 HIS A2412 Details of bonding type rmsd covalent geometry : bond 0.00309 (22776) covalent geometry : angle 0.58854 (30862) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.62511 ( 2) hydrogen bonds : bond 0.03817 ( 1019) hydrogen bonds : angle 4.68995 ( 2871) *********************** 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 322 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 242 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 TYR cc_start: 0.8279 (m-80) cc_final: 0.7963 (m-80) REVERT: A 330 SER cc_start: 0.9251 (t) cc_final: 0.8872 (p) REVERT: A 388 ASN cc_start: 0.8188 (m110) cc_final: 0.7892 (m110) REVERT: A 470 LYS cc_start: 0.8490 (tppt) cc_final: 0.8207 (tppt) REVERT: A 557 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 584 GLU cc_start: 0.8527 (pm20) cc_final: 0.8223 (pm20) REVERT: A 619 ASN cc_start: 0.8858 (t0) cc_final: 0.8489 (m110) REVERT: A 630 LYS cc_start: 0.9018 (pptt) cc_final: 0.8571 (ptpp) REVERT: A 693 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: A 695 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7797 (mtp-110) REVERT: A 1129 HIS cc_start: 0.7692 (m-70) cc_final: 0.7484 (m-70) REVERT: A 1330 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 1791 ASP cc_start: 0.8349 (m-30) cc_final: 0.7967 (m-30) REVERT: A 1863 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.5882 (pmm) REVERT: A 1928 ARG cc_start: 0.8369 (ptt90) cc_final: 0.8132 (ptt90) REVERT: A 1965 GLU cc_start: 0.8070 (tp30) cc_final: 0.7619 (tp30) REVERT: A 2123 ASN cc_start: 0.8320 (t0) cc_final: 0.8041 (t0) REVERT: A 2529 MET cc_start: 0.8729 (pmm) cc_final: 0.8420 (pmm) REVERT: A 2646 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7007 (pm20) REVERT: A 2962 GLN cc_start: 0.3411 (OUTLIER) cc_final: 0.1627 (pp30) REVERT: A 2986 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.4953 (t80) REVERT: A 3061 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8326 (ppp) outliers start: 80 outliers final: 58 residues processed: 299 average time/residue: 0.1692 time to fit residues: 79.3849 Evaluate side-chains 299 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 234 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1321 GLN Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1815 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1834 HIS Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1979 GLN Chi-restraints excluded: chain A residue 2036 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2532 VAL Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2793 ASP Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2949 TYR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 2973 ILE Chi-restraints excluded: chain A residue 2986 TYR Chi-restraints excluded: chain A residue 3032 PHE Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3061 MET Chi-restraints excluded: chain A residue 3063 TRP Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3177 LEU Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 210 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 222 optimal weight: 0.2980 chunk 163 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1834 HIS A2457 ASN ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2787 GLN ** A2856 HIS ** 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 = 0.4216 r_free = 0.4216 target = 0.141637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105749 restraints weight = 49606.535| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.82 r_work: 0.3466 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22777 Z= 0.118 Angle : 0.570 10.060 30864 Z= 0.289 Chirality : 0.042 0.160 3496 Planarity : 0.004 0.053 3983 Dihedral : 4.527 72.197 3060 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 3.09 % Allowed : 25.05 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2791 helix: 1.87 (0.16), residues: 1057 sheet: -0.70 (0.22), residues: 545 loop : -0.66 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2877 TYR 0.022 0.001 TYR A3154 PHE 0.023 0.001 PHE A3144 TRP 0.015 0.001 TRP A2746 HIS 0.015 0.001 HIS A1834 Details of bonding type rmsd covalent geometry : bond 0.00264 (22776) covalent geometry : angle 0.56970 (30862) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.52337 ( 2) hydrogen bonds : bond 0.03581 ( 1019) hydrogen bonds : angle 4.54724 ( 2871) *********************** 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 317 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 240 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 TYR cc_start: 0.8259 (m-80) cc_final: 0.8051 (m-80) REVERT: A 330 SER cc_start: 0.9338 (t) cc_final: 0.8946 (p) REVERT: A 388 ASN cc_start: 0.8131 (m110) cc_final: 0.7812 (m110) REVERT: A 470 LYS cc_start: 0.8449 (tppt) cc_final: 0.8101 (tppt) REVERT: A 557 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 584 GLU cc_start: 0.8577 (pm20) cc_final: 0.8214 (pm20) REVERT: A 619 ASN cc_start: 0.8860 (t0) cc_final: 0.8477 (m110) REVERT: A 630 LYS cc_start: 0.9021 (pptt) cc_final: 0.8621 (ptpp) REVERT: A 693 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: A 695 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7728 (mtp-110) REVERT: A 957 MET cc_start: 0.9015 (tpp) cc_final: 0.8747 (tpp) REVERT: A 1129 HIS cc_start: 0.7708 (m-70) cc_final: 0.7503 (m-70) REVERT: A 1330 CYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8132 (p) REVERT: A 1412 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7266 (pp) REVERT: A 1702 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8279 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8540 (m-30) cc_final: 0.8097 (m-30) REVERT: A 1863 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6004 (pmm) REVERT: A 1928 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8127 (ptt90) REVERT: A 1965 GLU cc_start: 0.8019 (tp30) cc_final: 0.7566 (tp30) REVERT: A 2123 ASN cc_start: 0.8479 (t0) cc_final: 0.8132 (t0) REVERT: A 2529 MET cc_start: 0.8914 (pmm) cc_final: 0.8590 (pmm) REVERT: A 2646 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7104 (pm20) REVERT: A 2962 GLN cc_start: 0.3472 (OUTLIER) cc_final: 0.1788 (pp30) REVERT: A 2986 TYR cc_start: 0.5353 (OUTLIER) cc_final: 0.4973 (t80) outliers start: 77 outliers final: 57 residues processed: 292 average time/residue: 0.1768 time to fit residues: 79.6423 Evaluate side-chains 298 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 805 THR 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 930 ILE Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1834 HIS Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1929 LEU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 2036 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2491 LEU Chi-restraints excluded: chain A residue 2532 VAL Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2648 MET Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2805 ARG Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2949 TYR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 2973 ILE Chi-restraints excluded: chain A residue 2986 TYR Chi-restraints excluded: chain A residue 3032 PHE Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3187 SER Chi-restraints excluded: chain A residue 3204 THR Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 229 optimal weight: 0.2980 chunk 270 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 172 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2457 ASN ** A2787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.142646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.106662 restraints weight = 49844.860| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.84 r_work: 0.3480 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22777 Z= 0.111 Angle : 0.588 14.636 30864 Z= 0.296 Chirality : 0.042 0.222 3496 Planarity : 0.004 0.058 3983 Dihedral : 4.457 70.767 3060 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.03 % Rotamer: Outliers : 2.81 % Allowed : 25.21 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2791 helix: 1.94 (0.16), residues: 1057 sheet: -0.60 (0.23), residues: 542 loop : -0.60 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A2458 TYR 0.015 0.001 TYR A2707 PHE 0.029 0.001 PHE A2506 TRP 0.014 0.001 TRP A2746 HIS 0.018 0.001 HIS A1834 Details of bonding type rmsd covalent geometry : bond 0.00245 (22776) covalent geometry : angle 0.58833 (30862) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.49432 ( 2) hydrogen bonds : bond 0.03447 ( 1019) hydrogen bonds : angle 4.44959 ( 2871) *********************** 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 310 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 TYR cc_start: 0.8373 (m-80) cc_final: 0.8104 (m-80) REVERT: A 330 SER cc_start: 0.9323 (t) cc_final: 0.8925 (p) REVERT: A 388 ASN cc_start: 0.8133 (m110) cc_final: 0.7798 (m110) REVERT: A 470 LYS cc_start: 0.8461 (tppt) cc_final: 0.8127 (tppt) REVERT: A 557 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: A 584 GLU cc_start: 0.8558 (pm20) cc_final: 0.8215 (pm20) REVERT: A 594 ASP cc_start: 0.8326 (t0) cc_final: 0.8082 (t0) REVERT: A 619 ASN cc_start: 0.8844 (t0) cc_final: 0.8455 (m110) REVERT: A 630 LYS cc_start: 0.9029 (pptt) cc_final: 0.8629 (ptpp) REVERT: A 693 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: A 695 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7737 (mtp-110) REVERT: A 957 MET cc_start: 0.9018 (tpp) cc_final: 0.8735 (tpp) REVERT: A 1129 HIS cc_start: 0.7679 (m-70) cc_final: 0.7473 (m-70) REVERT: A 1330 CYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 1412 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7286 (pp) REVERT: A 1702 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8294 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8529 (m-30) cc_final: 0.8081 (m-30) REVERT: A 1863 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6004 (pmm) REVERT: A 1928 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8136 (ptt90) REVERT: A 1965 GLU cc_start: 0.8024 (tp30) cc_final: 0.7576 (tp30) REVERT: A 2055 ASP cc_start: 0.8445 (m-30) cc_final: 0.8086 (m-30) REVERT: A 2123 ASN cc_start: 0.8528 (t0) cc_final: 0.8167 (t0) REVERT: A 2425 MET cc_start: 0.8112 (mtt) cc_final: 0.7717 (mmm) REVERT: A 2529 MET cc_start: 0.8885 (pmm) cc_final: 0.8517 (pmm) REVERT: A 2646 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7842 (mm-40) REVERT: A 2962 GLN cc_start: 0.3271 (OUTLIER) cc_final: 0.1546 (pp30) REVERT: A 2986 TYR cc_start: 0.5133 (OUTLIER) cc_final: 0.4716 (t80) outliers start: 70 outliers final: 53 residues processed: 293 average time/residue: 0.1746 time to fit residues: 81.2003 Evaluate side-chains 291 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 805 THR 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 898 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1330 CYS Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1850 LEU Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1929 LEU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 2036 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2532 VAL Chi-restraints excluded: chain A residue 2570 ASN Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2805 ARG Chi-restraints excluded: chain A residue 2861 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2949 TYR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 2986 TYR Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3204 THR Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 178 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 191 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 197 optimal weight: 0.0070 chunk 250 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2457 ASN ** A2787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.142855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107078 restraints weight = 49743.192| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.85 r_work: 0.3490 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22777 Z= 0.111 Angle : 0.590 15.233 30864 Z= 0.298 Chirality : 0.042 0.192 3496 Planarity : 0.004 0.060 3983 Dihedral : 4.394 69.294 3060 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 2.85 % Allowed : 25.25 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 2791 helix: 2.00 (0.16), residues: 1059 sheet: -0.52 (0.23), residues: 542 loop : -0.55 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2877 TYR 0.017 0.001 TYR A 305 PHE 0.029 0.001 PHE A2506 TRP 0.017 0.001 TRP A 662 HIS 0.005 0.001 HIS A2856 Details of bonding type rmsd covalent geometry : bond 0.00247 (22776) covalent geometry : angle 0.59029 (30862) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.47082 ( 2) hydrogen bonds : bond 0.03360 ( 1019) hydrogen bonds : angle 4.38084 ( 2871) ********************** 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 302 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 231 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.7877 (mmm) cc_final: 0.6506 (pmm) REVERT: A 330 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8902 (p) REVERT: A 388 ASN cc_start: 0.8124 (m110) cc_final: 0.7778 (m110) REVERT: A 470 LYS cc_start: 0.8448 (tppt) cc_final: 0.8108 (tppt) REVERT: A 557 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: A 584 GLU cc_start: 0.8568 (pm20) cc_final: 0.8224 (pm20) REVERT: A 594 ASP cc_start: 0.8261 (t0) cc_final: 0.8025 (t0) REVERT: A 619 ASN cc_start: 0.8828 (t0) cc_final: 0.8433 (m110) REVERT: A 630 LYS cc_start: 0.9063 (pptt) cc_final: 0.8596 (ptpp) REVERT: A 693 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: A 695 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7733 (mtp-110) REVERT: A 850 PHE cc_start: 0.8327 (m-80) cc_final: 0.8001 (m-80) REVERT: A 957 MET cc_start: 0.9010 (tpp) cc_final: 0.8694 (tpp) REVERT: A 1129 HIS cc_start: 0.7650 (m-70) cc_final: 0.7445 (m-70) REVERT: A 1412 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 1702 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8320 (mtm-85) REVERT: A 1791 ASP cc_start: 0.8540 (m-30) cc_final: 0.8079 (m-30) REVERT: A 1863 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6026 (pmm) REVERT: A 1910 MET cc_start: 0.8359 (mtp) cc_final: 0.8091 (mtp) REVERT: A 1928 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8119 (ptt90) REVERT: A 1965 GLU cc_start: 0.8011 (tp30) cc_final: 0.7553 (tp30) REVERT: A 2123 ASN cc_start: 0.8549 (t0) cc_final: 0.8176 (t0) REVERT: A 2529 MET cc_start: 0.8863 (pmm) cc_final: 0.8489 (pmm) REVERT: A 2646 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7359 (pm20) REVERT: A 2962 GLN cc_start: 0.3318 (OUTLIER) cc_final: 0.1700 (pp30) REVERT: A 2986 TYR cc_start: 0.5122 (OUTLIER) cc_final: 0.4711 (t80) outliers start: 71 outliers final: 56 residues processed: 282 average time/residue: 0.1681 time to fit residues: 73.9275 Evaluate side-chains 292 residues out of total 2491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 693 GLU Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 805 THR 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 898 GLU Chi-restraints excluded: chain A residue 941 ILE Chi-restraints excluded: chain A residue 942 ASN Chi-restraints excluded: chain A residue 948 HIS Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1412 ILE Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain A residue 1646 SER Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1764 THR Chi-restraints excluded: chain A residue 1813 ILE Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1862 ILE Chi-restraints excluded: chain A residue 1863 MET Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 ARG Chi-restraints excluded: chain A residue 1929 LEU Chi-restraints excluded: chain A residue 1931 SER Chi-restraints excluded: chain A residue 1939 SER Chi-restraints excluded: chain A residue 1984 THR Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2457 ASN Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain A residue 2532 VAL Chi-restraints excluded: chain A residue 2570 ASN Chi-restraints excluded: chain A residue 2576 ILE Chi-restraints excluded: chain A residue 2628 ARG Chi-restraints excluded: chain A residue 2678 LEU Chi-restraints excluded: chain A residue 2790 VAL Chi-restraints excluded: chain A residue 2861 LEU Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2949 TYR Chi-restraints excluded: chain A residue 2961 TYR Chi-restraints excluded: chain A residue 2962 GLN Chi-restraints excluded: chain A residue 2972 MET Chi-restraints excluded: chain A residue 2973 ILE Chi-restraints excluded: chain A residue 2986 TYR Chi-restraints excluded: chain A residue 3035 THR Chi-restraints excluded: chain A residue 3101 HIS Chi-restraints excluded: chain A residue 3110 VAL Chi-restraints excluded: chain A residue 3204 THR Chi-restraints excluded: chain A residue 3207 TRP Chi-restraints excluded: chain A residue 3221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 261 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 190 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1834 HIS ** A2457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.143387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107525 restraints weight = 49890.339| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.86 r_work: 0.3500 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22777 Z= 0.106 Angle : 0.585 16.066 30864 Z= 0.293 Chirality : 0.042 0.184 3496 Planarity : 0.004 0.057 3983 Dihedral : 4.344 68.690 3060 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 2.77 % Allowed : 25.37 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2791 helix: 2.06 (0.16), residues: 1059 sheet: -0.52 (0.23), residues: 546 loop : -0.52 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A2877 TYR 0.017 0.001 TYR A 305 PHE 0.020 0.001 PHE A 433 TRP 0.015 0.001 TRP A 662 HIS 0.004 0.001 HIS A2856 Details of bonding type rmsd covalent geometry : bond 0.00237 (22776) covalent geometry : angle 0.58541 (30862) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.44333 ( 2) hydrogen bonds : bond 0.03260 ( 1019) hydrogen bonds : angle 4.33218 ( 2871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8059.98 seconds wall clock time: 138 minutes 25.54 seconds (8305.54 seconds total)