Starting phenix.real_space_refine on Sun Feb 8 10:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743.map" model { file = "/net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pmw_71743/02_2026/9pmw_71743_neut_trim.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 5 Type Number sf(0) Gaussians S 134 5.16 5 C 13696 2.51 5 N 3683 2.21 5 O 3875 1.98 5 H 21934 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43322 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 292 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 1, 'TRANS': 15} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 267 Unusual residues: {'ACE': 1} Classifications: {'peptide': 17, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 16} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 256 Unusual residues: {'ACE': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 14} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2428, 38709 Classifications: {'peptide': 2428} Link IDs: {'PTRANS': 111, 'TRANS': 2316} Chain breaks: 19 Chain: "B" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3795 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 7.57, per 1000 atoms: 0.17 Number of scatterers: 43322 At special positions: 0 Unit cell: (117.12, 135.42, 144.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 O 3875 8.00 N 3683 7.00 C 13696 6.00 H 21934 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY D 2 " Number of C-beta restraints generated: 5214 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 2 sheets defined 78.1% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.260A pdb=" N LEU A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 4.232A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 200 through 219 removed outlier: 4.685A pdb=" N ARG A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Proline residue: A 206 - end of helix Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.504A pdb=" N ALA A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 265 through 283 Processing helix chain 'A' and resid 285 through 300 Processing helix chain 'A' and resid 309 through 324 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 352 through 367 Processing helix chain 'A' and resid 371 through 388 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 681 through 695 removed outlier: 4.012A pdb=" N HIS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 728 removed outlier: 3.818A pdb=" N LEU A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.630A pdb=" N SER A 734 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 761 Processing helix chain 'A' and resid 763 through 785 Processing helix chain 'A' and resid 788 through 801 Processing helix chain 'A' and resid 805 through 808 Processing helix chain 'A' and resid 809 through 818 removed outlier: 3.727A pdb=" N LYS A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 842 removed outlier: 5.672A pdb=" N MET A 837 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER A 838 " --> pdb=" O ASN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 856 removed outlier: 3.753A pdb=" N LEU A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 861 Processing helix chain 'A' and resid 863 through 877 removed outlier: 3.877A pdb=" N ILE A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 889 Processing helix chain 'A' and resid 890 through 898 removed outlier: 7.060A pdb=" N ALA A 896 " --> pdb=" O HIS A 893 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 897 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 898 " --> pdb=" O GLY A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 913 removed outlier: 3.523A pdb=" N VAL A 913 " --> pdb=" O VAL A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 937 Processing helix chain 'A' and resid 938 through 940 No H-bonds generated for 'chain 'A' and resid 938 through 940' Processing helix chain 'A' and resid 950 through 964 removed outlier: 4.181A pdb=" N VAL A 962 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR A 963 " --> pdb=" O GLN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1017 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1068 through 1078 removed outlier: 3.579A pdb=" N LEU A1075 " --> pdb=" O MET A1071 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1083 Processing helix chain 'A' and resid 1084 through 1101 Processing helix chain 'A' and resid 1102 through 1107 Processing helix chain 'A' and resid 1133 through 1135 No H-bonds generated for 'chain 'A' and resid 1133 through 1135' Processing helix chain 'A' and resid 1136 through 1160 Processing helix chain 'A' and resid 1235 through 1254 removed outlier: 3.537A pdb=" N TYR A1252 " --> pdb=" O THR A1248 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1280 Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'A' and resid 1291 through 1303 removed outlier: 3.574A pdb=" N SER A1301 " --> pdb=" O GLY A1297 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1322 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1355 through 1361 Processing helix chain 'A' and resid 1361 through 1375 Processing helix chain 'A' and resid 1376 through 1377 No H-bonds generated for 'chain 'A' and resid 1376 through 1377' Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 4.241A pdb=" N HIS A1423 " --> pdb=" O ILE A1420 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A1424 " --> pdb=" O HIS A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1441 removed outlier: 3.558A pdb=" N THR A1439 " --> pdb=" O LEU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1460 Processing helix chain 'A' and resid 1463 through 1468 Processing helix chain 'A' and resid 1471 through 1486 removed outlier: 3.685A pdb=" N PHE A1481 " --> pdb=" O VAL A1477 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A1482 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR A1483 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1494 Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1518 through 1532 removed outlier: 4.683A pdb=" N SER A1532 " --> pdb=" O GLY A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1538 Processing helix chain 'A' and resid 1539 through 1554 Proline residue: A1546 - end of helix Processing helix chain 'A' and resid 1564 through 1579 Processing helix chain 'A' and resid 1583 through 1601 removed outlier: 3.743A pdb=" N LYS A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1622 Proline residue: A1618 - end of helix Processing helix chain 'A' and resid 1629 through 1643 removed outlier: 3.642A pdb=" N GLU A1641 " --> pdb=" O ASN A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1649 removed outlier: 3.660A pdb=" N ARG A1649 " --> pdb=" O SER A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1659 Processing helix chain 'A' and resid 1667 through 1689 removed outlier: 3.585A pdb=" N VAL A1684 " --> pdb=" O ALA A1680 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1701 Processing helix chain 'A' and resid 1704 through 1708 removed outlier: 4.074A pdb=" N ILE A1708 " --> pdb=" O PRO A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1718 Processing helix chain 'A' and resid 1737 through 1760 removed outlier: 3.560A pdb=" N GLY A1751 " --> pdb=" O LEU A1747 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1760 " --> pdb=" O ASP A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1792 removed outlier: 4.443A pdb=" N GLY A1792 " --> pdb=" O ILE A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1806 removed outlier: 3.684A pdb=" N ARG A1806 " --> pdb=" O THR A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1827 Processing helix chain 'A' and resid 1828 through 1830 No H-bonds generated for 'chain 'A' and resid 1828 through 1830' Processing helix chain 'A' and resid 1831 through 1845 Processing helix chain 'A' and resid 1849 through 1857 removed outlier: 4.959A pdb=" N GLU A1855 " --> pdb=" O ARG A1851 " (cutoff:3.500A) Processing helix chain 'A' and resid 1890 through 1909 Processing helix chain 'A' and resid 1915 through 1932 removed outlier: 7.410A pdb=" N GLN A1927 " --> pdb=" O VAL A1923 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP A1928 " --> pdb=" O ASN A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1947 Processing helix chain 'A' and resid 1948 through 1961 Processing helix chain 'A' and resid 1962 through 1967 Processing helix chain 'A' and resid 1968 through 1980 Processing helix chain 'A' and resid 1981 through 1982 No H-bonds generated for 'chain 'A' and resid 1981 through 1982' Processing helix chain 'A' and resid 1983 through 1985 No H-bonds generated for 'chain 'A' and resid 1983 through 1985' Processing helix chain 'A' and resid 1986 through 1997 Processing helix chain 'A' and resid 2003 through 2024 Processing helix chain 'A' and resid 2025 through 2033 removed outlier: 3.899A pdb=" N ALA A2031 " --> pdb=" O GLN A2027 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2048 Processing helix chain 'A' and resid 2049 through 2054 Processing helix chain 'A' and resid 2054 through 2067 Processing helix chain 'A' and resid 2098 through 2111 removed outlier: 3.636A pdb=" N GLN A2109 " --> pdb=" O LEU A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2117 through 2127 removed outlier: 3.577A pdb=" N ARG A2127 " --> pdb=" O GLU A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2139 removed outlier: 4.361A pdb=" N ASN A2134 " --> pdb=" O ALA A2130 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA A2135 " --> pdb=" O GLU A2131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A2139 " --> pdb=" O ALA A2135 " (cutoff:3.500A) Processing helix chain 'A' and resid 2143 through 2145 No H-bonds generated for 'chain 'A' and resid 2143 through 2145' Processing helix chain 'A' and resid 2146 through 2159 Processing helix chain 'A' and resid 2164 through 2183 Processing helix chain 'A' and resid 2203 through 2211 Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.719A pdb=" N SER A2219 " --> pdb=" O ALA A2215 " (cutoff:3.500A) Proline residue: A2221 - end of helix removed outlier: 3.560A pdb=" N ALA A2226 " --> pdb=" O THR A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2242 Processing helix chain 'A' and resid 2244 through 2246 No H-bonds generated for 'chain 'A' and resid 2244 through 2246' Processing helix chain 'A' and resid 2247 through 2269 Processing helix chain 'A' and resid 2273 through 2290 removed outlier: 3.508A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) Processing helix chain 'A' and resid 2290 through 2298 removed outlier: 3.893A pdb=" N VAL A2296 " --> pdb=" O GLY A2292 " (cutoff:3.500A) Processing helix chain 'A' and resid 2299 through 2301 No H-bonds generated for 'chain 'A' and resid 2299 through 2301' Processing helix chain 'A' and resid 2302 through 2322 Processing helix chain 'A' and resid 2355 through 2372 removed outlier: 3.928A pdb=" N THR A2359 " --> pdb=" O PRO A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2402 Processing helix chain 'A' and resid 2404 through 2413 removed outlier: 4.690A pdb=" N SER A2409 " --> pdb=" O PRO A2405 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A2410 " --> pdb=" O LEU A2406 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A2413 " --> pdb=" O SER A2409 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2420 removed outlier: 4.046A pdb=" N TRP A2418 " --> pdb=" O PRO A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2440 through 2443 removed outlier: 3.643A pdb=" N GLN A2443 " --> pdb=" O GLU A2440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2440 through 2443' Processing helix chain 'A' and resid 2444 through 2459 Processing helix chain 'A' and resid 2462 through 2478 removed outlier: 3.622A pdb=" N VAL A2476 " --> pdb=" O THR A2472 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A2477 " --> pdb=" O LEU A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2514 Processing helix chain 'A' and resid 2515 through 2517 No H-bonds generated for 'chain 'A' and resid 2515 through 2517' Processing helix chain 'A' and resid 2539 through 2542 Processing helix chain 'A' and resid 2543 through 2565 removed outlier: 3.552A pdb=" N LYS A2548 " --> pdb=" O ARG A2544 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.940A pdb=" N LEU A2600 " --> pdb=" O GLU A2597 " (cutoff:3.500A) Processing helix chain 'A' and resid 2620 through 2629 Processing helix chain 'A' and resid 2669 through 2686 removed outlier: 3.770A pdb=" N CYS A2673 " --> pdb=" O ASP A2669 " (cutoff:3.500A) Processing helix chain 'A' and resid 2695 through 2710 removed outlier: 4.068A pdb=" N SER A2700 " --> pdb=" O ALA A2696 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU A2701 " --> pdb=" O ILE A2697 " (cutoff:3.500A) Processing helix chain 'A' and resid 2711 through 2713 No H-bonds generated for 'chain 'A' and resid 2711 through 2713' Processing helix chain 'A' and resid 2715 through 2733 removed outlier: 3.969A pdb=" N PHE A2719 " --> pdb=" O GLU A2715 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A2731 " --> pdb=" O THR A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2740 through 2755 Proline residue: A2746 - end of helix Processing helix chain 'A' and resid 2758 through 2773 removed outlier: 4.202A pdb=" N GLU A2763 " --> pdb=" O LYS A2759 " (cutoff:3.500A) Proline residue: A2764 - end of helix Processing helix chain 'A' and resid 2777 through 2792 Processing helix chain 'A' and resid 2797 through 2820 removed outlier: 4.361A pdb=" N GLN A2803 " --> pdb=" O ASP A2799 " (cutoff:3.500A) Proline residue: A2806 - end of helix removed outlier: 3.526A pdb=" N LYS A2817 " --> pdb=" O LEU A2813 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A2818 " --> pdb=" O SER A2814 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A2819 " --> pdb=" O ASN A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2822 through 2826 Processing helix chain 'A' and resid 2827 through 2845 Processing helix chain 'A' and resid 2854 through 2866 Processing helix chain 'A' and resid 2873 through 2890 removed outlier: 3.526A pdb=" N LEU A2889 " --> pdb=" O GLU A2885 " (cutoff:3.500A) Processing helix chain 'A' and resid 2894 through 2910 removed outlier: 3.729A pdb=" N VAL A2906 " --> pdb=" O VAL A2902 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A2907 " --> pdb=" O LYS A2903 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A2908 " --> pdb=" O LEU A2904 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A2909 " --> pdb=" O SER A2905 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A2910 " --> pdb=" O VAL A2906 " (cutoff:3.500A) Processing helix chain 'A' and resid 2913 through 2931 Processing helix chain 'A' and resid 2954 through 2970 removed outlier: 3.885A pdb=" N GLU A2958 " --> pdb=" O ILE A2954 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A2959 " --> pdb=" O VAL A2955 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A2962 " --> pdb=" O GLU A2958 " (cutoff:3.500A) Processing helix chain 'A' and resid 2971 through 2990 removed outlier: 4.311A pdb=" N VAL A2977 " --> pdb=" O CYS A2973 " (cutoff:3.500A) Proline residue: A2983 - end of helix Processing helix chain 'A' and resid 2991 through 2994 Processing helix chain 'A' and resid 2995 through 3005 Processing helix chain 'A' and resid 3010 through 3028 removed outlier: 4.274A pdb=" N THR A3016 " --> pdb=" O GLN A3012 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A3017 " --> pdb=" O PHE A3013 " (cutoff:3.500A) Processing helix chain 'A' and resid 3030 through 3046 removed outlier: 4.061A pdb=" N VAL A3034 " --> pdb=" O GLN A3030 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER A3043 " --> pdb=" O MET A3039 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN A3044 " --> pdb=" O LEU A3040 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3066 removed outlier: 4.105A pdb=" N SER A3057 " --> pdb=" O MET A3053 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A3058 " --> pdb=" O ALA A3054 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N CYS A3060 " --> pdb=" O TRP A3056 " (cutoff:3.500A) Processing helix chain 'A' and resid 3068 through 3073 Processing helix chain 'A' and resid 3074 through 3080 Processing helix chain 'A' and resid 3086 through 3104 Processing helix chain 'A' and resid 3108 through 3120 removed outlier: 3.916A pdb=" N GLN A3115 " --> pdb=" O ARG A3111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A3120 " --> pdb=" O SER A3116 " (cutoff:3.500A) Processing helix chain 'A' and resid 3126 through 3137 Processing helix chain 'B' and resid 84 through 106 removed outlier: 3.600A pdb=" N PHE B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 135 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.751A pdb=" N LEU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 173 Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 216 Processing helix chain 'B' and resid 259 through 281 removed outlier: 3.505A pdb=" N VAL B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.081A pdb=" N LYS B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 331 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.513A pdb=" N VAL B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 349 through 365 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6 1394 hydrogen bonds defined for protein. 4068 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: 11.68 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 21863 1.12 - 1.31: 3763 1.31 - 1.49: 8383 1.49 - 1.67: 9536 1.67 - 1.85: 194 Bond restraints: 43739 Sorted by residual: bond pdb=" C ACE E 1 " pdb=" N TYR E 2 " ideal model delta sigma weight residual 1.329 1.547 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C ACE D 1 " pdb=" O ACE D 1 " ideal model delta sigma weight residual 1.199 1.417 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C ACE C 1 " pdb=" O ACE C 1 " ideal model delta sigma weight residual 1.199 1.406 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" N TYR C 2 " pdb=" H TYR C 2 " ideal model delta sigma weight residual 0.860 1.039 -0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" N CYS D 6 " pdb=" H CYS D 6 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.05e+01 ... (remaining 43734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.52: 79022 7.52 - 15.03: 282 15.03 - 22.55: 8 22.55 - 30.06: 2 30.06 - 37.58: 6 Bond angle restraints: 79320 Sorted by residual: angle pdb=" CA CYS E 17 " pdb=" C CYS E 17 " pdb=" O CYS E 17 " ideal model delta sigma weight residual 120.80 90.44 30.36 1.70e+00 3.46e-01 3.19e+02 angle pdb=" CB LEU B 314 " pdb=" CG LEU B 314 " pdb=" HG LEU B 314 " ideal model delta sigma weight residual 109.00 71.42 37.58 3.00e+00 1.11e-01 1.57e+02 angle pdb=" CD1 LEU B 314 " pdb=" CG LEU B 314 " pdb=" HG LEU B 314 " ideal model delta sigma weight residual 108.00 72.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CD1 LEU A 695 " pdb=" CG LEU A 695 " pdb=" HG LEU A 695 " ideal model delta sigma weight residual 108.00 74.29 33.71 3.00e+00 1.11e-01 1.26e+02 angle pdb=" CB LEU A 695 " pdb=" CG LEU A 695 " pdb=" HG LEU A 695 " ideal model delta sigma weight residual 109.00 75.66 33.34 3.00e+00 1.11e-01 1.24e+02 ... (remaining 79315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 19591 31.35 - 62.70: 780 62.70 - 94.05: 167 94.05 - 125.40: 0 125.40 - 156.76: 1 Dihedral angle restraints: 20539 sinusoidal: 11256 harmonic: 9283 Sorted by residual: dihedral pdb=" CH3 ACE E 1 " pdb=" C ACE E 1 " pdb=" N TYR E 2 " pdb=" CA TYR E 2 " ideal model delta sinusoidal sigma weight residual -180.00 -23.24 -156.76 1 5.00e+00 4.00e-02 7.37e+02 dihedral pdb=" CA GLN A3104 " pdb=" C GLN A3104 " pdb=" N ILE A3105 " pdb=" CA ILE A3105 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA THR A2517 " pdb=" C THR A2517 " pdb=" N VAL A2518 " pdb=" CA VAL A2518 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 20536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 3227 0.156 - 0.312: 281 0.312 - 0.468: 11 0.468 - 0.624: 1 0.624 - 0.781: 2 Chirality restraints: 3522 Sorted by residual: chirality pdb=" CG LEU A 695 " pdb=" CB LEU A 695 " pdb=" CD1 LEU A 695 " pdb=" CD2 LEU A 695 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CB VAL A1586 " pdb=" CA VAL A1586 " pdb=" CG1 VAL A1586 " pdb=" CG2 VAL A1586 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CG LEU B 314 " pdb=" CB LEU B 314 " pdb=" CD1 LEU B 314 " pdb=" CD2 LEU B 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 3519 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE C 1 " 0.537 2.00e-02 2.50e+03 4.00e-01 2.00e+03 pdb=" O ACE C 1 " -0.416 2.00e-02 2.50e+03 pdb=" N TYR C 2 " 0.323 2.00e-02 2.50e+03 pdb=" CA TYR C 2 " 0.035 2.00e-02 2.50e+03 pdb=" H TYR C 2 " -0.480 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE D 1 " 0.389 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" O ACE D 1 " -0.153 2.00e-02 2.50e+03 pdb=" CH3 ACE D 1 " -0.086 2.00e-02 2.50e+03 pdb=" N DTY D 2 " -0.208 2.00e-02 2.50e+03 pdb=" CA DTY D 2 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE E 1 " 0.029 2.00e-02 2.50e+03 1.59e-01 3.79e+02 pdb=" O ACE E 1 " -0.076 2.00e-02 2.50e+03 pdb=" CH3 ACE E 1 " 0.088 2.00e-02 2.50e+03 pdb=" N TYR E 2 " -0.280 2.00e-02 2.50e+03 pdb=" CA TYR E 2 " -0.004 2.00e-02 2.50e+03 pdb=" H TYR E 2 " 0.243 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 2070 2.18 - 2.78: 76943 2.78 - 3.39: 128178 3.39 - 3.99: 170590 3.99 - 4.60: 247107 Nonbonded interactions: 624888 Sorted by model distance: nonbonded pdb=" HG SER A2152 " pdb=" OXT VAL B 371 " model vdw 1.569 2.450 nonbonded pdb=" HG1 THR A1816 " pdb=" OD1 ASP A1818 " model vdw 1.583 2.450 nonbonded pdb=" HH TYR A2929 " pdb=" OD2 ASP A2988 " model vdw 1.592 2.450 nonbonded pdb=" HG SER A 805 " pdb=" OD1 ASP A 808 " model vdw 1.605 2.450 nonbonded pdb=" OE1 GLU A 361 " pdb=" HG SER A 675 " model vdw 1.608 2.450 ... (remaining 624883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.940 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: 0.290 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 41.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 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 : 0.013 0.218 21811 Z= 0.790 Angle : 1.842 30.355 29616 Z= 1.247 Chirality : 0.094 0.781 3522 Planarity : 0.015 0.232 3736 Dihedral : 13.768 156.756 8010 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 0.76 % Allowed : 4.03 % Favored : 95.21 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 2676 helix: -0.54 (0.10), residues: 1880 sheet: -2.83 (1.14), residues: 9 loop : 0.20 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A 833 TYR 0.206 0.023 TYR A2811 PHE 0.083 0.013 PHE A 879 TRP 0.100 0.021 TRP A1853 HIS 0.018 0.003 HIS A2878 Details of bonding type rmsd covalent geometry : bond 0.01248 (21805) covalent geometry : angle 1.84224 (29616) hydrogen bonds : bond 0.19153 ( 1394) hydrogen bonds : angle 6.67304 ( 4068) Misc. bond : bond 0.08188 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 678 time to evaluate : 1.175 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1308 MET cc_start: 0.7414 (tmm) cc_final: 0.7172 (tmm) REVERT: A 2618 GLN cc_start: 0.7566 (mm110) cc_final: 0.7225 (tp40) REVERT: A 2675 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6880 (mm-40) REVERT: A 2685 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 2767 ARG cc_start: 0.6923 (mtp180) cc_final: 0.6656 (mtp180) REVERT: A 2770 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6201 (mt-10) REVERT: A 3047 GLN cc_start: 0.7510 (mt0) cc_final: 0.7195 (mt0) outliers start: 18 outliers final: 2 residues processed: 689 average time/residue: 1.3861 time to fit residues: 1096.2694 Evaluate side-chains 587 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 584 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2454 ARG Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2685 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 ASN A 111 ASN A 210 ASN A 246 ASN A 383 GLN A1445 GLN A1840 GLN A1892 ASN A2501 ASN A2535 ASN A2815 ASN B 182 GLN B 191 GLN B 313 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.151860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.137500 restraints weight = 68562.117| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.20 r_work: 0.3803 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21811 Z= 0.215 Angle : 0.706 10.146 29616 Z= 0.374 Chirality : 0.060 1.626 3522 Planarity : 0.006 0.059 3736 Dihedral : 6.655 177.899 2931 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.06 % Allowed : 10.80 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2676 helix: 0.69 (0.11), residues: 1900 sheet: -2.55 (1.30), residues: 9 loop : 0.27 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1656 TYR 0.020 0.002 TYR A3101 PHE 0.019 0.002 PHE A1500 TRP 0.026 0.002 TRP B 300 HIS 0.013 0.002 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00487 (21805) covalent geometry : angle 0.70621 (29616) hydrogen bonds : bond 0.06552 ( 1394) hydrogen bonds : angle 4.76518 ( 4068) Misc. bond : bond 0.00138 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 606 time to evaluate : 1.384 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: symmetry clash REVERT: A 833 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7456 (ttt180) REVERT: A 1317 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 1470 ASP cc_start: 0.7223 (m-30) cc_final: 0.7021 (m-30) REVERT: A 1511 TYR cc_start: 0.7135 (m-80) cc_final: 0.6677 (m-80) REVERT: A 1766 MET cc_start: 0.8780 (ptt) cc_final: 0.8460 (ptp) REVERT: A 2618 GLN cc_start: 0.7940 (mm110) cc_final: 0.7595 (tp-100) REVERT: A 2767 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7363 (mtp180) REVERT: A 2770 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6370 (mt-10) REVERT: A 2957 MET cc_start: 0.7664 (tpt) cc_final: 0.7440 (tpt) REVERT: B 86 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5995 (tm-30) REVERT: B 98 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7645 (mp) outliers start: 49 outliers final: 18 residues processed: 621 average time/residue: 1.4250 time to fit residues: 1010.5284 Evaluate side-chains 600 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 578 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 784 ARG Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 833 ARG Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1642 ILE Chi-restraints excluded: chain A residue 1968 THR Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2717 ASN Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2890 SER Chi-restraints excluded: chain A residue 2965 ASP Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3098 THR Chi-restraints excluded: chain A residue 3105 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 192 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 260 optimal weight: 0.9980 chunk 231 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 ASN A 210 ASN A 912 ASN A1624 GLN A2373 GLN B 182 GLN B 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.151149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136754 restraints weight = 67919.936| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.19 r_work: 0.3796 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21811 Z= 0.197 Angle : 0.642 10.572 29616 Z= 0.335 Chirality : 0.060 1.724 3522 Planarity : 0.005 0.076 3736 Dihedral : 6.182 177.940 2925 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 12.10 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2676 helix: 0.99 (0.11), residues: 1906 sheet: -2.39 (1.38), residues: 9 loop : 0.25 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1893 TYR 0.020 0.002 TYR A2357 PHE 0.019 0.002 PHE A1500 TRP 0.018 0.002 TRP B 300 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00461 (21805) covalent geometry : angle 0.64195 (29616) hydrogen bonds : bond 0.05911 ( 1394) hydrogen bonds : angle 4.47429 ( 4068) Misc. bond : bond 0.00137 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 590 time to evaluate : 1.041 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: symmetry clash REVERT: A 284 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6851 (ttm170) REVERT: A 1511 TYR cc_start: 0.7234 (m-80) cc_final: 0.6660 (m-80) REVERT: A 1766 MET cc_start: 0.8750 (ptt) cc_final: 0.8447 (ptt) REVERT: A 2062 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: A 2767 ARG cc_start: 0.7487 (mtp180) cc_final: 0.7274 (mtp180) REVERT: A 2770 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6405 (mt-10) outliers start: 57 outliers final: 26 residues processed: 616 average time/residue: 1.3761 time to fit residues: 969.7626 Evaluate side-chains 598 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 570 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1968 THR Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2062 ASP Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2277 LEU Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2674 SER Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3026 HIS Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3098 THR Chi-restraints excluded: chain A residue 3105 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 210 ASN A 906 GLN A1463 ASN A2042 GLN A2373 GLN A2628 ASN B 182 GLN B 191 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.150392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136063 restraints weight = 68283.132| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.19 r_work: 0.3789 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21811 Z= 0.220 Angle : 0.625 10.730 29616 Z= 0.327 Chirality : 0.062 1.752 3522 Planarity : 0.005 0.069 3736 Dihedral : 6.090 177.354 2925 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.02 % Allowed : 13.66 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.16), residues: 2676 helix: 1.07 (0.12), residues: 1905 sheet: -2.25 (1.30), residues: 9 loop : 0.26 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1656 TYR 0.020 0.002 TYR A2357 PHE 0.020 0.002 PHE A2839 TRP 0.016 0.002 TRP B 300 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00513 (21805) covalent geometry : angle 0.62547 (29616) hydrogen bonds : bond 0.05758 ( 1394) hydrogen bonds : angle 4.40563 ( 4068) Misc. bond : bond 0.00058 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 577 time to evaluate : 1.033 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 1766 MET cc_start: 0.8724 (ptt) cc_final: 0.8514 (ptt) REVERT: A 2618 GLN cc_start: 0.8050 (mm110) cc_final: 0.7689 (tp-100) REVERT: A 2767 ARG cc_start: 0.7560 (mtp180) cc_final: 0.7341 (mtp180) REVERT: A 2770 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6477 (mt-10) REVERT: B 86 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6372 (tm-30) outliers start: 48 outliers final: 28 residues processed: 593 average time/residue: 1.1851 time to fit residues: 804.8514 Evaluate side-chains 593 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 564 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1968 THR Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3036 ASP Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3105 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 94 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 701 ASN A 757 ASN A 959 GLN A1463 ASN A1624 GLN A2055 GLN A2373 GLN A2628 ASN A2815 ASN A3047 GLN B 182 GLN B 191 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.150199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135886 restraints weight = 68038.056| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.19 r_work: 0.3784 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 21811 Z= 0.215 Angle : 0.621 10.697 29616 Z= 0.322 Chirality : 0.062 1.765 3522 Planarity : 0.005 0.086 3736 Dihedral : 6.013 177.352 2925 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 14.03 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.16), residues: 2676 helix: 1.07 (0.12), residues: 1917 sheet: -2.09 (1.23), residues: 9 loop : 0.16 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1656 TYR 0.019 0.002 TYR A2357 PHE 0.022 0.002 PHE A2839 TRP 0.015 0.002 TRP B 300 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00509 (21805) covalent geometry : angle 0.62072 (29616) hydrogen bonds : bond 0.05644 ( 1394) hydrogen bonds : angle 4.37240 ( 4068) Misc. bond : bond 0.00059 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 579 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1766 MET cc_start: 0.8697 (ptt) cc_final: 0.8446 (ptt) REVERT: A 2618 GLN cc_start: 0.8064 (mm110) cc_final: 0.7799 (tp-100) REVERT: A 2770 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6512 (mt-10) REVERT: A 3036 ASP cc_start: 0.7349 (m-30) cc_final: 0.7147 (m-30) outliers start: 51 outliers final: 30 residues processed: 597 average time/residue: 1.0666 time to fit residues: 732.6513 Evaluate side-chains 601 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 571 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2159 SER Chi-restraints excluded: chain A residue 2356 LYS Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3016 THR Chi-restraints excluded: chain A residue 3096 VAL Chi-restraints excluded: chain A residue 3105 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 224 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 GLN A1463 ASN A1927 GLN A2055 GLN A2373 GLN ** A2561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2628 ASN ** A2878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3047 GLN B 191 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.148915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.134654 restraints weight = 67850.879| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.18 r_work: 0.3767 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 21811 Z= 0.300 Angle : 0.674 10.966 29616 Z= 0.354 Chirality : 0.065 1.752 3522 Planarity : 0.006 0.090 3736 Dihedral : 6.143 176.057 2925 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.27 % Allowed : 14.71 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2676 helix: 0.73 (0.11), residues: 1921 sheet: -1.87 (1.19), residues: 9 loop : -0.03 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1656 TYR 0.024 0.003 TYR A2357 PHE 0.024 0.003 PHE A1500 TRP 0.019 0.003 TRP B 300 HIS 0.018 0.002 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00718 (21805) covalent geometry : angle 0.67409 (29616) hydrogen bonds : bond 0.06331 ( 1394) hydrogen bonds : angle 4.50526 ( 4068) Misc. bond : bond 0.00084 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 580 time to evaluate : 0.676 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: C 5 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7213 (mtm-85) REVERT: A 321 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (ttm170) REVERT: A 738 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7816 (ttpp) REVERT: A 1911 ASN cc_start: 0.8141 (m-40) cc_final: 0.7909 (m-40) REVERT: A 2770 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6516 (mt-10) REVERT: A 3036 ASP cc_start: 0.7335 (m-30) cc_final: 0.7126 (m-30) REVERT: A 3061 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7641 (t80) outliers start: 54 outliers final: 35 residues processed: 601 average time/residue: 0.8646 time to fit residues: 602.0014 Evaluate side-chains 610 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 572 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1524 GLN Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1855 GLU Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1968 THR Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2356 LYS Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2767 ARG Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3016 THR Chi-restraints excluded: chain A residue 3061 PHE Chi-restraints excluded: chain A residue 3098 THR Chi-restraints excluded: chain A residue 3105 ILE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 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 210 ASN A 959 GLN A1624 GLN A1927 GLN A2055 GLN A2373 GLN A2561 GLN A3047 GLN B 191 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.150126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135877 restraints weight = 67895.876| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.18 r_work: 0.3784 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21811 Z= 0.197 Angle : 0.613 10.738 29616 Z= 0.317 Chirality : 0.061 1.737 3522 Planarity : 0.005 0.098 3736 Dihedral : 5.976 177.136 2925 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.81 % Allowed : 15.88 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2676 helix: 1.06 (0.12), residues: 1917 sheet: -1.92 (1.17), residues: 9 loop : 0.02 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1656 TYR 0.017 0.002 TYR A2357 PHE 0.018 0.002 PHE A1500 TRP 0.015 0.002 TRP A1853 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00462 (21805) covalent geometry : angle 0.61295 (29616) hydrogen bonds : bond 0.05433 ( 1394) hydrogen bonds : angle 4.36242 ( 4068) Misc. bond : bond 0.00059 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 573 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7803 (ttpp) REVERT: A 1911 ASN cc_start: 0.8117 (m-40) cc_final: 0.7896 (m-40) REVERT: A 2770 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6537 (mt-10) REVERT: A 3036 ASP cc_start: 0.7321 (m-30) cc_final: 0.7116 (m-30) REVERT: A 3061 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7560 (t80) REVERT: B 86 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.5900 (tm-30) outliers start: 43 outliers final: 29 residues processed: 586 average time/residue: 0.8126 time to fit residues: 551.9435 Evaluate side-chains 592 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 560 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1855 GLU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2168 GLU Chi-restraints excluded: chain A residue 2356 LYS Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2767 ARG Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3061 PHE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 210 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 190 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 959 GLN A1463 ASN A1840 GLN A1927 GLN A2055 GLN A2373 GLN A2618 GLN A2628 ASN ** A2878 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2915 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 191 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.149375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135111 restraints weight = 68186.651| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.18 r_work: 0.3775 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 21811 Z= 0.260 Angle : 0.645 10.756 29616 Z= 0.336 Chirality : 0.063 1.750 3522 Planarity : 0.006 0.099 3736 Dihedral : 6.039 176.366 2925 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.97 % Allowed : 15.97 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2676 helix: 0.91 (0.11), residues: 1915 sheet: -1.96 (1.18), residues: 9 loop : -0.04 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1656 TYR 0.021 0.002 TYR A2357 PHE 0.022 0.002 PHE A1500 TRP 0.016 0.002 TRP A2579 HIS 0.017 0.002 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00623 (21805) covalent geometry : angle 0.64457 (29616) hydrogen bonds : bond 0.05909 ( 1394) hydrogen bonds : angle 4.42740 ( 4068) Misc. bond : bond 0.00071 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 565 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7299 (ttm170) REVERT: A 738 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: A 1661 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7419 (p) REVERT: A 1911 ASN cc_start: 0.8123 (m-40) cc_final: 0.7907 (m-40) REVERT: A 2770 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 3036 ASP cc_start: 0.7324 (m-30) cc_final: 0.7111 (m-30) REVERT: A 3061 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 47 outliers final: 37 residues processed: 579 average time/residue: 0.8131 time to fit residues: 545.1947 Evaluate side-chains 604 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 563 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1855 GLU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2168 GLU Chi-restraints excluded: chain A residue 2356 LYS Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2767 ARG Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3016 THR Chi-restraints excluded: chain A residue 3061 PHE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 317 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 36 optimal weight: 0.0070 chunk 234 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A1927 GLN A2055 GLN A2373 GLN A2628 ASN B 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136262 restraints weight = 68154.549| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.18 r_work: 0.3794 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21811 Z= 0.168 Angle : 0.594 10.827 29616 Z= 0.306 Chirality : 0.060 1.743 3522 Planarity : 0.005 0.108 3736 Dihedral : 5.882 177.441 2925 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.68 % Allowed : 16.47 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2676 helix: 1.26 (0.12), residues: 1906 sheet: -2.04 (1.18), residues: 9 loop : 0.08 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1656 TYR 0.014 0.002 TYR A2357 PHE 0.018 0.002 PHE A2839 TRP 0.015 0.002 TRP A1853 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00390 (21805) covalent geometry : angle 0.59431 (29616) hydrogen bonds : bond 0.05086 ( 1394) hydrogen bonds : angle 4.29675 ( 4068) Misc. bond : bond 0.00054 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 570 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2770 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6507 (mt-10) REVERT: A 3036 ASP cc_start: 0.7303 (m-30) cc_final: 0.7086 (m-30) REVERT: A 3061 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7557 (t80) REVERT: B 86 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6013 (tm-30) outliers start: 40 outliers final: 33 residues processed: 585 average time/residue: 0.8025 time to fit residues: 544.6610 Evaluate side-chains 599 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 564 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1855 GLU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2168 GLU Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3061 PHE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 222 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 259 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A1637 ASN A2055 GLN A2373 GLN A2577 GLN A2628 ASN B 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.150275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136047 restraints weight = 68180.423| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.19 r_work: 0.3788 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21811 Z= 0.186 Angle : 0.608 10.839 29616 Z= 0.313 Chirality : 0.060 1.727 3522 Planarity : 0.005 0.108 3736 Dihedral : 5.856 177.221 2925 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.76 % Allowed : 16.76 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 2676 helix: 1.29 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1656 TYR 0.016 0.002 TYR A2357 PHE 0.019 0.002 PHE A1500 TRP 0.015 0.002 TRP A2579 HIS 0.016 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00441 (21805) covalent geometry : angle 0.60833 (29616) hydrogen bonds : bond 0.05195 ( 1394) hydrogen bonds : angle 4.28699 ( 4068) Misc. bond : bond 0.00057 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 564 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1661 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7380 (p) REVERT: A 2770 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6551 (mt-10) REVERT: A 3036 ASP cc_start: 0.7297 (m-30) cc_final: 0.7088 (m-30) REVERT: A 3061 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 86 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5907 (tm-30) outliers start: 42 outliers final: 32 residues processed: 578 average time/residue: 0.7988 time to fit residues: 535.2667 Evaluate side-chains 594 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 559 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 815 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1604 LYS Chi-restraints excluded: chain A residue 1610 ARG Chi-restraints excluded: chain A residue 1661 THR Chi-restraints excluded: chain A residue 1855 GLU Chi-restraints excluded: chain A residue 1901 LEU Chi-restraints excluded: chain A residue 1904 PHE Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain A residue 2042 GLN Chi-restraints excluded: chain A residue 2156 SER Chi-restraints excluded: chain A residue 2168 GLU Chi-restraints excluded: chain A residue 2621 ILE Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2714 THR Chi-restraints excluded: chain A residue 2804 LEU Chi-restraints excluded: chain A residue 2823 VAL Chi-restraints excluded: chain A residue 2960 VAL Chi-restraints excluded: chain A residue 3004 LEU Chi-restraints excluded: chain A residue 3061 PHE Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 261 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 247 optimal weight: 0.0570 chunk 264 optimal weight: 1.9990 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A2055 GLN A2373 GLN A2628 ASN A3047 GLN B 191 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.150934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136698 restraints weight = 68400.863| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.19 r_work: 0.3799 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21811 Z= 0.155 Angle : 0.585 10.910 29616 Z= 0.299 Chirality : 0.060 1.728 3522 Planarity : 0.005 0.109 3736 Dihedral : 5.764 177.636 2925 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.60 % Allowed : 16.85 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.16), residues: 2676 helix: 1.47 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1656 TYR 0.013 0.002 TYR A2357 PHE 0.018 0.002 PHE A2839 TRP 0.016 0.002 TRP A2579 HIS 0.015 0.001 HIS A2915 Details of bonding type rmsd covalent geometry : bond 0.00359 (21805) covalent geometry : angle 0.58517 (29616) hydrogen bonds : bond 0.04832 ( 1394) hydrogen bonds : angle 4.21174 ( 4068) Misc. bond : bond 0.00051 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17640.86 seconds wall clock time: 297 minutes 30.66 seconds (17850.66 seconds total)