Starting phenix.real_space_refine on Sun Feb 18 02:15:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_30911_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_30911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_30911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_30911_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxj_30911/02_2024/7dxj_30911_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A ARG 951": "NH1" <-> "NH2" Residue "A ARG 981": "NH1" <-> "NH2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1573": "NH1" <-> "NH2" Residue "A ARG 1604": "NH1" <-> "NH2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A ARG 1691": "NH1" <-> "NH2" Residue "A ARG 1709": "NH1" <-> "NH2" Residue "A ARG 1738": "NH1" <-> "NH2" Residue "A ARG 1789": "NH1" <-> "NH2" Residue "A ARG 1800": "NH1" <-> "NH2" Residue "A ARG 1817": "NH1" <-> "NH2" Residue "A ARG 1891": "NH1" <-> "NH2" Residue "A ARG 1991": "NH1" <-> "NH2" Residue "A ARG 1998": "NH1" <-> "NH2" Residue "A ARG 2011": "NH1" <-> "NH2" Residue "A ARG 2059": "NH1" <-> "NH2" Residue "A TYR 2351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2389": "NH1" <-> "NH2" Residue "A ARG 2397": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "A ARG 2457": "NH1" <-> "NH2" Residue "A ARG 2547": "NH1" <-> "NH2" Residue "A ARG 2698": "NH1" <-> "NH2" Residue "A ARG 2902": "NH1" <-> "NH2" Residue "A ARG 2910": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 10.84, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 8.35 Conformation dependent library (CDL) restraints added in 3.8 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: 2.66 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: 7.88 Time building geometry restraints manager: 9.03 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: 96.67 - 104.24: 334 104.24 - 111.81: 9899 111.81 - 119.38: 7894 119.38 - 126.94: 9959 126.94 - 134.51: 288 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 2.440 nonbonded pdb=" O ASN A2517 " pdb=" OG SER A2521 " model vdw 2.271 2.440 nonbonded pdb=" OE2 GLU A1275 " pdb=" NE2 GLN A1310 " model vdw 2.278 2.520 nonbonded pdb=" OH TYR A1502 " pdb=" O ASP A1544 " model vdw 2.284 2.440 nonbonded pdb=" O HIS A2299 " pdb=" OG SER A2302 " model vdw 2.286 2.440 ... (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 ========== 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: 0.310 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: 2.080 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 56.870 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.460 ------------------------------------------------------------------------------- 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 20885 Z= 0.446 Angle : 1.165 16.501 28374 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.003 TRP A2454 HIS 0.018 0.002 HIS A1940 PHE 0.050 0.004 PHE A3039 TYR 0.038 0.003 TYR A1292 ARG 0.012 0.001 ARG A2528 *********************** 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 fitting. rotamer outliers: 22 poor density : 748 time to evaluate : 2.466 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: 0.3598 time to fit residues: 407.3981 Evaluate side-chains 485 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 475 time to evaluate : 2.225 ------------------------------------------------------------------------------- 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 220 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 133 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 237 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 377 GLN A 399 GLN A 755 HIS A 900 GLN A 905 ASN A1091 ASN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 ASN A1272 GLN A1352 HIS A1492 ASN A1589 GLN ** A1605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1624 HIS A1708 ASN ** 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** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2526 GLN A2555 GLN A2563 ASN A2568 HIS A2571 GLN A2596 GLN A2616 HIS A2622 ASN ** A2727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20885 Z= 0.215 Angle : 0.702 16.787 28374 Z= 0.347 Chirality : 0.041 0.227 3395 Planarity : 0.006 0.081 3576 Dihedral : 6.511 65.472 2817 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 4.26 % Allowed : 11.42 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 2575 helix: -0.20 (0.11), residues: 1872 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1122 HIS 0.011 0.001 HIS A 276 PHE 0.021 0.002 PHE A3039 TYR 0.022 0.002 TYR B 114 ARG 0.009 0.001 ARG A3029 *********************** 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 611 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 514 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8749 (tp) cc_final: 0.8161 (tp) REVERT: A 356 LEU cc_start: 0.9062 (tm) cc_final: 0.8756 (tp) REVERT: A 724 GLU cc_start: 0.7693 (mp0) cc_final: 0.7328 (mt-10) REVERT: A 848 ASP cc_start: 0.7710 (m-30) cc_final: 0.7215 (m-30) REVERT: A 937 LYS cc_start: 0.8539 (tptm) cc_final: 0.8244 (tttm) REVERT: A 1077 LEU cc_start: 0.8136 (mt) cc_final: 0.7777 (mp) REVERT: A 1270 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8369 (tp) REVERT: A 1315 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8904 (tp) REVERT: A 1350 LEU cc_start: 0.8634 (tm) cc_final: 0.8007 (tp) REVERT: A 1611 LEU cc_start: 0.8733 (mt) cc_final: 0.8433 (mt) REVERT: A 1621 ILE cc_start: 0.8945 (mt) cc_final: 0.8451 (mt) REVERT: A 1772 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8813 (tp) REVERT: A 1838 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 1915 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 1923 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8030 (tm) REVERT: A 1974 GLU cc_start: 0.6956 (tt0) cc_final: 0.6622 (tt0) REVERT: A 2323 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7727 (pp) REVERT: A 2596 GLN cc_start: 0.8423 (mm-40) cc_final: 0.7726 (mt0) REVERT: A 2620 LEU cc_start: 0.8603 (tp) cc_final: 0.8362 (tt) REVERT: A 2700 LEU cc_start: 0.9158 (tp) cc_final: 0.8889 (tp) REVERT: A 2717 TYR cc_start: 0.8247 (t80) cc_final: 0.8033 (t80) REVERT: A 2731 ASP cc_start: 0.7683 (t0) cc_final: 0.7063 (t0) REVERT: A 2839 TYR cc_start: 0.8285 (m-80) cc_final: 0.7369 (m-80) REVERT: A 3076 MET cc_start: 0.7284 (ttp) cc_final: 0.6639 (ttt) REVERT: B 178 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8248 (tp) REVERT: B 286 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7516 (mttp) REVERT: B 320 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.7925 (mm) REVERT: B 339 SER cc_start: 0.9452 (m) cc_final: 0.8762 (t) outliers start: 97 outliers final: 35 residues processed: 573 average time/residue: 0.3250 time to fit residues: 291.3755 Evaluate side-chains 489 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 445 time to evaluate : 2.330 ------------------------------------------------------------------------------- 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 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 988 SER 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 1270 LEU Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain A residue 1698 SER 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 1922 ASP 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 2616 HIS 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 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 131 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 237 optimal weight: 20.0000 chunk 256 optimal weight: 0.7980 chunk 211 optimal weight: 0.2980 chunk 235 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A1091 ASN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN ** A1605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 HIS A1852 GLN A1951 GLN A2033 ASN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2616 HIS A2727 HIS A2838 ASN A2872 HIS B 137 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20885 Z= 0.191 Angle : 0.654 14.841 28374 Z= 0.319 Chirality : 0.040 0.239 3395 Planarity : 0.005 0.075 3576 Dihedral : 5.787 61.845 2807 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.18 % Rotamer: Outliers : 4.00 % Allowed : 14.67 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2575 helix: 0.61 (0.12), residues: 1880 sheet: None (None), residues: 0 loop : -2.22 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2454 HIS 0.013 0.001 HIS A 98 PHE 0.020 0.001 PHE A1495 TYR 0.016 0.001 TYR B 114 ARG 0.007 0.000 ARG A3029 *********************** 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 554 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 463 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 202 LEU cc_start: 0.8668 (tp) cc_final: 0.8119 (tp) REVERT: A 232 MET cc_start: 0.7098 (mmm) cc_final: 0.6835 (mmm) REVERT: A 356 LEU cc_start: 0.9021 (tm) cc_final: 0.8731 (tp) REVERT: A 724 GLU cc_start: 0.7759 (mp0) cc_final: 0.7527 (mp0) REVERT: A 848 ASP cc_start: 0.7545 (m-30) cc_final: 0.7172 (m-30) REVERT: A 1077 LEU cc_start: 0.8214 (mt) cc_final: 0.7889 (mp) REVERT: A 1315 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8801 (tp) REVERT: A 1611 LEU cc_start: 0.8777 (mt) cc_final: 0.8405 (mt) REVERT: A 1621 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 1772 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8653 (tp) REVERT: A 1838 LEU cc_start: 0.8758 (mt) cc_final: 0.8403 (mt) REVERT: A 1923 LEU cc_start: 0.8490 (tm) cc_final: 0.8032 (tp) REVERT: A 1974 GLU cc_start: 0.6884 (tt0) cc_final: 0.6658 (tt0) REVERT: A 2530 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7489 (mmmt) REVERT: A 2596 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7700 (mt0) REVERT: A 2698 ARG cc_start: 0.8105 (tmm-80) cc_final: 0.7870 (ttt90) REVERT: A 2717 TYR cc_start: 0.8271 (t80) cc_final: 0.8027 (t80) REVERT: A 2731 ASP cc_start: 0.7661 (t0) cc_final: 0.7118 (t0) REVERT: A 2839 TYR cc_start: 0.8331 (m-80) cc_final: 0.7286 (m-80) REVERT: A 2854 MET cc_start: 0.7310 (mtm) cc_final: 0.7022 (mtt) REVERT: A 2912 MET cc_start: 0.6990 (mmm) cc_final: 0.6673 (mmm) REVERT: A 2951 MET cc_start: 0.7467 (tmm) cc_final: 0.7160 (tmm) REVERT: A 3076 MET cc_start: 0.7068 (ttp) cc_final: 0.6648 (ttt) REVERT: A 3087 PHE cc_start: 0.8748 (t80) cc_final: 0.8510 (t80) REVERT: B 178 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 286 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7475 (mttp) REVERT: B 288 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 316 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6587 (mt-10) REVERT: B 320 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.7831 (mm) outliers start: 91 outliers final: 50 residues processed: 514 average time/residue: 0.3154 time to fit residues: 253.1208 Evaluate side-chains 479 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 423 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 104 GLU 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 400 LEU Chi-restraints excluded: chain A residue 703 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 1315 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1531 VAL Chi-restraints excluded: chain A residue 1621 ILE 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 1922 ASP 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 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 2468 LEU Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2616 HIS 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 2711 ASN Chi-restraints excluded: chain A residue 2727 HIS Chi-restraints excluded: chain A residue 2786 LEU 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 234 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** A1310 GLN ** A1742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2616 HIS A2727 HIS B 137 GLN B 353 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20885 Z= 0.197 Angle : 0.654 13.752 28374 Z= 0.313 Chirality : 0.040 0.213 3395 Planarity : 0.005 0.083 3576 Dihedral : 5.520 61.066 2805 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 4.04 % Allowed : 15.46 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2575 helix: 1.01 (0.12), residues: 1887 sheet: None (None), residues: 0 loop : -2.06 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1122 HIS 0.008 0.001 HIS A 276 PHE 0.015 0.001 PHE A2984 TYR 0.016 0.001 TYR B 114 ARG 0.007 0.000 ARG A3029 *********************** 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 534 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 442 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7757 (tm-30) cc_final: 0.6967 (tm-30) REVERT: A 202 LEU cc_start: 0.8580 (tp) cc_final: 0.8060 (tp) REVERT: A 274 CYS cc_start: 0.8123 (m) cc_final: 0.7737 (m) REVERT: A 356 LEU cc_start: 0.9053 (tm) cc_final: 0.8747 (tp) REVERT: A 848 ASP cc_start: 0.7509 (m-30) cc_final: 0.7294 (m-30) REVERT: A 937 LYS cc_start: 0.8528 (tptm) cc_final: 0.8204 (tttm) REVERT: A 1077 LEU cc_start: 0.8283 (mt) cc_final: 0.7941 (mp) REVERT: A 1263 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 1315 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8826 (tp) REVERT: A 1611 LEU cc_start: 0.8777 (mt) cc_final: 0.8423 (mt) REVERT: A 1621 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 1772 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 1838 LEU cc_start: 0.8779 (mt) cc_final: 0.8402 (mt) REVERT: A 1923 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 2530 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7447 (mmmt) REVERT: A 2596 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7783 (mt0) REVERT: A 2698 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7917 (ttt90) REVERT: A 2717 TYR cc_start: 0.8268 (t80) cc_final: 0.8008 (t80) REVERT: A 2731 ASP cc_start: 0.7689 (t0) cc_final: 0.7054 (t0) REVERT: A 2839 TYR cc_start: 0.8349 (m-80) cc_final: 0.7299 (m-80) REVERT: A 2854 MET cc_start: 0.7157 (mtm) cc_final: 0.6813 (mtt) REVERT: A 2912 MET cc_start: 0.6929 (mmm) cc_final: 0.6619 (mmm) REVERT: A 2952 GLU cc_start: 0.7335 (tp30) cc_final: 0.7109 (tp30) REVERT: A 3029 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8109 (mtm110) REVERT: A 3076 MET cc_start: 0.6908 (ttp) cc_final: 0.6588 (ttt) REVERT: A 3087 PHE cc_start: 0.8707 (t80) cc_final: 0.8356 (t80) REVERT: B 178 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8129 (tp) outliers start: 92 outliers final: 60 residues processed: 493 average time/residue: 0.3214 time to fit residues: 247.9800 Evaluate side-chains 482 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 416 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1315 LEU 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 1698 SER 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 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1922 ASP 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 2118 LEU Chi-restraints excluded: chain A residue 2153 SER 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 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 2616 HIS 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 2710 ARG Chi-restraints excluded: chain A residue 2807 LEU 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 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 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 210 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN ** A1742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN A1951 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2377 ASN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2616 HIS A2727 HIS B 137 GLN B 353 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20885 Z= 0.193 Angle : 0.647 13.979 28374 Z= 0.308 Chirality : 0.040 0.205 3395 Planarity : 0.005 0.086 3576 Dihedral : 5.360 59.999 2803 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 4.26 % Allowed : 16.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2575 helix: 1.28 (0.12), residues: 1889 sheet: None (None), residues: 0 loop : -1.96 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1122 HIS 0.008 0.001 HIS A 276 PHE 0.020 0.001 PHE A2833 TYR 0.017 0.001 TYR A2211 ARG 0.007 0.000 ARG A1738 *********************** 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 529 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 432 time to evaluate : 2.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7782 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 202 LEU cc_start: 0.8492 (tp) cc_final: 0.7998 (tp) REVERT: A 274 CYS cc_start: 0.8104 (m) cc_final: 0.7734 (m) REVERT: A 356 LEU cc_start: 0.9051 (tm) cc_final: 0.8761 (tp) REVERT: A 1077 LEU cc_start: 0.8437 (mt) cc_final: 0.8152 (mp) REVERT: A 1263 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8253 (tp) REVERT: A 1315 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8808 (tp) REVERT: A 1611 LEU cc_start: 0.8804 (mt) cc_final: 0.8435 (mt) REVERT: A 1621 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 1682 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7790 (mm110) REVERT: A 1768 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 1772 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 1838 LEU cc_start: 0.8827 (mt) cc_final: 0.8458 (mt) REVERT: A 1923 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8365 (tp) REVERT: A 2530 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7460 (mmmt) REVERT: A 2596 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7779 (mt0) REVERT: A 2717 TYR cc_start: 0.8412 (t80) cc_final: 0.8188 (t80) REVERT: A 2731 ASP cc_start: 0.7716 (t0) cc_final: 0.7038 (t0) REVERT: A 2807 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 2839 TYR cc_start: 0.8128 (m-80) cc_final: 0.7615 (m-80) REVERT: A 2854 MET cc_start: 0.7190 (mtm) cc_final: 0.6870 (mtt) REVERT: A 2912 MET cc_start: 0.7027 (mmm) cc_final: 0.6696 (mmm) REVERT: A 2952 GLU cc_start: 0.7358 (tp30) cc_final: 0.7051 (tp30) REVERT: A 3087 PHE cc_start: 0.8820 (t80) cc_final: 0.8462 (t80) REVERT: B 178 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8117 (tp) outliers start: 97 outliers final: 57 residues processed: 488 average time/residue: 0.3122 time to fit residues: 239.2832 Evaluate side-chains 469 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 404 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 698 VAL 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 1074 TRP Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1315 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1621 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR 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 1922 ASP 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 2118 LEU Chi-restraints excluded: chain A residue 2153 SER 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 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 2468 LEU Chi-restraints excluded: chain A residue 2514 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2614 SER Chi-restraints excluded: chain A residue 2616 HIS 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 2701 LEU Chi-restraints excluded: chain A residue 2708 THR Chi-restraints excluded: chain A residue 2807 LEU 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 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 314 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 84 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 62 optimal weight: 0.0020 chunk 252 optimal weight: 7.9990 chunk 209 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 A1042 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A1742 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20885 Z= 0.175 Angle : 0.640 14.186 28374 Z= 0.303 Chirality : 0.039 0.199 3395 Planarity : 0.004 0.086 3576 Dihedral : 5.237 59.787 2803 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 4.52 % Allowed : 16.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2575 helix: 1.43 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1122 HIS 0.008 0.001 HIS A 276 PHE 0.015 0.001 PHE A2983 TYR 0.015 0.001 TYR A 740 ARG 0.013 0.000 ARG A3029 *********************** 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 538 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 435 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7057 (tm-30) REVERT: A 274 CYS cc_start: 0.8014 (m) cc_final: 0.7662 (m) REVERT: A 356 LEU cc_start: 0.9047 (tm) cc_final: 0.8768 (tp) REVERT: A 1077 LEU cc_start: 0.8417 (mt) cc_final: 0.8167 (mp) REVERT: A 1292 TYR cc_start: 0.6937 (m-10) cc_final: 0.6346 (m-10) REVERT: A 1315 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 1584 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7128 (t80) REVERT: A 1611 LEU cc_start: 0.8775 (mt) cc_final: 0.8382 (mt) REVERT: A 1621 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 1768 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 1772 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8573 (tp) REVERT: A 1838 LEU cc_start: 0.8840 (mt) cc_final: 0.8470 (mt) REVERT: A 1923 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8362 (tp) REVERT: A 2468 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 2530 LYS cc_start: 0.7719 (mmmt) cc_final: 0.7437 (mmmt) REVERT: A 2596 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7778 (mt0) REVERT: A 2717 TYR cc_start: 0.8413 (t80) cc_final: 0.8180 (t80) REVERT: A 2731 ASP cc_start: 0.7625 (t0) cc_final: 0.7064 (t0) REVERT: A 2807 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 2839 TYR cc_start: 0.8179 (m-80) cc_final: 0.7672 (m-80) REVERT: A 2854 MET cc_start: 0.7226 (mtm) cc_final: 0.6953 (mtt) REVERT: A 2912 MET cc_start: 0.7052 (mmm) cc_final: 0.6783 (mmm) REVERT: A 2952 GLU cc_start: 0.7379 (tp30) cc_final: 0.6986 (tp30) REVERT: A 3087 PHE cc_start: 0.8927 (t80) cc_final: 0.8564 (t80) REVERT: B 178 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7791 (tt) REVERT: B 325 LEU cc_start: 0.9017 (tt) cc_final: 0.8443 (tp) outliers start: 103 outliers final: 67 residues processed: 494 average time/residue: 0.3132 time to fit residues: 244.3641 Evaluate side-chains 487 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 411 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 770 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 790 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 984 ASN 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 1315 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1499 LEU 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 1649 LEU Chi-restraints excluded: chain A residue 1698 SER Chi-restraints excluded: chain A residue 1768 TYR 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 1910 GLU Chi-restraints excluded: chain A residue 1922 ASP 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 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2153 SER 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 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 2605 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 2691 ILE Chi-restraints excluded: chain A residue 2692 LEU 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 2807 LEU 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 101 GLU 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 288 LEU 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 243 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 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 118 GLN A 366 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A2187 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2612 GLN A2616 HIS A2665 HIS A2727 HIS A2780 HIS A2838 ASN A3081 GLN A3085 ASN B 137 GLN B 341 GLN B 353 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20885 Z= 0.248 Angle : 0.682 13.923 28374 Z= 0.323 Chirality : 0.042 0.250 3395 Planarity : 0.005 0.088 3576 Dihedral : 5.205 59.509 2803 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Rotamer: Outliers : 4.70 % Allowed : 16.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2575 helix: 1.44 (0.12), residues: 1901 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1122 HIS 0.026 0.001 HIS A 98 PHE 0.016 0.001 PHE A2983 TYR 0.018 0.001 TYR B 114 ARG 0.008 0.000 ARG A2528 *********************** 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 526 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 419 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A 356 LEU cc_start: 0.9113 (tm) cc_final: 0.8867 (tp) REVERT: A 1077 LEU cc_start: 0.8478 (mt) cc_final: 0.8228 (mp) REVERT: A 1292 TYR cc_start: 0.7060 (m-10) cc_final: 0.6377 (m-10) REVERT: A 1315 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 1487 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 1584 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 1611 LEU cc_start: 0.8787 (mt) cc_final: 0.8413 (mt) REVERT: A 1621 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8466 (mt) REVERT: A 1768 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 1838 LEU cc_start: 0.8908 (mt) cc_final: 0.8522 (mt) REVERT: A 1923 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8434 (tp) REVERT: A 2256 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 2377 ASN cc_start: 0.8854 (t0) cc_final: 0.8603 (t0) REVERT: A 2530 LYS cc_start: 0.7784 (mmmt) cc_final: 0.7429 (mmmt) REVERT: A 2596 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7853 (mt0) REVERT: A 2606 MET cc_start: 0.8302 (mmm) cc_final: 0.7416 (mmt) REVERT: A 2674 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 2717 TYR cc_start: 0.8455 (t80) cc_final: 0.8171 (t80) REVERT: A 2731 ASP cc_start: 0.7673 (t0) cc_final: 0.7112 (t0) REVERT: A 2732 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: A 2807 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 2839 TYR cc_start: 0.8317 (m-80) cc_final: 0.7605 (m-80) REVERT: A 2952 GLU cc_start: 0.7367 (tp30) cc_final: 0.6966 (tp30) REVERT: A 3087 PHE cc_start: 0.8962 (t80) cc_final: 0.8598 (t80) REVERT: B 178 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8242 (tp) REVERT: B 325 LEU cc_start: 0.9043 (tt) cc_final: 0.8692 (tp) outliers start: 107 outliers final: 73 residues processed: 479 average time/residue: 0.2995 time to fit residues: 227.0868 Evaluate side-chains 484 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 401 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 343 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 698 VAL 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 984 ASN 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 1315 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1499 LEU 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 1630 LEU Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1649 LEU 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 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1922 ASP 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 2153 SER 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 2514 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2616 HIS 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 2691 ILE 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 2732 GLU Chi-restraints excluded: chain A residue 2807 LEU 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 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 288 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.0000 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN A2187 GLN ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2563 ASN A2616 HIS A2669 GLN A2727 HIS A2809 ASN A2838 ASN B 137 GLN B 341 GLN B 353 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20885 Z= 0.188 Angle : 0.684 14.217 28374 Z= 0.321 Chirality : 0.041 0.321 3395 Planarity : 0.005 0.088 3576 Dihedral : 5.158 58.342 2803 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 3.78 % Allowed : 17.83 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2575 helix: 1.56 (0.12), residues: 1898 sheet: None (None), residues: 0 loop : -1.71 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A1122 HIS 0.022 0.001 HIS A2616 PHE 0.016 0.001 PHE A2983 TYR 0.018 0.001 TYR A2211 ARG 0.009 0.000 ARG A3029 *********************** 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 510 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 424 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.6190 (mp0) cc_final: 0.5922 (mp0) REVERT: A 196 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 202 LEU cc_start: 0.8502 (tp) cc_final: 0.8165 (tp) REVERT: A 206 LEU cc_start: 0.7528 (tp) cc_final: 0.7320 (tp) REVERT: A 356 LEU cc_start: 0.9074 (tm) cc_final: 0.8854 (tp) REVERT: A 1077 LEU cc_start: 0.8438 (mt) cc_final: 0.8194 (mp) REVERT: A 1292 TYR cc_start: 0.6984 (m-10) cc_final: 0.6328 (m-10) REVERT: A 1315 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8846 (tp) REVERT: A 1584 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 1608 ASP cc_start: 0.7715 (p0) cc_final: 0.7488 (t0) REVERT: A 1611 LEU cc_start: 0.8835 (mt) cc_final: 0.8375 (mt) REVERT: A 1621 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 1768 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 1838 LEU cc_start: 0.8922 (mt) cc_final: 0.8528 (mt) REVERT: A 1923 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 2256 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 2596 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7855 (mt0) REVERT: A 2717 TYR cc_start: 0.8437 (t80) cc_final: 0.8165 (t80) REVERT: A 2731 ASP cc_start: 0.7652 (t0) cc_final: 0.7083 (t0) REVERT: A 2807 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 2811 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7734 (ttpp) REVERT: A 2839 TYR cc_start: 0.8315 (m-80) cc_final: 0.7634 (m-80) REVERT: A 2854 MET cc_start: 0.7223 (mtt) cc_final: 0.6833 (mtt) REVERT: A 2912 MET cc_start: 0.7157 (mmm) cc_final: 0.6795 (mmm) REVERT: A 2952 GLU cc_start: 0.7426 (tp30) cc_final: 0.6985 (tp30) REVERT: A 3087 PHE cc_start: 0.8950 (t80) cc_final: 0.8579 (t80) REVERT: B 178 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7833 (tt) outliers start: 86 outliers final: 60 residues processed: 474 average time/residue: 0.3058 time to fit residues: 230.4744 Evaluate side-chains 474 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 406 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 698 VAL 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 984 ASN 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 1315 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1499 LEU 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 1649 LEU 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 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1922 ASP 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 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2153 SER 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 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL 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 2708 THR Chi-restraints excluded: chain A residue 2710 ARG Chi-restraints excluded: chain A residue 2807 LEU 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 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 228 optimal weight: 8.9990 chunk 241 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 234 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 HIS ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS B 137 GLN B 353 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20885 Z= 0.190 Angle : 0.679 14.316 28374 Z= 0.319 Chirality : 0.041 0.432 3395 Planarity : 0.004 0.095 3576 Dihedral : 5.035 57.852 2802 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 3.56 % Allowed : 18.09 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2575 helix: 1.64 (0.12), residues: 1901 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1122 HIS 0.008 0.001 HIS A 276 PHE 0.015 0.001 PHE A2983 TYR 0.018 0.001 TYR A2211 ARG 0.008 0.000 ARG A3029 *********************** 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 499 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 418 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 356 LEU cc_start: 0.9048 (tm) cc_final: 0.8812 (tp) REVERT: A 771 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8644 (tp) REVERT: A 1077 LEU cc_start: 0.8485 (mt) cc_final: 0.8257 (mp) REVERT: A 1292 TYR cc_start: 0.7034 (m-10) cc_final: 0.6416 (m-10) REVERT: A 1315 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8811 (tp) REVERT: A 1584 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 1611 LEU cc_start: 0.8818 (mt) cc_final: 0.8462 (mt) REVERT: A 1621 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 1768 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6323 (t80) REVERT: A 1821 MET cc_start: 0.7950 (mtm) cc_final: 0.7685 (mtp) REVERT: A 1838 LEU cc_start: 0.8942 (mt) cc_final: 0.8530 (mt) REVERT: A 1923 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 2256 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 2320 GLU cc_start: 0.7047 (tt0) cc_final: 0.6810 (tt0) REVERT: A 2596 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7843 (mt0) REVERT: A 2717 TYR cc_start: 0.8445 (t80) cc_final: 0.8157 (t80) REVERT: A 2731 ASP cc_start: 0.7626 (t0) cc_final: 0.7033 (t0) REVERT: A 2807 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8000 (mt) REVERT: A 2811 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7622 (ttpp) REVERT: A 2839 TYR cc_start: 0.8422 (m-80) cc_final: 0.7689 (m-80) REVERT: A 2854 MET cc_start: 0.7262 (mtt) cc_final: 0.6912 (mtt) REVERT: A 2952 GLU cc_start: 0.7519 (tp30) cc_final: 0.7089 (tp30) REVERT: B 178 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7831 (tt) outliers start: 81 outliers final: 60 residues processed: 467 average time/residue: 0.3062 time to fit residues: 226.9601 Evaluate side-chains 467 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 398 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 698 VAL 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 872 ASP Chi-restraints excluded: chain A residue 984 ASN 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 1315 LEU 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 1649 LEU 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 1850 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1922 ASP 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 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2131 MET Chi-restraints excluded: chain A residue 2153 SER 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 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2692 LEU Chi-restraints excluded: chain A residue 2701 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 2807 LEU 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 137 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 LEU 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 233 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 172 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 159 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2727 HIS B 137 GLN B 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20885 Z= 0.184 Angle : 0.695 15.535 28374 Z= 0.323 Chirality : 0.041 0.443 3395 Planarity : 0.005 0.092 3576 Dihedral : 4.994 57.569 2802 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 3.12 % Allowed : 19.32 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2575 helix: 1.68 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1122 HIS 0.007 0.001 HIS A2727 PHE 0.018 0.001 PHE A1495 TYR 0.018 0.001 TYR A 740 ARG 0.014 0.000 ARG A3029 ********************** 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 500 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 429 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7142 (tm-30) REVERT: A 356 LEU cc_start: 0.9029 (tm) cc_final: 0.8808 (tp) REVERT: A 771 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8621 (tp) REVERT: A 1251 ASP cc_start: 0.7299 (t0) cc_final: 0.6524 (t0) REVERT: A 1292 TYR cc_start: 0.7004 (m-10) cc_final: 0.6422 (m-10) REVERT: A 1315 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 1584 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7033 (t80) REVERT: A 1611 LEU cc_start: 0.8749 (mt) cc_final: 0.8418 (mt) REVERT: A 1621 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 1768 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6273 (t80) REVERT: A 1821 MET cc_start: 0.7952 (mtm) cc_final: 0.7742 (mtp) REVERT: A 1838 LEU cc_start: 0.8936 (mt) cc_final: 0.8526 (mt) REVERT: A 1923 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8383 (tp) REVERT: A 2256 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 2320 GLU cc_start: 0.6972 (tt0) cc_final: 0.6753 (tt0) REVERT: A 2596 GLN cc_start: 0.8435 (mm-40) cc_final: 0.7839 (mt0) REVERT: A 2717 TYR cc_start: 0.8408 (t80) cc_final: 0.8130 (t80) REVERT: A 2731 ASP cc_start: 0.7668 (t0) cc_final: 0.7058 (t0) REVERT: A 2807 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 2811 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7528 (ttpp) REVERT: A 2839 TYR cc_start: 0.8378 (m-80) cc_final: 0.7584 (m-80) REVERT: A 2854 MET cc_start: 0.7296 (mtt) cc_final: 0.6960 (mtt) REVERT: A 2952 GLU cc_start: 0.7535 (tp30) cc_final: 0.7076 (tp30) REVERT: A 3013 TYR cc_start: 0.8922 (t80) cc_final: 0.8602 (t80) REVERT: A 3087 PHE cc_start: 0.8804 (t80) cc_final: 0.8483 (t80) REVERT: B 173 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8088 (tp) REVERT: B 178 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7767 (tt) outliers start: 71 outliers final: 54 residues processed: 474 average time/residue: 0.3214 time to fit residues: 240.9442 Evaluate side-chains 467 residues out of total 2280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 403 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 698 VAL 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 872 ASP Chi-restraints excluded: chain A residue 984 ASN 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 1071 SER Chi-restraints excluded: chain A residue 1074 TRP Chi-restraints excluded: chain A residue 1271 SER Chi-restraints excluded: chain A residue 1315 LEU 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 1649 LEU 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 1850 VAL Chi-restraints excluded: chain A residue 1922 ASP 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 2100 VAL Chi-restraints excluded: chain A residue 2118 LEU Chi-restraints excluded: chain A residue 2153 SER 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 2311 LEU Chi-restraints excluded: chain A residue 2323 LEU Chi-restraints excluded: chain A residue 2401 VAL Chi-restraints excluded: chain A residue 2678 TRP Chi-restraints excluded: chain A residue 2701 LEU Chi-restraints excluded: chain A residue 2708 THR Chi-restraints excluded: chain A residue 2710 ARG Chi-restraints excluded: chain A residue 2807 LEU 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 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 126 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 57 optimal weight: 0.0770 chunk 207 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 281 GLN ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1708 ASN ** A2026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.171609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137760 restraints weight = 24318.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.138285 restraints weight = 24572.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139641 restraints weight = 20314.224| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20885 Z= 0.177 Angle : 0.679 14.319 28374 Z= 0.315 Chirality : 0.040 0.420 3395 Planarity : 0.004 0.091 3576 Dihedral : 4.914 57.495 2802 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 2.99 % Allowed : 19.72 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2575 helix: 1.78 (0.12), residues: 1894 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1122 HIS 0.010 0.001 HIS A3071 PHE 0.014 0.001 PHE A2984 TYR 0.018 0.001 TYR A 740 ARG 0.008 0.000 ARG A2724 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.80 seconds wall clock time: 86 minutes 32.23 seconds (5192.23 seconds total)