Starting phenix.real_space_refine on Thu Mar 5 07:31:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911.map" model { file = "/net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxj_30911/03_2026/7dxj_30911_neut.cif" } resolution = 3.6 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= 0.000 sd= 0.019 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 129 5.16 5 C 13129 2.51 5 N 3524 2.21 5 O 3709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20491 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2353, 18458 Classifications: {'peptide': 2353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 106, 'TRANS': 2246} Chain breaks: 19 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2033 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.40, per 1000 atoms: 0.21 Number of scatterers: 20491 At special positions: 0 Unit cell: (140.4, 106.65, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 3709 8.00 N 3524 7.00 C 13129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 768 " - pdb=" SG CYS A 803 " 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: 1.59 Conformation dependent library (CDL) restraints added in 1.0 seconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5014 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 91 through 108 removed outlier: 3.679A pdb=" N ALA A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.799A pdb=" N ARG A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.699A pdb=" N LYS A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 189 Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.808A pdb=" N VAL A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 197 through 213 removed outlier: 3.709A pdb=" N TYR A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 236 through 239 removed outlier: 3.813A pdb=" N ALA A 239 " --> pdb=" O GLY A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 240 through 253 removed outlier: 3.611A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 276 removed outlier: 3.583A pdb=" N ARG A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.687A pdb=" N LEU A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.107A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 382 Processing helix chain 'A' and resid 384 through 393 removed outlier: 3.642A pdb=" N ALA A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.659A pdb=" N HIS A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 762 through 779 Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 815 through 835 removed outlier: 5.289A pdb=" N MET A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 835 " --> pdb=" O MET A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 857 through 868 Processing helix chain 'A' and resid 872 through 883 Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.522A pdb=" N GLY A 913 " --> pdb=" O HIS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 931 Processing helix chain 'A' and resid 932 through 934 No H-bonds generated for 'chain 'A' and resid 932 through 934' Processing helix chain 'A' and resid 944 through 957 Processing helix chain 'A' and resid 991 through 1011 removed outlier: 3.764A pdb=" N GLU A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1032 removed outlier: 4.388A pdb=" N THR A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A1023 " --> pdb=" O PHE A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1062 through 1070 removed outlier: 4.070A pdb=" N ILE A1066 " --> pdb=" O MET A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1095 removed outlier: 3.513A pdb=" N HIS A1082 " --> pdb=" O ASP A1078 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A1084 " --> pdb=" O SER A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 4.051A pdb=" N LEU A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1130 through 1153 removed outlier: 3.691A pdb=" N VAL A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 Processing helix chain 'A' and resid 1259 through 1275 removed outlier: 3.882A pdb=" N LEU A1270 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1304 through 1314 removed outlier: 3.623A pdb=" N VAL A1308 " --> pdb=" O ALA A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1369 Processing helix chain 'A' and resid 1421 through 1435 Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.943A pdb=" N GLN A1441 " --> pdb=" O CYS A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1481 Processing helix chain 'A' and resid 1485 through 1488 removed outlier: 3.510A pdb=" N ALA A1488 " --> pdb=" O GLU A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1485 through 1488' Processing helix chain 'A' and resid 1489 through 1502 Processing helix chain 'A' and resid 1512 through 1526 removed outlier: 3.575A pdb=" N SER A1526 " --> pdb=" O GLY A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1544 Proline residue: A1540 - end of helix Processing helix chain 'A' and resid 1558 through 1574 Processing helix chain 'A' and resid 1577 through 1595 removed outlier: 3.863A pdb=" N GLU A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1616 removed outlier: 3.537A pdb=" N TRP A1599 " --> pdb=" O ASN A1595 " (cutoff:3.500A) Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1623 through 1637 removed outlier: 3.557A pdb=" N LEU A1627 " --> pdb=" O SER A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1642 Processing helix chain 'A' and resid 1645 through 1651 removed outlier: 3.567A pdb=" N LEU A1649 " --> pdb=" O VAL A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1682 removed outlier: 3.578A pdb=" N VAL A1665 " --> pdb=" O SER A1661 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A1678 " --> pdb=" O ALA A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1695 removed outlier: 3.993A pdb=" N VAL A1688 " --> pdb=" O THR A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1713 Processing helix chain 'A' and resid 1731 through 1753 Processing helix chain 'A' and resid 1761 through 1785 removed outlier: 3.510A pdb=" N HIS A1765 " --> pdb=" O SER A1761 " (cutoff:3.500A) Processing helix chain 'A' and resid 1789 through 1797 Processing helix chain 'A' and resid 1810 through 1820 Processing helix chain 'A' and resid 1825 through 1839 removed outlier: 3.743A pdb=" N VAL A1829 " --> pdb=" O HIS A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1852 Processing helix chain 'A' and resid 1884 through 1905 removed outlier: 4.129A pdb=" N GLU A1888 " --> pdb=" O MET A1884 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A1889 " --> pdb=" O CYS A1885 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A1890 " --> pdb=" O ASN A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1919 removed outlier: 3.574A pdb=" N THR A1913 " --> pdb=" O SER A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1926 removed outlier: 3.549A pdb=" N LEU A1926 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1940 Processing helix chain 'A' and resid 1942 through 1956 Processing helix chain 'A' and resid 1962 through 1973 Processing helix chain 'A' and resid 1980 through 1991 removed outlier: 3.726A pdb=" N THR A1986 " --> pdb=" O GLY A1982 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A1991 " --> pdb=" O LEU A1987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 1995 removed outlier: 3.628A pdb=" N THR A1995 " --> pdb=" O LEU A1992 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1992 through 1995' Processing helix chain 'A' and resid 1997 through 2017 Processing helix chain 'A' and resid 2019 through 2025 removed outlier: 3.512A pdb=" N ALA A2025 " --> pdb=" O GLN A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2042 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2062 removed outlier: 4.211A pdb=" N TYR A2052 " --> pdb=" O HIS A2048 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A2062 " --> pdb=" O PHE A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2103 Processing helix chain 'A' and resid 2112 through 2121 removed outlier: 3.837A pdb=" N ARG A2121 " --> pdb=" O GLU A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2140 through 2153 Processing helix chain 'A' and resid 2158 through 2178 removed outlier: 4.123A pdb=" N GLU A2162 " --> pdb=" O SER A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2204 removed outlier: 3.776A pdb=" N LYS A2200 " --> pdb=" O ALA A2196 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A2204 " --> pdb=" O LYS A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2228 Proline residue: A2215 - end of helix Processing helix chain 'A' and resid 2229 through 2231 No H-bonds generated for 'chain 'A' and resid 2229 through 2231' Processing helix chain 'A' and resid 2241 through 2263 Processing helix chain 'A' and resid 2269 through 2284 removed outlier: 3.559A pdb=" N LEU A2284 " --> pdb=" O LEU A2280 " (cutoff:3.500A) Processing helix chain 'A' and resid 2284 through 2292 Processing helix chain 'A' and resid 2296 through 2313 Processing helix chain 'A' and resid 2351 through 2369 removed outlier: 4.145A pdb=" N GLU A2357 " --> pdb=" O THR A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2374 through 2379 removed outlier: 3.716A pdb=" N SER A2378 " --> pdb=" O LYS A2375 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A2379 " --> pdb=" O ARG A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2396 Processing helix chain 'A' and resid 2401 through 2406 Processing helix chain 'A' and resid 2408 through 2414 removed outlier: 3.661A pdb=" N TRP A2412 " --> pdb=" O PRO A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2453 removed outlier: 3.518A pdb=" N GLY A2453 " --> pdb=" O ILE A2449 " (cutoff:3.500A) Processing helix chain 'A' and resid 2456 through 2471 removed outlier: 3.907A pdb=" N PHE A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A2471 " --> pdb=" O LEU A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2509 Processing helix chain 'A' and resid 2539 through 2558 removed outlier: 3.736A pdb=" N LEU A2543 " --> pdb=" O PHE A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2622 removed outlier: 3.887A pdb=" N ASN A2622 " --> pdb=" O VAL A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2680 removed outlier: 3.992A pdb=" N CYS A2667 " --> pdb=" O ASP A2663 " (cutoff:3.500A) Processing helix chain 'A' and resid 2689 through 2704 Processing helix chain 'A' and resid 2709 through 2727 removed outlier: 3.570A pdb=" N PHE A2713 " --> pdb=" O GLU A2709 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2749 Proline residue: A2740 - end of helix removed outlier: 3.633A pdb=" N LEU A2749 " --> pdb=" O ALA A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2767 Proline residue: A2758 - end of helix Processing helix chain 'A' and resid 2771 through 2786 Processing helix chain 'A' and resid 2795 through 2798 Processing helix chain 'A' and resid 2799 through 2812 Processing helix chain 'A' and resid 2822 through 2839 Processing helix chain 'A' and resid 2844 through 2860 removed outlier: 3.879A pdb=" N SER A2848 " --> pdb=" O GLY A2844 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2884 Processing helix chain 'A' and resid 2888 through 2904 Processing helix chain 'A' and resid 2907 through 2922 Processing helix chain 'A' and resid 2946 through 2963 Processing helix chain 'A' and resid 2965 through 2984 Proline residue: A2977 - end of helix removed outlier: 4.091A pdb=" N PHE A2984 " --> pdb=" O LEU A2980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2985 through 2998 removed outlier: 4.201A pdb=" N ILE A2989 " --> pdb=" O PRO A2985 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A2998 " --> pdb=" O ILE A2994 " (cutoff:3.500A) Processing helix chain 'A' and resid 3005 through 3018 Processing helix chain 'A' and resid 3021 through 3040 removed outlier: 3.696A pdb=" N MET A3027 " --> pdb=" O GLY A3023 " (cutoff:3.500A) Processing helix chain 'A' and resid 3044 through 3059 Processing helix chain 'A' and resid 3065 through 3067 No H-bonds generated for 'chain 'A' and resid 3065 through 3067' Processing helix chain 'A' and resid 3068 through 3073 Processing helix chain 'A' and resid 3080 through 3096 removed outlier: 3.567A pdb=" N ARG A3096 " --> pdb=" O THR A3092 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.598A pdb=" N LEU B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 106 Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.946A pdb=" N GLN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.923A pdb=" N ALA B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.750A pdb=" N ALA B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.983A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 280 removed outlier: 3.572A pdb=" N ASP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.673A pdb=" N GLU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 1300 hydrogen bonds defined for protein. 3867 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: 3.60 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5808 1.34 - 1.47: 5432 1.47 - 1.60: 9458 1.60 - 1.73: 0 1.73 - 1.86: 187 Bond restraints: 20885 Sorted by residual: bond pdb=" C PRO A1930 " pdb=" N PRO A1931 " ideal model delta sigma weight residual 1.336 1.398 -0.062 1.20e-02 6.94e+03 2.64e+01 bond pdb=" C ILE A1513 " pdb=" N PRO A1514 " ideal model delta sigma weight residual 1.335 1.400 -0.065 1.28e-02 6.10e+03 2.59e+01 bond pdb=" C GLN A1539 " pdb=" N PRO A1540 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" C LEU A2976 " pdb=" N PRO A2977 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.30e-02 5.92e+03 1.11e+01 bond pdb=" C VAL A 193 " pdb=" N ARG A 194 " ideal model delta sigma weight residual 1.339 1.205 0.135 5.57e-02 3.22e+02 5.85e+00 ... (remaining 20880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 27735 3.30 - 6.60: 530 6.60 - 9.90: 95 9.90 - 13.20: 11 13.20 - 16.50: 3 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N VAL A1645 " pdb=" CA VAL A1645 " pdb=" C VAL A1645 " ideal model delta sigma weight residual 111.91 106.26 5.65 8.90e-01 1.26e+00 4.03e+01 angle pdb=" N THR A 670 " pdb=" CA THR A 670 " pdb=" C THR A 670 " ideal model delta sigma weight residual 114.75 107.11 7.64 1.26e+00 6.30e-01 3.68e+01 angle pdb=" C ILE A2975 " pdb=" N LEU A2976 " pdb=" CA LEU A2976 " ideal model delta sigma weight residual 120.06 126.53 -6.47 1.19e+00 7.06e-01 2.96e+01 angle pdb=" C LEU A2593 " pdb=" N LEU A2594 " pdb=" CA LEU A2594 " ideal model delta sigma weight residual 120.82 128.21 -7.39 1.50e+00 4.44e-01 2.43e+01 angle pdb=" C ALA A 227 " pdb=" N VAL A 228 " pdb=" CA VAL A 228 " ideal model delta sigma weight residual 120.24 123.34 -3.10 6.30e-01 2.52e+00 2.42e+01 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 12031 18.09 - 36.18: 548 36.18 - 54.28: 82 54.28 - 72.37: 12 72.37 - 90.46: 7 Dihedral angle restraints: 12680 sinusoidal: 5006 harmonic: 7674 Sorted by residual: dihedral pdb=" CA VAL A1045 " pdb=" C VAL A1045 " pdb=" N PRO A1046 " pdb=" CA PRO A1046 " ideal model delta harmonic sigma weight residual -180.00 -108.17 -71.83 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA VAL A 296 " pdb=" C VAL A 296 " pdb=" N PRO A 297 " pdb=" CA PRO A 297 " ideal model delta harmonic sigma weight residual -180.00 -121.27 -58.73 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CA ALA B 162 " pdb=" C ALA B 162 " pdb=" N GLY B 163 " pdb=" CA GLY B 163 " ideal model delta harmonic sigma weight residual 180.00 127.51 52.49 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3110 0.099 - 0.199: 272 0.199 - 0.298: 9 0.298 - 0.397: 3 0.397 - 0.496: 1 Chirality restraints: 3395 Sorted by residual: chirality pdb=" CG LEU A 166 " pdb=" CB LEU A 166 " pdb=" CD1 LEU A 166 " pdb=" CD2 LEU A 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CG LEU A2543 " pdb=" CB LEU A2543 " pdb=" CD1 LEU A2543 " pdb=" CD2 LEU A2543 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CG LEU A 320 " pdb=" CB LEU A 320 " pdb=" CD1 LEU A 320 " pdb=" CD2 LEU A 320 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 3392 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1045 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A1046 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A1046 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A1046 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 296 " -0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 297 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1138 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C PHE A1138 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE A1138 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A1139 " -0.021 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4932 2.80 - 3.32: 19294 3.32 - 3.85: 33209 3.85 - 4.37: 37698 4.37 - 4.90: 65338 Nonbonded interactions: 160471 Sorted by model distance: nonbonded pdb=" O LEU A 807 " pdb=" OG1 THR A 810 " model vdw 2.271 3.040 nonbonded pdb=" O ASN A2517 " pdb=" OG SER A2521 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A1275 " pdb=" NE2 GLN A1310 " model vdw 2.278 3.120 nonbonded pdb=" OH TYR A1502 " pdb=" O ASP A1544 " model vdw 2.284 3.040 nonbonded pdb=" O HIS A2299 " pdb=" OG SER A2302 " model vdw 2.286 3.040 ... (remaining 160466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.030 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.007 0.135 20887 Z= 0.301 Angle : 1.166 16.501 28378 Z= 0.620 Chirality : 0.058 0.496 3395 Planarity : 0.009 0.101 3576 Dihedral : 11.072 81.100 7660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.90 % Favored : 93.86 % Rotamer: Outliers : 0.97 % Allowed : 5.09 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.13), residues: 2575 helix: -2.19 (0.09), residues: 1848 sheet: -4.87 (0.92), residues: 11 loop : -3.11 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A2528 TYR 0.038 0.003 TYR A1292 PHE 0.050 0.004 PHE A3039 TRP 0.030 0.003 TRP A2454 HIS 0.018 0.002 HIS A1940 Details of bonding type rmsd covalent geometry : bond 0.00694 (20885) covalent geometry : angle 1.16522 (28374) SS BOND : bond 0.00681 ( 2) SS BOND : angle 3.72448 ( 4) hydrogen bonds : bond 0.15159 ( 1300) hydrogen bonds : angle 6.46038 ( 3867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 748 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.8172 (mp) cc_final: 0.7799 (mp) REVERT: A 356 LEU cc_start: 0.8832 (tm) cc_final: 0.8611 (tp) REVERT: A 766 ILE cc_start: 0.8741 (tt) cc_final: 0.8333 (mt) REVERT: A 787 MET cc_start: 0.8015 (mmt) cc_final: 0.6697 (mmt) REVERT: A 793 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 844 GLN cc_start: 0.7584 (tp-100) cc_final: 0.7349 (mt0) REVERT: A 848 ASP cc_start: 0.7584 (m-30) cc_final: 0.7108 (m-30) REVERT: A 866 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7182 (tp30) REVERT: A 870 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7102 (tt0) REVERT: A 900 GLN cc_start: 0.8584 (tt0) cc_final: 0.8029 (tt0) REVERT: A 1002 ILE cc_start: 0.9157 (mt) cc_final: 0.8854 (mt) REVERT: A 1088 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8757 (tp) REVERT: A 1251 ASP cc_start: 0.7438 (t0) cc_final: 0.6885 (t0) REVERT: A 1281 ASP cc_start: 0.8405 (t70) cc_final: 0.7961 (t0) REVERT: A 1592 HIS cc_start: 0.8397 (t70) cc_final: 0.8018 (t-170) REVERT: A 1611 LEU cc_start: 0.8877 (mt) cc_final: 0.8472 (mt) REVERT: A 1621 ILE cc_start: 0.8811 (mt) cc_final: 0.8345 (mt) REVERT: A 2201 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7897 (tm) REVERT: A 2323 LEU cc_start: 0.7917 (pp) cc_final: 0.7514 (pt) REVERT: A 2391 ILE cc_start: 0.9120 (tt) cc_final: 0.8890 (tt) REVERT: A 2455 THR cc_start: 0.7069 (p) cc_final: 0.6823 (p) REVERT: A 2596 GLN cc_start: 0.8354 (mm110) cc_final: 0.7869 (mt0) REVERT: A 2606 MET cc_start: 0.6743 (mmm) cc_final: 0.6440 (tpp) REVERT: A 2839 TYR cc_start: 0.8021 (m-80) cc_final: 0.7544 (m-80) REVERT: A 2854 MET cc_start: 0.4196 (mmp) cc_final: 0.3978 (mmp) REVERT: A 3087 PHE cc_start: 0.8730 (t80) cc_final: 0.8499 (t80) REVERT: B 201 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 320 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.7959 (mm) outliers start: 22 outliers final: 5 residues processed: 762 average time/residue: 0.1662 time to fit residues: 188.5730 Evaluate side-chains 485 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 475 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 2201 LEU Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 113 ASN A 240 ASN A 254 ASN A 399 GLN A 755 HIS A 900 GLN A 905 ASN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN A1352 HIS A1443 GLN A1492 ASN A1589 GLN ** A1605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1624 HIS ** A1742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1825 HIS A1841 HIS A2019 ASN A2033 ASN A2133 ASN A2236 HIS ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2299 HIS ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2526 GLN A2563 ASN A2568 HIS A2571 GLN ** A2616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS A2820 HIS A2978 GLN ** A3006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3085 ASN B 353 ASN B 357 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.170928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136650 restraints weight = 24301.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.137238 restraints weight = 25597.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138631 restraints weight = 21881.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.139033 restraints weight = 17057.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139677 restraints weight = 16076.099| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20887 Z= 0.155 Angle : 0.722 16.285 28378 Z= 0.359 Chirality : 0.042 0.224 3395 Planarity : 0.006 0.082 3576 Dihedral : 6.588 66.492 2817 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.78 % Favored : 94.99 % Rotamer: Outliers : 4.26 % Allowed : 11.33 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 2575 helix: -0.30 (0.11), residues: 1873 sheet: None (None), residues: 0 loop : -2.53 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A3029 TYR 0.022 0.002 TYR B 114 PHE 0.024 0.002 PHE A 238 TRP 0.026 0.002 TRP A1122 HIS 0.011 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00355 (20885) covalent geometry : angle 0.72190 (28374) SS BOND : bond 0.00815 ( 2) SS BOND : angle 2.45928 ( 4) hydrogen bonds : bond 0.04755 ( 1300) hydrogen bonds : angle 4.44810 ( 3867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 506 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8034 (mttt) cc_final: 0.7816 (mttp) REVERT: A 202 LEU cc_start: 0.8764 (tp) cc_final: 0.8260 (tp) REVERT: A 356 LEU cc_start: 0.9167 (tm) cc_final: 0.8888 (tp) REVERT: A 724 GLU cc_start: 0.7866 (mp0) cc_final: 0.7538 (mt-10) REVERT: A 844 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7218 (mt0) REVERT: A 848 ASP cc_start: 0.7860 (m-30) cc_final: 0.7355 (m-30) REVERT: A 1077 LEU cc_start: 0.8441 (mt) cc_final: 0.8109 (mp) REVERT: A 1102 ARG cc_start: 0.7034 (tpp-160) cc_final: 0.6624 (tpm170) REVERT: A 1152 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 1270 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 1316 PHE cc_start: 0.8113 (m-80) cc_final: 0.7898 (m-80) REVERT: A 1611 LEU cc_start: 0.8738 (mt) cc_final: 0.8418 (mt) REVERT: A 1621 ILE cc_start: 0.9041 (mt) cc_final: 0.8527 (mt) REVERT: A 1649 LEU cc_start: 0.9551 (mt) cc_final: 0.9348 (mt) REVERT: A 1738 ARG cc_start: 0.7453 (mmm160) cc_final: 0.7220 (mmt90) REVERT: A 1772 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8691 (tp) REVERT: A 1838 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8683 (mt) REVERT: A 1910 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6873 (mt-10) REVERT: A 1915 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8104 (tp) REVERT: A 1923 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8108 (tm) REVERT: A 1974 GLU cc_start: 0.7480 (tt0) cc_final: 0.7048 (tt0) REVERT: A 2596 GLN cc_start: 0.8474 (mm110) cc_final: 0.7734 (mt0) REVERT: A 2620 LEU cc_start: 0.8674 (tp) cc_final: 0.8409 (tt) REVERT: A 2695 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7362 (mm-30) REVERT: A 2700 LEU cc_start: 0.9130 (tp) cc_final: 0.8899 (tp) REVERT: A 2731 ASP cc_start: 0.7707 (t0) cc_final: 0.7105 (t0) REVERT: A 2839 TYR cc_start: 0.8448 (m-80) cc_final: 0.7443 (m-80) REVERT: A 3076 MET cc_start: 0.7398 (ttp) cc_final: 0.6736 (ttt) REVERT: B 178 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 286 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7472 (mttp) REVERT: B 316 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6659 (mt-10) REVERT: B 320 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 339 SER cc_start: 0.9572 (m) cc_final: 0.8878 (t) outliers start: 97 outliers final: 34 residues processed: 565 average time/residue: 0.1455 time to fit residues: 128.3514 Evaluate side-chains 479 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 436 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1838 LEU Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2468 LEU Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2696 VAL Chi-restraints excluded: chain A residue 2708 THR Chi-restraints excluded: chain A residue 2786 LEU Chi-restraints excluded: chain A residue 2802 ILE Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2983 PHE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 4 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 188 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 HIS A 984 ASN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 HIS A1852 GLN A1951 GLN A2033 ASN A2555 GLN A2665 HIS A2727 HIS A2780 HIS A2872 HIS B 137 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.175326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139968 restraints weight = 24621.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.141973 restraints weight = 18794.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142917 restraints weight = 13591.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.143376 restraints weight = 12846.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.143725 restraints weight = 11397.864| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20887 Z= 0.130 Angle : 0.654 14.064 28378 Z= 0.322 Chirality : 0.041 0.242 3395 Planarity : 0.005 0.074 3576 Dihedral : 5.776 60.860 2807 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 14.32 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2575 helix: 0.59 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3029 TYR 0.024 0.002 TYR A 167 PHE 0.023 0.001 PHE A1495 TRP 0.016 0.001 TRP A2454 HIS 0.012 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00285 (20885) covalent geometry : angle 0.65267 (28374) SS BOND : bond 0.01317 ( 2) SS BOND : angle 4.09428 ( 4) hydrogen bonds : bond 0.04005 ( 1300) hydrogen bonds : angle 4.05219 ( 3867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 470 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 202 LEU cc_start: 0.8547 (tp) cc_final: 0.8087 (tp) REVERT: A 232 MET cc_start: 0.7900 (mmm) cc_final: 0.7680 (mmm) REVERT: A 724 GLU cc_start: 0.8070 (mp0) cc_final: 0.7767 (mt-10) REVERT: A 844 GLN cc_start: 0.7525 (tp-100) cc_final: 0.6994 (mt0) REVERT: A 848 ASP cc_start: 0.7838 (m-30) cc_final: 0.7374 (m-30) REVERT: A 1077 LEU cc_start: 0.8617 (mt) cc_final: 0.8333 (mp) REVERT: A 1102 ARG cc_start: 0.6831 (tpp-160) cc_final: 0.6476 (tpm170) REVERT: A 1251 ASP cc_start: 0.7258 (t0) cc_final: 0.6271 (t0) REVERT: A 1611 LEU cc_start: 0.8578 (mt) cc_final: 0.8204 (mt) REVERT: A 1621 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 1649 LEU cc_start: 0.9571 (mt) cc_final: 0.9352 (mt) REVERT: A 1682 GLN cc_start: 0.8348 (mm110) cc_final: 0.7991 (mm-40) REVERT: A 1733 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7896 (mt-10) REVERT: A 1772 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 1838 LEU cc_start: 0.8867 (mt) cc_final: 0.8605 (mt) REVERT: A 1923 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (tp) REVERT: A 2000 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 2056 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: A 2467 LEU cc_start: 0.8921 (mt) cc_final: 0.8712 (mt) REVERT: A 2596 GLN cc_start: 0.8424 (mm110) cc_final: 0.7796 (mt0) REVERT: A 2620 LEU cc_start: 0.8809 (tp) cc_final: 0.8584 (tt) REVERT: A 2698 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.8014 (ttt90) REVERT: A 2709 GLU cc_start: 0.6909 (tp30) cc_final: 0.6606 (mm-30) REVERT: A 2731 ASP cc_start: 0.7787 (t0) cc_final: 0.7295 (t0) REVERT: A 2811 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7696 (ttpp) REVERT: A 2839 TYR cc_start: 0.8497 (m-80) cc_final: 0.7275 (m-80) REVERT: A 2854 MET cc_start: 0.7587 (mtm) cc_final: 0.7283 (mtt) REVERT: A 2912 MET cc_start: 0.7196 (mmm) cc_final: 0.6917 (mmm) REVERT: A 2951 MET cc_start: 0.7617 (tmm) cc_final: 0.7346 (tmm) REVERT: A 2952 GLU cc_start: 0.7547 (tp30) cc_final: 0.7286 (tp30) REVERT: A 3076 MET cc_start: 0.7523 (ttp) cc_final: 0.7109 (ttt) REVERT: B 178 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7869 (tp) REVERT: B 286 LYS cc_start: 0.7833 (mtpp) cc_final: 0.7342 (mttp) REVERT: B 288 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7959 (mt) REVERT: B 316 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6825 (mt-10) REVERT: B 320 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7788 (mm) outliers start: 90 outliers final: 47 residues processed: 519 average time/residue: 0.1473 time to fit residues: 118.9353 Evaluate side-chains 469 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 414 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2267 LEU Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2708 THR Chi-restraints excluded: chain A residue 2710 ARG Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 344 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 253 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN A1007 HIS A1042 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 GLN A1921 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2616 HIS A2665 HIS A2727 HIS A2838 ASN A2906 HIS B 137 GLN B 353 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.169401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.134777 restraints weight = 24825.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.136426 restraints weight = 22119.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.137643 restraints weight = 17527.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.137947 restraints weight = 13955.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138389 restraints weight = 13696.087| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20887 Z= 0.135 Angle : 0.658 12.789 28378 Z= 0.318 Chirality : 0.041 0.210 3395 Planarity : 0.005 0.081 3576 Dihedral : 5.517 60.794 2805 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 4.26 % Allowed : 15.20 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2575 helix: 0.98 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.018 0.002 TYR B 114 PHE 0.017 0.001 PHE A3087 TRP 0.024 0.001 TRP A1122 HIS 0.010 0.001 HIS A2727 Details of bonding type rmsd covalent geometry : bond 0.00313 (20885) covalent geometry : angle 0.65687 (28374) SS BOND : bond 0.00947 ( 2) SS BOND : angle 3.27813 ( 4) hydrogen bonds : bond 0.03926 ( 1300) hydrogen bonds : angle 3.91928 ( 3867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 445 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 232 MET cc_start: 0.8069 (mmm) cc_final: 0.7868 (mmm) REVERT: A 274 CYS cc_start: 0.8492 (m) cc_final: 0.7987 (m) REVERT: A 356 LEU cc_start: 0.9125 (tm) cc_final: 0.8898 (tp) REVERT: A 752 TYR cc_start: 0.8310 (m-10) cc_final: 0.7941 (m-80) REVERT: A 802 ASP cc_start: 0.7238 (m-30) cc_final: 0.6939 (m-30) REVERT: A 844 GLN cc_start: 0.7426 (tp-100) cc_final: 0.7160 (mt0) REVERT: A 848 ASP cc_start: 0.7860 (m-30) cc_final: 0.7541 (m-30) REVERT: A 1077 LEU cc_start: 0.8675 (mt) cc_final: 0.8391 (mp) REVERT: A 1102 ARG cc_start: 0.6642 (tpp-160) cc_final: 0.6412 (tpm170) REVERT: A 1251 ASP cc_start: 0.7314 (t0) cc_final: 0.6352 (t0) REVERT: A 1611 LEU cc_start: 0.8629 (mt) cc_final: 0.8288 (mt) REVERT: A 1621 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 1738 ARG cc_start: 0.7732 (mmt180) cc_final: 0.7253 (mmp-170) REVERT: A 1772 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 1838 LEU cc_start: 0.8961 (mt) cc_final: 0.8700 (mt) REVERT: A 1923 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8398 (tp) REVERT: A 1965 MET cc_start: 0.8182 (mmm) cc_final: 0.7956 (mmm) REVERT: A 2000 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 2056 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: A 2211 TYR cc_start: 0.7466 (t80) cc_final: 0.7218 (t80) REVERT: A 2468 LEU cc_start: 0.8788 (mt) cc_final: 0.8584 (mt) REVERT: A 2596 GLN cc_start: 0.8476 (mm110) cc_final: 0.7753 (mt0) REVERT: A 2698 ARG cc_start: 0.8391 (tmm-80) cc_final: 0.8026 (ttt90) REVERT: A 2709 GLU cc_start: 0.6915 (tp30) cc_final: 0.6635 (mm-30) REVERT: A 2731 ASP cc_start: 0.7733 (t0) cc_final: 0.7149 (t0) REVERT: A 2839 TYR cc_start: 0.8655 (m-80) cc_final: 0.7356 (m-80) REVERT: A 2854 MET cc_start: 0.7416 (mtm) cc_final: 0.6994 (mtt) REVERT: A 2912 MET cc_start: 0.7183 (mmm) cc_final: 0.6918 (mmm) REVERT: A 2952 GLU cc_start: 0.7557 (tp30) cc_final: 0.7164 (tp30) REVERT: A 3029 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8207 (mtm110) REVERT: A 3076 MET cc_start: 0.7080 (ttp) cc_final: 0.6804 (ttp) REVERT: B 178 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7945 (tp) REVERT: B 286 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7619 (mttp) REVERT: B 288 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7952 (mt) REVERT: B 332 LYS cc_start: 0.7549 (mttt) cc_final: 0.7155 (mmtt) outliers start: 97 outliers final: 57 residues processed: 502 average time/residue: 0.1415 time to fit residues: 112.1584 Evaluate side-chains 483 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 419 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1133 MET Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2056 ASP Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2176 VAL Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2267 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2391 ILE Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2696 VAL Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2708 THR Chi-restraints excluded: chain A residue 2711 ASN Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 2983 PHE Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 344 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 135 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 GLN A2187 GLN A2377 ASN A2665 HIS A2727 HIS B 353 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.165430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130862 restraints weight = 24536.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.131085 restraints weight = 24888.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132477 restraints weight = 22906.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.132742 restraints weight = 18524.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.133131 restraints weight = 17307.620| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20887 Z= 0.166 Angle : 0.681 13.721 28378 Z= 0.328 Chirality : 0.042 0.199 3395 Planarity : 0.005 0.083 3576 Dihedral : 5.401 60.972 2803 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.50 % Favored : 95.38 % Rotamer: Outliers : 4.70 % Allowed : 16.43 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2575 helix: 1.18 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2724 TYR 0.020 0.002 TYR B 114 PHE 0.019 0.002 PHE A2833 TRP 0.033 0.002 TRP A1122 HIS 0.008 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00403 (20885) covalent geometry : angle 0.68000 (28374) SS BOND : bond 0.00911 ( 2) SS BOND : angle 3.02916 ( 4) hydrogen bonds : bond 0.04254 ( 1300) hydrogen bonds : angle 3.90079 ( 3867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 444 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 274 CYS cc_start: 0.8389 (m) cc_final: 0.8067 (m) REVERT: A 356 LEU cc_start: 0.9183 (tm) cc_final: 0.8926 (tp) REVERT: A 695 ASN cc_start: 0.7432 (p0) cc_final: 0.7210 (p0) REVERT: A 752 TYR cc_start: 0.8450 (m-10) cc_final: 0.8144 (m-10) REVERT: A 831 MET cc_start: 0.7650 (mmm) cc_final: 0.7357 (mmm) REVERT: A 998 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 1077 LEU cc_start: 0.8702 (mt) cc_final: 0.8426 (mp) REVERT: A 1102 ARG cc_start: 0.6457 (tpp-160) cc_final: 0.6070 (tpm170) REVERT: A 1135 GLU cc_start: 0.6971 (tp30) cc_final: 0.6688 (mm-30) REVERT: A 1584 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 1600 LYS cc_start: 0.8441 (ptpp) cc_final: 0.8235 (ptpp) REVERT: A 1611 LEU cc_start: 0.8847 (mt) cc_final: 0.8442 (mt) REVERT: A 1621 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 1738 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7344 (mmp-170) REVERT: A 1768 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 1838 LEU cc_start: 0.9087 (mt) cc_final: 0.8818 (mt) REVERT: A 1909 SER cc_start: 0.8185 (m) cc_final: 0.7932 (t) REVERT: A 1923 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8565 (tp) REVERT: A 1974 GLU cc_start: 0.7434 (tt0) cc_final: 0.7082 (tt0) REVERT: A 2034 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7962 (ttt-90) REVERT: A 2596 GLN cc_start: 0.8531 (mm110) cc_final: 0.7906 (mt0) REVERT: A 2674 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 2698 ARG cc_start: 0.8404 (tmm-80) cc_final: 0.8095 (ttt90) REVERT: A 2731 ASP cc_start: 0.7821 (t0) cc_final: 0.7212 (t0) REVERT: A 2807 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8054 (mt) REVERT: A 2838 ASN cc_start: 0.8422 (m-40) cc_final: 0.8021 (m110) REVERT: A 2839 TYR cc_start: 0.8345 (m-80) cc_final: 0.7636 (m-80) REVERT: A 2854 MET cc_start: 0.7401 (mtm) cc_final: 0.7181 (mtt) REVERT: A 2952 GLU cc_start: 0.7602 (tp30) cc_final: 0.7193 (tp30) REVERT: B 119 GLN cc_start: 0.8341 (mt0) cc_final: 0.8039 (mt0) REVERT: B 288 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8058 (mt) REVERT: B 316 GLU cc_start: 0.8231 (tp30) cc_final: 0.7928 (tp30) REVERT: B 332 LYS cc_start: 0.7489 (mttt) cc_final: 0.7270 (mmmt) REVERT: B 361 GLN cc_start: 0.8338 (tt0) cc_final: 0.8031 (tt0) outliers start: 107 outliers final: 67 residues processed: 505 average time/residue: 0.1376 time to fit residues: 109.5221 Evaluate side-chains 487 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 412 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2006 ILE Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2267 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2391 ILE Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2696 VAL Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2711 ASN Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 60 optimal weight: 0.0970 chunk 222 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 204 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN A2669 GLN A2727 HIS ** A2824 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.166436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.132371 restraints weight = 24292.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.132957 restraints weight = 23873.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134492 restraints weight = 21552.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134565 restraints weight = 17479.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.135044 restraints weight = 16495.440| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20887 Z= 0.147 Angle : 0.676 13.271 28378 Z= 0.324 Chirality : 0.041 0.192 3395 Planarity : 0.005 0.084 3576 Dihedral : 5.309 60.397 2803 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 4.17 % Allowed : 17.30 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2575 helix: 1.33 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3029 TYR 0.028 0.002 TYR A2211 PHE 0.018 0.001 PHE A2058 TRP 0.027 0.001 TRP A1122 HIS 0.012 0.001 HIS A2824 Details of bonding type rmsd covalent geometry : bond 0.00352 (20885) covalent geometry : angle 0.67536 (28374) SS BOND : bond 0.00880 ( 2) SS BOND : angle 2.74744 ( 4) hydrogen bonds : bond 0.04015 ( 1300) hydrogen bonds : angle 3.87623 ( 3867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 440 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 CYS cc_start: 0.8362 (m) cc_final: 0.8138 (m) REVERT: A 694 LYS cc_start: 0.7365 (tptt) cc_final: 0.7158 (ttpt) REVERT: A 1077 LEU cc_start: 0.8668 (mt) cc_final: 0.8394 (mp) REVERT: A 1102 ARG cc_start: 0.6122 (tpp-160) cc_final: 0.5891 (tpm170) REVERT: A 1584 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6758 (t80) REVERT: A 1600 LYS cc_start: 0.8392 (ptpp) cc_final: 0.8177 (ptpp) REVERT: A 1611 LEU cc_start: 0.8776 (mt) cc_final: 0.8407 (mt) REVERT: A 1621 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 1733 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 1738 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7342 (mmp-170) REVERT: A 1768 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6639 (t80) REVERT: A 1838 LEU cc_start: 0.9079 (mt) cc_final: 0.8783 (mt) REVERT: A 1909 SER cc_start: 0.8140 (m) cc_final: 0.7923 (t) REVERT: A 1923 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 2034 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7892 (ttt-90) REVERT: A 2103 GLN cc_start: 0.8212 (mm-40) cc_final: 0.8005 (mm-40) REVERT: A 2256 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8241 (mt) REVERT: A 2455 THR cc_start: 0.7873 (p) cc_final: 0.7029 (t) REVERT: A 2596 GLN cc_start: 0.8545 (mm110) cc_final: 0.7778 (mt0) REVERT: A 2674 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 2731 ASP cc_start: 0.7807 (t0) cc_final: 0.7206 (t0) REVERT: A 2807 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7986 (mt) REVERT: A 2839 TYR cc_start: 0.8393 (m-80) cc_final: 0.7520 (m-80) REVERT: A 2952 GLU cc_start: 0.7569 (tp30) cc_final: 0.7031 (tp30) REVERT: A 3013 TYR cc_start: 0.8899 (t80) cc_final: 0.8644 (t80) REVERT: B 178 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 280 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8208 (pt) REVERT: B 286 LYS cc_start: 0.8073 (mttp) cc_final: 0.7861 (mttp) REVERT: B 316 GLU cc_start: 0.8209 (tp30) cc_final: 0.7871 (tp30) REVERT: B 325 LEU cc_start: 0.8883 (tt) cc_final: 0.8350 (tp) REVERT: B 361 GLN cc_start: 0.8270 (tt0) cc_final: 0.7964 (tt0) outliers start: 95 outliers final: 65 residues processed: 499 average time/residue: 0.1411 time to fit residues: 110.5160 Evaluate side-chains 488 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 414 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1984 VAL Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2006 ILE Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2229 SER Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2267 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2391 ILE Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2691 ILE Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 134 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1951 GLN A2727 HIS B 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.164163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.129858 restraints weight = 24648.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.129535 restraints weight = 25159.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131249 restraints weight = 24926.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.131271 restraints weight = 18274.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.131630 restraints weight = 16985.638| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20887 Z= 0.162 Angle : 0.697 13.042 28378 Z= 0.334 Chirality : 0.043 0.474 3395 Planarity : 0.005 0.097 3576 Dihedral : 5.299 60.370 2803 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.30 % Rotamer: Outliers : 4.35 % Allowed : 17.61 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2575 helix: 1.36 (0.12), residues: 1891 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2724 TYR 0.021 0.002 TYR A2211 PHE 0.022 0.002 PHE A2428 TRP 0.032 0.001 TRP A1122 HIS 0.025 0.001 HIS A2727 Details of bonding type rmsd covalent geometry : bond 0.00393 (20885) covalent geometry : angle 0.69659 (28374) SS BOND : bond 0.00899 ( 2) SS BOND : angle 2.75574 ( 4) hydrogen bonds : bond 0.04123 ( 1300) hydrogen bonds : angle 3.87752 ( 3867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 422 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 LYS cc_start: 0.7372 (tptt) cc_final: 0.7064 (ttpt) REVERT: A 998 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8373 (tt) REVERT: A 1077 LEU cc_start: 0.8650 (mt) cc_final: 0.8373 (mp) REVERT: A 1102 ARG cc_start: 0.6060 (tpp-160) cc_final: 0.5823 (tpm170) REVERT: A 1251 ASP cc_start: 0.7656 (t0) cc_final: 0.6718 (t0) REVERT: A 1430 LYS cc_start: 0.8242 (mmtp) cc_final: 0.8037 (ttmm) REVERT: A 1584 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 1600 LYS cc_start: 0.8335 (ptpp) cc_final: 0.8086 (ptpp) REVERT: A 1611 LEU cc_start: 0.8813 (mt) cc_final: 0.8471 (mt) REVERT: A 1621 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 1733 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 1738 ARG cc_start: 0.7935 (mmt180) cc_final: 0.7465 (mmp-170) REVERT: A 1768 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6839 (t80) REVERT: A 1821 MET cc_start: 0.8222 (mtm) cc_final: 0.7950 (mtp) REVERT: A 1838 LEU cc_start: 0.9106 (mt) cc_final: 0.8849 (mt) REVERT: A 1909 SER cc_start: 0.8187 (m) cc_final: 0.7963 (t) REVERT: A 1923 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 2034 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7872 (ttt-90) REVERT: A 2256 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 2596 GLN cc_start: 0.8530 (mm110) cc_final: 0.7765 (mt0) REVERT: A 2674 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8837 (tt) REVERT: A 2731 ASP cc_start: 0.7949 (t0) cc_final: 0.7374 (t0) REVERT: A 2807 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7980 (mt) REVERT: A 2811 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7570 (ttpp) REVERT: A 2839 TYR cc_start: 0.8550 (m-80) cc_final: 0.7567 (m-80) REVERT: A 2854 MET cc_start: 0.7387 (mtt) cc_final: 0.7000 (mtt) REVERT: A 2952 GLU cc_start: 0.7562 (tp30) cc_final: 0.7015 (tp30) REVERT: A 3013 TYR cc_start: 0.8922 (t80) cc_final: 0.8695 (t80) REVERT: B 173 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 178 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 280 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8254 (pt) REVERT: B 286 LYS cc_start: 0.8055 (mttp) cc_final: 0.7826 (mttp) REVERT: B 316 GLU cc_start: 0.8241 (tp30) cc_final: 0.7877 (tp30) REVERT: B 325 LEU cc_start: 0.8876 (tt) cc_final: 0.8581 (tp) REVERT: B 344 MET cc_start: 0.8057 (mtp) cc_final: 0.7836 (ttm) REVERT: B 361 GLN cc_start: 0.8308 (tt0) cc_final: 0.8099 (tt0) outliers start: 99 outliers final: 72 residues processed: 481 average time/residue: 0.1404 time to fit residues: 106.9872 Evaluate side-chains 488 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 405 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 366 HIS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1955 SER Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2006 ILE Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2229 SER Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2267 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2622 ASN Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2691 ILE Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2798 LEU Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3072 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 6.9990 chunk 193 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A2612 GLN A2727 HIS B 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.166869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.131921 restraints weight = 24635.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.133084 restraints weight = 23318.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.134133 restraints weight = 20461.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.134546 restraints weight = 16186.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134765 restraints weight = 15180.539| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20887 Z= 0.130 Angle : 0.692 14.639 28378 Z= 0.330 Chirality : 0.041 0.420 3395 Planarity : 0.005 0.098 3576 Dihedral : 5.215 59.059 2802 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 4.04 % Allowed : 18.36 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2575 helix: 1.46 (0.12), residues: 1893 sheet: None (None), residues: 0 loop : -1.55 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A3029 TYR 0.019 0.001 TYR A2211 PHE 0.018 0.001 PHE A3087 TRP 0.021 0.001 TRP A1122 HIS 0.031 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00303 (20885) covalent geometry : angle 0.68880 (28374) SS BOND : bond 0.00929 ( 2) SS BOND : angle 5.87652 ( 4) hydrogen bonds : bond 0.03813 ( 1300) hydrogen bonds : angle 3.83364 ( 3867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 423 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 LYS cc_start: 0.7351 (tptt) cc_final: 0.7066 (ttpt) REVERT: A 771 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8615 (tp) REVERT: A 1077 LEU cc_start: 0.8678 (mt) cc_final: 0.8402 (mp) REVERT: A 1102 ARG cc_start: 0.5841 (tpp-160) cc_final: 0.5569 (tpm170) REVERT: A 1251 ASP cc_start: 0.7601 (t0) cc_final: 0.6671 (t0) REVERT: A 1292 TYR cc_start: 0.7295 (m-10) cc_final: 0.6603 (m-10) REVERT: A 1430 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7998 (ttmm) REVERT: A 1584 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 1600 LYS cc_start: 0.8342 (ptpp) cc_final: 0.8089 (ptpp) REVERT: A 1611 LEU cc_start: 0.8823 (mt) cc_final: 0.8463 (mt) REVERT: A 1621 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 1768 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 1838 LEU cc_start: 0.9104 (mt) cc_final: 0.8815 (mt) REVERT: A 1909 SER cc_start: 0.8124 (m) cc_final: 0.7900 (t) REVERT: A 1923 LEU cc_start: 0.8873 (tm) cc_final: 0.8562 (tp) REVERT: A 2000 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8125 (mp) REVERT: A 2034 ARG cc_start: 0.8291 (ttp80) cc_final: 0.8016 (ttt-90) REVERT: A 2256 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8232 (mt) REVERT: A 2455 THR cc_start: 0.7784 (p) cc_final: 0.6966 (t) REVERT: A 2539 PHE cc_start: 0.7931 (t80) cc_final: 0.7623 (t80) REVERT: A 2596 GLN cc_start: 0.8403 (mm110) cc_final: 0.7690 (mt0) REVERT: A 2674 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 2731 ASP cc_start: 0.7837 (t0) cc_final: 0.7195 (t0) REVERT: A 2807 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 2811 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7552 (ttpp) REVERT: A 2839 TYR cc_start: 0.8518 (m-80) cc_final: 0.7496 (m-80) REVERT: A 2854 MET cc_start: 0.7433 (mtt) cc_final: 0.7052 (mtt) REVERT: A 2923 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6421 (t80) REVERT: A 2952 GLU cc_start: 0.7561 (tp30) cc_final: 0.7009 (tp30) REVERT: B 173 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8084 (tp) REVERT: B 178 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 286 LYS cc_start: 0.8039 (mttp) cc_final: 0.7810 (mttp) REVERT: B 361 GLN cc_start: 0.8146 (tt0) cc_final: 0.7927 (tt0) outliers start: 92 outliers final: 62 residues processed: 477 average time/residue: 0.1309 time to fit residues: 100.1840 Evaluate side-chains 477 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 404 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2229 SER Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2674 LEU Chi-restraints excluded: chain A residue 2691 ILE Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2798 LEU Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2879 GLU Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2923 TYR Chi-restraints excluded: chain A residue 2961 ILE Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3068 ILE Chi-restraints excluded: chain A residue 3072 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 21 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 118 GLN A 755 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1951 GLN A2026 GLN A2555 GLN A2590 HIS A2616 HIS A2727 HIS B 353 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.162608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.128330 restraints weight = 24574.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.127802 restraints weight = 25327.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.128994 restraints weight = 24390.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.129727 restraints weight = 17146.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.129866 restraints weight = 15902.822| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20887 Z= 0.186 Angle : 0.744 14.345 28378 Z= 0.355 Chirality : 0.044 0.388 3395 Planarity : 0.005 0.099 3576 Dihedral : 5.292 60.534 2802 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.54 % Favored : 95.38 % Rotamer: Outliers : 4.17 % Allowed : 18.80 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2575 helix: 1.42 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3029 TYR 0.020 0.002 TYR A3013 PHE 0.019 0.002 PHE A3087 TRP 0.032 0.002 TRP A1122 HIS 0.006 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00459 (20885) covalent geometry : angle 0.74174 (28374) SS BOND : bond 0.01504 ( 2) SS BOND : angle 4.95672 ( 4) hydrogen bonds : bond 0.04324 ( 1300) hydrogen bonds : angle 3.92046 ( 3867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 420 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.8741 (mp) cc_final: 0.8432 (mp) REVERT: A 694 LYS cc_start: 0.7371 (tptt) cc_final: 0.7078 (ttpt) REVERT: A 752 TYR cc_start: 0.8507 (m-10) cc_final: 0.8206 (m-10) REVERT: A 771 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8704 (tp) REVERT: A 1077 LEU cc_start: 0.8719 (mt) cc_final: 0.8445 (mp) REVERT: A 1102 ARG cc_start: 0.5932 (tpp-160) cc_final: 0.5606 (tpm170) REVERT: A 1135 GLU cc_start: 0.7165 (tp30) cc_final: 0.6931 (mm-30) REVERT: A 1584 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 1600 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8139 (ptpp) REVERT: A 1611 LEU cc_start: 0.8864 (mt) cc_final: 0.8541 (mt) REVERT: A 1621 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 1652 MET cc_start: 0.8465 (ttt) cc_final: 0.8196 (ttt) REVERT: A 1768 TYR cc_start: 0.8281 (OUTLIER) cc_final: 0.6803 (t80) REVERT: A 1838 LEU cc_start: 0.9112 (mt) cc_final: 0.8854 (mt) REVERT: A 1909 SER cc_start: 0.8153 (m) cc_final: 0.7927 (t) REVERT: A 1923 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 2000 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 2034 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8014 (ttt-90) REVERT: A 2256 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 2280 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 2596 GLN cc_start: 0.8394 (mm110) cc_final: 0.7822 (mt0) REVERT: A 2709 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6895 (mm-30) REVERT: A 2731 ASP cc_start: 0.7922 (t0) cc_final: 0.7310 (t0) REVERT: A 2807 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7970 (mt) REVERT: A 2811 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7573 (ttpp) REVERT: A 2839 TYR cc_start: 0.8636 (m-80) cc_final: 0.7713 (m-80) REVERT: A 2854 MET cc_start: 0.7443 (mtt) cc_final: 0.7078 (mtt) REVERT: A 2952 GLU cc_start: 0.7557 (tp30) cc_final: 0.6988 (tp30) REVERT: A 3029 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.7850 (mtm110) REVERT: B 173 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 178 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (tp) REVERT: B 280 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8289 (pt) REVERT: B 286 LYS cc_start: 0.8093 (mttp) cc_final: 0.7856 (mttp) REVERT: B 325 LEU cc_start: 0.8954 (tt) cc_final: 0.8387 (tp) REVERT: B 344 MET cc_start: 0.8670 (ttm) cc_final: 0.8450 (ttp) REVERT: B 361 GLN cc_start: 0.8231 (tt0) cc_final: 0.8002 (tt0) outliers start: 95 outliers final: 69 residues processed: 480 average time/residue: 0.1390 time to fit residues: 106.3796 Evaluate side-chains 492 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 411 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 1670 SER Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1976 ILE Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2006 ILE Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2229 SER Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2280 LEU Chi-restraints excluded: chain A residue 2291 VAL Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2798 LEU Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2879 GLU Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3068 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 224 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 174 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN B 137 GLN B 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.167870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134278 restraints weight = 24445.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.134462 restraints weight = 24312.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.135673 restraints weight = 22855.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.135960 restraints weight = 19282.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.136280 restraints weight = 17044.713| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20887 Z= 0.130 Angle : 0.711 14.197 28378 Z= 0.336 Chirality : 0.041 0.379 3395 Planarity : 0.005 0.099 3576 Dihedral : 5.112 58.690 2800 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.38 % Allowed : 19.89 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2575 helix: 1.54 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -1.38 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2677 TYR 0.019 0.001 TYR A 740 PHE 0.020 0.001 PHE A3087 TRP 0.037 0.002 TRP A2095 HIS 0.028 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00301 (20885) covalent geometry : angle 0.70826 (28374) SS BOND : bond 0.00980 ( 2) SS BOND : angle 4.84723 ( 4) hydrogen bonds : bond 0.03747 ( 1300) hydrogen bonds : angle 3.84253 ( 3867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 431 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.8683 (mp) cc_final: 0.8349 (mp) REVERT: A 665 ASP cc_start: 0.7530 (t0) cc_final: 0.7070 (t0) REVERT: A 771 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8494 (tp) REVERT: A 802 ASP cc_start: 0.6584 (m-30) cc_final: 0.6176 (m-30) REVERT: A 1077 LEU cc_start: 0.8710 (mt) cc_final: 0.8421 (mp) REVERT: A 1102 ARG cc_start: 0.5742 (tpp-160) cc_final: 0.5254 (tpm170) REVERT: A 1251 ASP cc_start: 0.7630 (t0) cc_final: 0.6673 (t0) REVERT: A 1584 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 1600 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8135 (ptpp) REVERT: A 1611 LEU cc_start: 0.8835 (mt) cc_final: 0.8492 (mt) REVERT: A 1621 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 1652 MET cc_start: 0.8475 (ttt) cc_final: 0.8226 (ttt) REVERT: A 1768 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.6551 (t80) REVERT: A 1838 LEU cc_start: 0.9099 (mt) cc_final: 0.8837 (mt) REVERT: A 1909 SER cc_start: 0.8113 (m) cc_final: 0.7878 (t) REVERT: A 1923 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 2000 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 2034 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7994 (ttt-90) REVERT: A 2256 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 2440 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7595 (mm-30) REVERT: A 2455 THR cc_start: 0.7755 (p) cc_final: 0.6933 (t) REVERT: A 2559 SER cc_start: 0.9454 (t) cc_final: 0.9080 (p) REVERT: A 2596 GLN cc_start: 0.8276 (mm110) cc_final: 0.7721 (mt0) REVERT: A 2678 TRP cc_start: 0.7958 (m-10) cc_final: 0.7709 (m-10) REVERT: A 2709 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 2731 ASP cc_start: 0.7816 (t0) cc_final: 0.7161 (t0) REVERT: A 2807 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7879 (mt) REVERT: A 2839 TYR cc_start: 0.8398 (m-80) cc_final: 0.7489 (m-80) REVERT: A 2923 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6685 (t80) REVERT: A 2952 GLU cc_start: 0.7590 (tp30) cc_final: 0.6996 (tp30) REVERT: A 2976 LEU cc_start: 0.8113 (mt) cc_final: 0.7425 (mt) REVERT: B 173 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8323 (tp) REVERT: B 178 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7352 (tt) REVERT: B 286 LYS cc_start: 0.8026 (mttp) cc_final: 0.7805 (mttp) REVERT: B 361 GLN cc_start: 0.8171 (tt0) cc_final: 0.7935 (tt0) outliers start: 77 outliers final: 56 residues processed: 485 average time/residue: 0.1415 time to fit residues: 110.3820 Evaluate side-chains 473 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 406 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 302 HIS Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 MET Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1502 TYR Chi-restraints excluded: chain A residue 1584 PHE Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1768 TYR Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1814 LEU Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1923 LEU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 1993 LEU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2229 SER Chi-restraints excluded: chain A residue 2253 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2578 SER Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2618 VAL Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2798 LEU Chi-restraints excluded: chain A residue 2807 LEU Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2879 GLU Chi-restraints excluded: chain A residue 2905 VAL Chi-restraints excluded: chain A residue 2917 LEU Chi-restraints excluded: chain A residue 2923 TYR Chi-restraints excluded: chain A residue 3008 MET Chi-restraints excluded: chain A residue 3068 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 248 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 194 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1951 GLN A2838 ASN B 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.164775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.130844 restraints weight = 24542.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.130634 restraints weight = 26203.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.132553 restraints weight = 24408.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.132518 restraints weight = 17797.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132734 restraints weight = 16651.617| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20887 Z= 0.164 Angle : 0.744 14.237 28378 Z= 0.350 Chirality : 0.043 0.367 3395 Planarity : 0.005 0.099 3576 Dihedral : 5.116 59.181 2800 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 3.38 % Allowed : 20.47 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2575 helix: 1.52 (0.12), residues: 1889 sheet: None (None), residues: 0 loop : -1.40 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3029 TYR 0.021 0.002 TYR A2717 PHE 0.024 0.002 PHE A2670 TRP 0.033 0.002 TRP A2095 HIS 0.016 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00401 (20885) covalent geometry : angle 0.74147 (28374) SS BOND : bond 0.01105 ( 2) SS BOND : angle 4.83004 ( 4) hydrogen bonds : bond 0.04062 ( 1300) hydrogen bonds : angle 3.88163 ( 3867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.30 seconds wall clock time: 59 minutes 34.17 seconds (3574.17 seconds total)