Starting phenix.real_space_refine on Sun Aug 24 14:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxk_30912/08_2025/7dxk_30912.map" } resolution = 4.1 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 13129 2.51 5 N 3524 2.21 5 O 3709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20491 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2353, 18458 Classifications: {'peptide': 2353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 106, 'TRANS': 2246} Chain breaks: 19 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2033 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.12, per 1000 atoms: 0.20 Number of scatterers: 20491 At special positions: 0 Unit cell: (139.05, 108, 144.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 3709 8.00 N 3524 7.00 C 13129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 768 " - pdb=" SG CYS A 803 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 818.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5014 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 91 through 108 Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.527A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.547A pdb=" N ARG A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 175 through 189 Processing helix chain 'A' and resid 190 through 193 removed outlier: 3.718A pdb=" N VAL A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 197 through 214 removed outlier: 3.707A pdb=" N TYR A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 236 Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.629A pdb=" N ARG A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 304 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.821A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.866A pdb=" N GLY A 398 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.710A pdb=" N HIS A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.550A pdb=" N TYR A 752 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 779 Processing helix chain 'A' and resid 782 through 794 Processing helix chain 'A' and resid 799 through 802 Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.716A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 834 removed outlier: 3.582A pdb=" N CYS A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N MET A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.783A pdb=" N ARG A 861 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.716A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.711A pdb=" N ASP A 914 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 931 Processing helix chain 'A' and resid 944 through 958 removed outlier: 3.560A pdb=" N ALA A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1011 Processing helix chain 'A' and resid 1015 through 1032 removed outlier: 4.133A pdb=" N PHE A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1024 " --> pdb=" O GLY A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.054A pdb=" N ILE A1066 " --> pdb=" O MET A1062 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 3.801A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1130 through 1153 removed outlier: 3.871A pdb=" N VAL A1134 " --> pdb=" O LEU A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.712A pdb=" N LEU A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A1249 " --> pdb=" O ASN A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1274 Processing helix chain 'A' and resid 1275 through 1277 No H-bonds generated for 'chain 'A' and resid 1275 through 1277' Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1285 through 1296 removed outlier: 3.591A pdb=" N ILE A1289 " --> pdb=" O CYS A1285 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1295 " --> pdb=" O GLY A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1315 removed outlier: 3.563A pdb=" N THR A1305 " --> pdb=" O PRO A1301 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A1306 " --> pdb=" O MET A1302 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS A1307 " --> pdb=" O MET A1303 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1308 " --> pdb=" O ALA A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1370 Processing helix chain 'A' and resid 1421 through 1435 Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.702A pdb=" N GLN A1441 " --> pdb=" O CYS A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1462 removed outlier: 3.802A pdb=" N LEU A1461 " --> pdb=" O TYR A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1480 Processing helix chain 'A' and resid 1489 through 1501 Processing helix chain 'A' and resid 1512 through 1526 removed outlier: 3.851A pdb=" N ILE A1516 " --> pdb=" O GLY A1512 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A1526 " --> pdb=" O GLY A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1544 Proline residue: A1540 - end of helix Processing helix chain 'A' and resid 1558 through 1574 removed outlier: 3.842A pdb=" N LEU A1574 " --> pdb=" O MET A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1595 removed outlier: 3.694A pdb=" N LYS A1593 " --> pdb=" O GLN A1589 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1616 Proline residue: A1612 - end of helix Processing helix chain 'A' and resid 1623 through 1637 Processing helix chain 'A' and resid 1645 through 1651 Processing helix chain 'A' and resid 1661 through 1682 removed outlier: 3.528A pdb=" N VAL A1665 " --> pdb=" O SER A1661 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A1678 " --> pdb=" O ALA A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1695 removed outlier: 3.740A pdb=" N VAL A1688 " --> pdb=" O THR A1684 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1695 " --> pdb=" O ARG A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1703 through 1713 Processing helix chain 'A' and resid 1731 through 1753 removed outlier: 4.093A pdb=" N THR A1753 " --> pdb=" O GLU A1749 " (cutoff:3.500A) Processing helix chain 'A' and resid 1761 through 1785 Processing helix chain 'A' and resid 1788 through 1800 removed outlier: 3.943A pdb=" N THR A1792 " --> pdb=" O PHE A1788 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1822 Processing helix chain 'A' and resid 1826 through 1839 Processing helix chain 'A' and resid 1843 through 1852 Processing helix chain 'A' and resid 1885 through 1905 Processing helix chain 'A' and resid 1910 through 1919 Processing helix chain 'A' and resid 1920 through 1925 Processing helix chain 'A' and resid 1929 through 1940 Processing helix chain 'A' and resid 1943 through 1956 Processing helix chain 'A' and resid 1962 through 1973 Processing helix chain 'A' and resid 1977 through 1979 No H-bonds generated for 'chain 'A' and resid 1977 through 1979' Processing helix chain 'A' and resid 1980 through 1991 Processing helix chain 'A' and resid 1997 through 2018 removed outlier: 3.807A pdb=" N ALA A2018 " --> pdb=" O MET A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2027 removed outlier: 3.545A pdb=" N GLN A2026 " --> pdb=" O SER A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2042 Processing helix chain 'A' and resid 2043 through 2048 Processing helix chain 'A' and resid 2048 through 2062 removed outlier: 4.131A pdb=" N TYR A2052 " --> pdb=" O HIS A2048 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A2062 " --> pdb=" O PHE A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2112 through 2121 removed outlier: 3.697A pdb=" N ARG A2121 " --> pdb=" O GLU A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2132 Processing helix chain 'A' and resid 2137 through 2139 No H-bonds generated for 'chain 'A' and resid 2137 through 2139' Processing helix chain 'A' and resid 2140 through 2155 Processing helix chain 'A' and resid 2158 through 2178 removed outlier: 4.209A pdb=" N GLU A2162 " --> pdb=" O SER A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2204 removed outlier: 3.982A pdb=" N LYS A2200 " --> pdb=" O ALA A2196 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A2204 " --> pdb=" O LYS A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2228 Proline residue: A2215 - end of helix Processing helix chain 'A' and resid 2229 through 2231 No H-bonds generated for 'chain 'A' and resid 2229 through 2231' Processing helix chain 'A' and resid 2238 through 2240 No H-bonds generated for 'chain 'A' and resid 2238 through 2240' Processing helix chain 'A' and resid 2241 through 2263 Processing helix chain 'A' and resid 2267 through 2282 Processing helix chain 'A' and resid 2284 through 2292 Processing helix chain 'A' and resid 2296 through 2313 Processing helix chain 'A' and resid 2350 through 2369 removed outlier: 3.847A pdb=" N GLU A2357 " --> pdb=" O THR A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2380 removed outlier: 4.305A pdb=" N GLY A2379 " --> pdb=" O ARG A2376 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2397 removed outlier: 3.638A pdb=" N ARG A2397 " --> pdb=" O ILE A2393 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2406 Processing helix chain 'A' and resid 2408 through 2414 removed outlier: 3.769A pdb=" N TRP A2412 " --> pdb=" O PRO A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2437 removed outlier: 3.805A pdb=" N GLN A2437 " --> pdb=" O GLU A2434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2434 through 2437' Processing helix chain 'A' and resid 2438 through 2453 removed outlier: 3.722A pdb=" N PHE A2442 " --> pdb=" O GLU A2438 " (cutoff:3.500A) Processing helix chain 'A' and resid 2456 through 2471 removed outlier: 4.074A pdb=" N PHE A2460 " --> pdb=" O SER A2456 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A2471 " --> pdb=" O LEU A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2508 Processing helix chain 'A' and resid 2539 through 2558 removed outlier: 4.164A pdb=" N LEU A2543 " --> pdb=" O PHE A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2593 Processing helix chain 'A' and resid 2614 through 2621 Processing helix chain 'A' and resid 2663 through 2680 removed outlier: 4.070A pdb=" N CYS A2667 " --> pdb=" O ASP A2663 " (cutoff:3.500A) Processing helix chain 'A' and resid 2689 through 2704 Processing helix chain 'A' and resid 2705 through 2707 No H-bonds generated for 'chain 'A' and resid 2705 through 2707' Processing helix chain 'A' and resid 2709 through 2727 removed outlier: 3.699A pdb=" N PHE A2713 " --> pdb=" O GLU A2709 " (cutoff:3.500A) Processing helix chain 'A' and resid 2731 through 2749 Proline residue: A2740 - end of helix removed outlier: 3.626A pdb=" N LEU A2749 " --> pdb=" O ALA A2745 " (cutoff:3.500A) Processing helix chain 'A' and resid 2752 through 2767 Proline residue: A2758 - end of helix Processing helix chain 'A' and resid 2771 through 2786 Processing helix chain 'A' and resid 2795 through 2799 removed outlier: 3.586A pdb=" N LEU A2798 " --> pdb=" O ALA A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2800 through 2812 removed outlier: 3.852A pdb=" N GLY A2812 " --> pdb=" O SER A2808 " (cutoff:3.500A) Processing helix chain 'A' and resid 2823 through 2839 Processing helix chain 'A' and resid 2844 through 2860 removed outlier: 3.779A pdb=" N SER A2848 " --> pdb=" O GLY A2844 " (cutoff:3.500A) Processing helix chain 'A' and resid 2867 through 2884 Processing helix chain 'A' and resid 2888 through 2903 removed outlier: 3.833A pdb=" N ALA A2892 " --> pdb=" O SER A2888 " (cutoff:3.500A) Processing helix chain 'A' and resid 2907 through 2922 removed outlier: 3.857A pdb=" N MET A2922 " --> pdb=" O MET A2918 " (cutoff:3.500A) Processing helix chain 'A' and resid 2946 through 2963 Processing helix chain 'A' and resid 2965 through 2984 Proline residue: A2977 - end of helix removed outlier: 4.223A pdb=" N PHE A2984 " --> pdb=" O LEU A2980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2985 through 2996 removed outlier: 4.391A pdb=" N ILE A2989 " --> pdb=" O PRO A2985 " (cutoff:3.500A) Processing helix chain 'A' and resid 3005 through 3018 Processing helix chain 'A' and resid 3021 through 3039 Processing helix chain 'A' and resid 3044 through 3059 removed outlier: 3.518A pdb=" N ALA A3059 " --> pdb=" O PHE A3055 " (cutoff:3.500A) Processing helix chain 'A' and resid 3065 through 3067 No H-bonds generated for 'chain 'A' and resid 3065 through 3067' Processing helix chain 'A' and resid 3068 through 3073 Processing helix chain 'A' and resid 3080 through 3096 removed outlier: 3.598A pdb=" N ARG A3096 " --> pdb=" O THR A3092 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 64 through 80 removed outlier: 3.660A pdb=" N LEU B 80 " --> pdb=" O CYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 106 removed outlier: 3.791A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.844A pdb=" N GLN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 154 removed outlier: 4.010A pdb=" N ALA B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.962A pdb=" N ALA B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 194 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 260 through 280 removed outlier: 4.016A pdb=" N ASP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 299 Processing helix chain 'B' and resid 315 through 332 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.513A pdb=" N ILE B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 362 1303 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6603 1.34 - 1.47: 4606 1.47 - 1.59: 9489 1.59 - 1.71: 0 1.71 - 1.84: 187 Bond restraints: 20885 Sorted by residual: bond pdb=" CG1 ILE A1002 " pdb=" CD1 ILE A1002 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.61e+00 bond pdb=" C VAL A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.29e+00 bond pdb=" C ILE A2122 " pdb=" N PRO A2123 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.19e-02 7.06e+03 6.78e+00 bond pdb=" C VAL A 318 " pdb=" N PRO A 319 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.26e+00 bond pdb=" CB MET A2828 " pdb=" CG MET A2828 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.14e+00 ... (remaining 20880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 27982 3.51 - 7.01: 331 7.01 - 10.52: 55 10.52 - 14.02: 5 14.02 - 17.53: 1 Bond angle restraints: 28374 Sorted by residual: angle pdb=" N VAL A2514 " pdb=" CA VAL A2514 " pdb=" C VAL A2514 " ideal model delta sigma weight residual 113.10 104.81 8.29 9.70e-01 1.06e+00 7.30e+01 angle pdb=" N LEU B 63 " pdb=" CA LEU B 63 " pdb=" C LEU B 63 " ideal model delta sigma weight residual 109.81 121.05 -11.24 2.21e+00 2.05e-01 2.59e+01 angle pdb=" CA LEU A 852 " pdb=" CB LEU A 852 " pdb=" CG LEU A 852 " ideal model delta sigma weight residual 116.30 133.83 -17.53 3.50e+00 8.16e-02 2.51e+01 angle pdb=" C LEU A1130 " pdb=" N VAL A1131 " pdb=" CA VAL A1131 " ideal model delta sigma weight residual 120.43 124.97 -4.54 9.60e-01 1.09e+00 2.24e+01 angle pdb=" N VAL A2512 " pdb=" CA VAL A2512 " pdb=" C VAL A2512 " ideal model delta sigma weight residual 108.88 117.92 -9.04 2.16e+00 2.14e-01 1.75e+01 ... (remaining 28369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11126 17.81 - 35.61: 1273 35.61 - 53.42: 225 53.42 - 71.23: 31 71.23 - 89.03: 25 Dihedral angle restraints: 12680 sinusoidal: 5006 harmonic: 7674 Sorted by residual: dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual 180.00 132.83 47.17 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA VAL A 296 " pdb=" C VAL A 296 " pdb=" N PRO A 297 " pdb=" CA PRO A 297 " ideal model delta harmonic sigma weight residual -180.00 -135.33 -44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA SER A3062 " pdb=" C SER A3062 " pdb=" N PRO A3063 " pdb=" CA PRO A3063 " ideal model delta harmonic sigma weight residual -180.00 -143.40 -36.60 0 5.00e+00 4.00e-02 5.36e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2404 0.053 - 0.106: 787 0.106 - 0.158: 173 0.158 - 0.211: 23 0.211 - 0.264: 8 Chirality restraints: 3395 Sorted by residual: chirality pdb=" CB ILE A1490 " pdb=" CA ILE A1490 " pdb=" CG1 ILE A1490 " pdb=" CG2 ILE A1490 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL A2512 " pdb=" N VAL A2512 " pdb=" C VAL A2512 " pdb=" CB VAL A2512 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A2624 " pdb=" CA ILE A2624 " pdb=" CG1 ILE A2624 " pdb=" CG2 ILE A2624 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3392 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 63 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO B 64 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1138 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C PHE A1138 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A1138 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A1139 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1136 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C GLN A1136 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN A1136 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A1137 " 0.016 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4754 2.78 - 3.31: 19390 3.31 - 3.84: 34217 3.84 - 4.37: 38116 4.37 - 4.90: 64734 Nonbonded interactions: 161211 Sorted by model distance: nonbonded pdb=" OH TYR A 983 " pdb=" O GLN A1272 " model vdw 2.251 3.040 nonbonded pdb=" O SER A2614 " pdb=" OG SER A2617 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A2400 " pdb=" OG1 THR A2426 " model vdw 2.270 3.040 nonbonded pdb=" O SER A2378 " pdb=" OG SER A2378 " model vdw 2.306 3.040 nonbonded pdb=" O MET A1647 " pdb=" OG SER A1651 " model vdw 2.312 3.040 ... (remaining 161206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.120 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 20887 Z= 0.298 Angle : 1.050 17.528 28378 Z= 0.565 Chirality : 0.055 0.264 3395 Planarity : 0.008 0.081 3576 Dihedral : 15.550 89.032 7660 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.60 % Rotamer: Outliers : 0.48 % Allowed : 11.24 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.75 (0.13), residues: 2575 helix: -2.17 (0.09), residues: 1833 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 268 TYR 0.026 0.002 TYR B 298 PHE 0.029 0.002 PHE B 165 TRP 0.026 0.002 TRP A 184 HIS 0.010 0.002 HIS A2616 Details of bonding type rmsd covalent geometry : bond 0.00679 (20885) covalent geometry : angle 1.04860 (28374) SS BOND : bond 0.01390 ( 2) SS BOND : angle 4.07342 ( 4) hydrogen bonds : bond 0.13148 ( 1303) hydrogen bonds : angle 6.23423 ( 3870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 523 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9026 (mmm) cc_final: 0.8410 (mmp) REVERT: A 145 GLU cc_start: 0.8488 (pp20) cc_final: 0.7901 (pp20) REVERT: A 874 ARG cc_start: 0.8697 (ptp-110) cc_final: 0.8302 (mtt90) REVERT: A 886 LEU cc_start: 0.7822 (tp) cc_final: 0.7437 (tt) REVERT: A 1235 LEU cc_start: 0.8439 (tp) cc_final: 0.8109 (tp) REVERT: A 1284 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8683 (mptt) REVERT: A 1356 MET cc_start: 0.7288 (tpt) cc_final: 0.6721 (tpp) REVERT: A 1563 GLN cc_start: 0.8181 (mt0) cc_final: 0.7894 (mp10) REVERT: A 1652 MET cc_start: 0.8750 (tpp) cc_final: 0.8110 (tpt) REVERT: A 1988 TYR cc_start: 0.7556 (m-10) cc_final: 0.7310 (m-10) REVERT: A 1998 ARG cc_start: 0.8439 (mmp-170) cc_final: 0.8195 (tpp-160) REVERT: A 2003 MET cc_start: 0.8112 (ttp) cc_final: 0.7883 (mmt) REVERT: A 2040 GLN cc_start: 0.8303 (mm110) cc_final: 0.7856 (mm110) REVERT: A 2179 LEU cc_start: 0.8325 (mt) cc_final: 0.7980 (mt) REVERT: A 2385 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (p) REVERT: A 2447 TYR cc_start: 0.8789 (t80) cc_final: 0.8588 (t80) REVERT: A 2524 GLU cc_start: 0.7497 (pp20) cc_final: 0.7238 (tm-30) REVERT: A 2593 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 2762 LEU cc_start: 0.9053 (tt) cc_final: 0.8451 (mm) REVERT: A 2839 TYR cc_start: 0.7432 (m-80) cc_final: 0.7215 (m-10) REVERT: A 2853 GLN cc_start: 0.9075 (mt0) cc_final: 0.8769 (pt0) REVERT: A 2879 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 2883 LEU cc_start: 0.9148 (mm) cc_final: 0.8421 (mm) REVERT: A 2953 ARG cc_start: 0.7809 (mpt180) cc_final: 0.7464 (mtm180) REVERT: A 2990 MET cc_start: 0.8850 (tpt) cc_final: 0.7893 (tpp) REVERT: A 3001 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 3031 TRP cc_start: 0.9470 (m100) cc_final: 0.8980 (m100) REVERT: A 3047 MET cc_start: 0.8292 (mmt) cc_final: 0.7912 (mpp) REVERT: A 3055 PHE cc_start: 0.9229 (t80) cc_final: 0.8853 (t80) REVERT: B 88 LEU cc_start: 0.8485 (mm) cc_final: 0.8226 (mm) REVERT: B 99 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7055 (tpp-160) REVERT: B 116 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 130 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7853 (tpm170) REVERT: B 279 LEU cc_start: 0.8945 (tp) cc_final: 0.8675 (tp) outliers start: 11 outliers final: 3 residues processed: 533 average time/residue: 0.1610 time to fit residues: 127.7162 Evaluate side-chains 355 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 350 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 148 ASN A 221 GLN A 281 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS A 399 GLN A 796 ASN A1140 HIS A1272 GLN A1352 HIS A1708 ASN A1742 GLN A1765 HIS A1841 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN A1959 ASN A2026 GLN A2040 GLN ** A2390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2495 ASN A2555 GLN A2568 HIS A2669 GLN A2838 ASN B 82 HIS B 119 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN B 352 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.123454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097146 restraints weight = 42679.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.099388 restraints weight = 27162.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100404 restraints weight = 18254.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100568 restraints weight = 19491.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100681 restraints weight = 16134.870| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20887 Z= 0.141 Angle : 0.689 10.320 28378 Z= 0.340 Chirality : 0.041 0.163 3395 Planarity : 0.006 0.089 3576 Dihedral : 5.543 42.113 2798 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.15), residues: 2575 helix: -0.42 (0.11), residues: 1855 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 791 TYR 0.026 0.002 TYR A 857 PHE 0.031 0.002 PHE B 165 TRP 0.029 0.001 TRP A2454 HIS 0.014 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00310 (20885) covalent geometry : angle 0.68864 (28374) SS BOND : bond 0.01443 ( 2) SS BOND : angle 2.85911 ( 4) hydrogen bonds : bond 0.04324 ( 1303) hydrogen bonds : angle 4.57040 ( 3870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 470 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8987 (mmm) cc_final: 0.8576 (mmm) REVERT: A 145 GLU cc_start: 0.8339 (pp20) cc_final: 0.7885 (pp20) REVERT: A 831 MET cc_start: 0.8350 (tpp) cc_final: 0.7508 (mmm) REVERT: A 886 LEU cc_start: 0.7983 (tp) cc_final: 0.7473 (tt) REVERT: A 1102 ARG cc_start: 0.4488 (mpt180) cc_final: 0.4149 (mmt180) REVERT: A 1235 LEU cc_start: 0.8332 (tp) cc_final: 0.8095 (tp) REVERT: A 1284 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8688 (mptt) REVERT: A 1356 MET cc_start: 0.7177 (tpt) cc_final: 0.6612 (tpp) REVERT: A 1570 MET cc_start: 0.8480 (mtm) cc_final: 0.8146 (mtp) REVERT: A 1590 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 1970 LEU cc_start: 0.8692 (mt) cc_final: 0.8479 (mm) REVERT: A 1988 TYR cc_start: 0.7377 (m-10) cc_final: 0.7063 (m-10) REVERT: A 2040 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7859 (mm110) REVERT: A 2179 LEU cc_start: 0.8301 (mt) cc_final: 0.7992 (mt) REVERT: A 2201 LEU cc_start: 0.8798 (tp) cc_final: 0.8402 (tp) REVERT: A 2378 SER cc_start: 0.8560 (t) cc_final: 0.8330 (t) REVERT: A 2459 GLN cc_start: 0.7690 (mp10) cc_final: 0.7384 (mp10) REVERT: A 2524 GLU cc_start: 0.7817 (pp20) cc_final: 0.7335 (tm-30) REVERT: A 2762 LEU cc_start: 0.8857 (tt) cc_final: 0.8324 (mm) REVERT: A 2775 ARG cc_start: 0.8491 (mtt90) cc_final: 0.8141 (mtt-85) REVERT: A 2922 MET cc_start: 0.7751 (ptp) cc_final: 0.7470 (ppp) REVERT: A 2990 MET cc_start: 0.8769 (tpt) cc_final: 0.7858 (tpp) REVERT: A 2992 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8662 (mmtm) REVERT: A 3001 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 3031 TRP cc_start: 0.9468 (m100) cc_final: 0.8997 (m100) REVERT: A 3047 MET cc_start: 0.8250 (mmt) cc_final: 0.7831 (mpp) REVERT: A 3052 LEU cc_start: 0.9529 (tp) cc_final: 0.9053 (mt) REVERT: B 68 TRP cc_start: 0.7157 (t-100) cc_final: 0.6927 (t60) REVERT: B 88 LEU cc_start: 0.8609 (mm) cc_final: 0.8336 (mm) REVERT: B 99 ARG cc_start: 0.7586 (ttm170) cc_final: 0.6854 (tpp-160) REVERT: B 279 LEU cc_start: 0.8698 (tp) cc_final: 0.8472 (tp) outliers start: 3 outliers final: 0 residues processed: 473 average time/residue: 0.1305 time to fit residues: 97.5530 Evaluate side-chains 311 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 4 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 232 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 HIS A1834 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1921 GLN A1959 ASN A2048 HIS A2367 GLN A2820 HIS A2824 HIS A3017 GLN B 341 GLN B 357 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094874 restraints weight = 43591.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096588 restraints weight = 30127.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097726 restraints weight = 23432.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098580 restraints weight = 19925.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099080 restraints weight = 17932.228| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20887 Z= 0.200 Angle : 0.713 9.618 28378 Z= 0.354 Chirality : 0.043 0.157 3395 Planarity : 0.005 0.067 3576 Dihedral : 5.309 39.699 2798 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.16), residues: 2575 helix: 0.25 (0.12), residues: 1857 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A2057 TYR 0.021 0.002 TYR A 857 PHE 0.028 0.002 PHE A2833 TRP 0.033 0.002 TRP A 786 HIS 0.009 0.001 HIS A2771 Details of bonding type rmsd covalent geometry : bond 0.00463 (20885) covalent geometry : angle 0.71191 (28374) SS BOND : bond 0.01042 ( 2) SS BOND : angle 2.95733 ( 4) hydrogen bonds : bond 0.04236 ( 1303) hydrogen bonds : angle 4.41553 ( 3870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 434 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8820 (mmm) cc_final: 0.8426 (mmm) REVERT: A 145 GLU cc_start: 0.8025 (pp20) cc_final: 0.7750 (pp20) REVERT: A 210 THR cc_start: 0.8873 (p) cc_final: 0.8420 (p) REVERT: A 813 ASP cc_start: 0.7059 (t0) cc_final: 0.6205 (t0) REVERT: A 831 MET cc_start: 0.8171 (tpp) cc_final: 0.7931 (mmm) REVERT: A 868 LEU cc_start: 0.8821 (mt) cc_final: 0.8573 (mt) REVERT: A 886 LEU cc_start: 0.7952 (tp) cc_final: 0.7503 (tt) REVERT: A 1065 MET cc_start: 0.6188 (tpt) cc_final: 0.5977 (tpt) REVERT: A 1102 ARG cc_start: 0.4735 (mpt180) cc_final: 0.4194 (mmt180) REVERT: A 1235 LEU cc_start: 0.8074 (tp) cc_final: 0.7870 (tp) REVERT: A 1284 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8569 (mptt) REVERT: A 1356 MET cc_start: 0.7165 (tpt) cc_final: 0.6607 (tpp) REVERT: A 1563 GLN cc_start: 0.7917 (mt0) cc_final: 0.7649 (mp10) REVERT: A 1570 MET cc_start: 0.8308 (mtm) cc_final: 0.8019 (mtp) REVERT: A 1590 GLN cc_start: 0.7518 (tm-30) cc_final: 0.6905 (tm-30) REVERT: A 1988 TYR cc_start: 0.7179 (m-10) cc_final: 0.6846 (m-10) REVERT: A 2201 LEU cc_start: 0.8779 (tp) cc_final: 0.8471 (tp) REVERT: A 2357 GLU cc_start: 0.8181 (mp0) cc_final: 0.7796 (pm20) REVERT: A 2593 LEU cc_start: 0.8588 (pp) cc_final: 0.8345 (pp) REVERT: A 2606 MET cc_start: 0.7426 (mmm) cc_final: 0.7222 (mpp) REVERT: A 2762 LEU cc_start: 0.8861 (tt) cc_final: 0.8234 (mm) REVERT: A 2833 PHE cc_start: 0.8348 (m-80) cc_final: 0.8132 (m-80) REVERT: A 2854 MET cc_start: 0.7867 (mtt) cc_final: 0.7502 (mtp) REVERT: A 2990 MET cc_start: 0.8631 (tpt) cc_final: 0.7910 (mmm) REVERT: A 3001 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 3031 TRP cc_start: 0.9362 (m100) cc_final: 0.8849 (m100) REVERT: A 3047 MET cc_start: 0.8318 (mmt) cc_final: 0.7734 (mpp) REVERT: B 68 TRP cc_start: 0.7300 (t-100) cc_final: 0.7054 (t-100) REVERT: B 88 LEU cc_start: 0.8606 (mm) cc_final: 0.8303 (mm) REVERT: B 99 ARG cc_start: 0.7484 (ttm170) cc_final: 0.6980 (tpp-160) REVERT: B 279 LEU cc_start: 0.8827 (tp) cc_final: 0.8491 (tp) outliers start: 2 outliers final: 0 residues processed: 435 average time/residue: 0.1447 time to fit residues: 99.6933 Evaluate side-chains 316 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 253 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN A1150 HIS ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1834 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2348 ASN ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098217 restraints weight = 43085.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098651 restraints weight = 33783.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098710 restraints weight = 26409.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099257 restraints weight = 25348.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099384 restraints weight = 22852.852| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20887 Z= 0.154 Angle : 0.684 12.635 28378 Z= 0.334 Chirality : 0.042 0.160 3395 Planarity : 0.005 0.067 3576 Dihedral : 5.121 39.700 2798 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2575 helix: 0.61 (0.12), residues: 1855 sheet: None (None), residues: 0 loop : -1.93 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1234 TYR 0.022 0.002 TYR A2737 PHE 0.036 0.002 PHE B 165 TRP 0.015 0.001 TRP A 184 HIS 0.004 0.001 HIS A2824 Details of bonding type rmsd covalent geometry : bond 0.00355 (20885) covalent geometry : angle 0.68360 (28374) SS BOND : bond 0.00850 ( 2) SS BOND : angle 2.62270 ( 4) hydrogen bonds : bond 0.03942 ( 1303) hydrogen bonds : angle 4.24495 ( 3870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8853 (mmm) cc_final: 0.8344 (mmp) REVERT: A 145 GLU cc_start: 0.8047 (pp20) cc_final: 0.7774 (pp20) REVERT: A 269 SER cc_start: 0.8929 (m) cc_final: 0.8355 (p) REVERT: A 813 ASP cc_start: 0.7001 (t0) cc_final: 0.6301 (t0) REVERT: A 831 MET cc_start: 0.8091 (tpp) cc_final: 0.7687 (tmm) REVERT: A 886 LEU cc_start: 0.7911 (tp) cc_final: 0.7515 (tt) REVERT: A 1102 ARG cc_start: 0.5356 (mpt180) cc_final: 0.4969 (mmt180) REVERT: A 1284 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8640 (mptt) REVERT: A 1356 MET cc_start: 0.7072 (tpt) cc_final: 0.6558 (tpp) REVERT: A 1570 MET cc_start: 0.8215 (mtm) cc_final: 0.8002 (mtp) REVERT: A 1926 LEU cc_start: 0.8701 (mt) cc_final: 0.8341 (pp) REVERT: A 1932 VAL cc_start: 0.7955 (p) cc_final: 0.7717 (p) REVERT: A 1988 TYR cc_start: 0.7148 (m-10) cc_final: 0.6854 (m-10) REVERT: A 2003 MET cc_start: 0.6902 (mmt) cc_final: 0.5899 (mmt) REVERT: A 2040 GLN cc_start: 0.8115 (mm110) cc_final: 0.7891 (mm110) REVERT: A 2201 LEU cc_start: 0.8751 (tp) cc_final: 0.8469 (tp) REVERT: A 2696 VAL cc_start: 0.9118 (p) cc_final: 0.8739 (p) REVERT: A 2854 MET cc_start: 0.7956 (mtt) cc_final: 0.7540 (mtp) REVERT: A 2875 LEU cc_start: 0.9164 (tp) cc_final: 0.8963 (tp) REVERT: A 2878 LEU cc_start: 0.9033 (mp) cc_final: 0.8570 (tp) REVERT: A 2990 MET cc_start: 0.8394 (tpt) cc_final: 0.7430 (mmm) REVERT: A 2992 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8638 (mmtm) REVERT: A 3001 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 3031 TRP cc_start: 0.9283 (m100) cc_final: 0.8837 (m100) REVERT: A 3047 MET cc_start: 0.8255 (mmt) cc_final: 0.7719 (mpp) REVERT: B 88 LEU cc_start: 0.8473 (mm) cc_final: 0.8185 (mm) REVERT: B 99 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7024 (tpp-160) REVERT: B 279 LEU cc_start: 0.8771 (tp) cc_final: 0.8437 (tp) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.1407 time to fit residues: 98.4847 Evaluate side-chains 302 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 236 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 HIS ** A1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1834 GLN A1852 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2212 GLN ** A2568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 GLN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.123456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099359 restraints weight = 42740.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100128 restraints weight = 31717.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100404 restraints weight = 23966.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100727 restraints weight = 23158.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100854 restraints weight = 21488.552| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20887 Z= 0.139 Angle : 0.669 11.421 28378 Z= 0.326 Chirality : 0.041 0.172 3395 Planarity : 0.005 0.068 3576 Dihedral : 4.947 39.299 2798 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 0.04 % Allowed : 2.81 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.17), residues: 2575 helix: 0.85 (0.12), residues: 1855 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2057 TYR 0.027 0.001 TYR A1768 PHE 0.051 0.002 PHE A 128 TRP 0.038 0.001 TRP A 786 HIS 0.006 0.001 HIS A2374 Details of bonding type rmsd covalent geometry : bond 0.00319 (20885) covalent geometry : angle 0.66842 (28374) SS BOND : bond 0.00789 ( 2) SS BOND : angle 2.59076 ( 4) hydrogen bonds : bond 0.03831 ( 1303) hydrogen bonds : angle 4.16039 ( 3870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8807 (mmm) cc_final: 0.8284 (mmp) REVERT: A 145 GLU cc_start: 0.7997 (pp20) cc_final: 0.7733 (pp20) REVERT: A 162 LEU cc_start: 0.8883 (mt) cc_final: 0.8678 (mt) REVERT: A 224 LEU cc_start: 0.8998 (tp) cc_final: 0.8712 (tp) REVERT: A 719 VAL cc_start: 0.8749 (p) cc_final: 0.8477 (m) REVERT: A 813 ASP cc_start: 0.6883 (t0) cc_final: 0.6273 (t0) REVERT: A 831 MET cc_start: 0.7956 (tpp) cc_final: 0.7474 (tmm) REVERT: A 886 LEU cc_start: 0.8108 (tp) cc_final: 0.7485 (tt) REVERT: A 1102 ARG cc_start: 0.5267 (mpt180) cc_final: 0.4915 (mmt180) REVERT: A 1263 LEU cc_start: 0.8535 (tp) cc_final: 0.7656 (tp) REVERT: A 1284 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8527 (mptt) REVERT: A 1356 MET cc_start: 0.7037 (tpt) cc_final: 0.6528 (tpp) REVERT: A 1563 GLN cc_start: 0.8059 (mt0) cc_final: 0.7807 (mp10) REVERT: A 1570 MET cc_start: 0.8199 (mtm) cc_final: 0.7999 (mtp) REVERT: A 1932 VAL cc_start: 0.7879 (p) cc_final: 0.7667 (p) REVERT: A 1988 TYR cc_start: 0.7055 (m-10) cc_final: 0.6711 (m-10) REVERT: A 2014 MET cc_start: 0.7705 (ppp) cc_final: 0.7504 (ptm) REVERT: A 2201 LEU cc_start: 0.8825 (tp) cc_final: 0.8463 (tp) REVERT: A 2606 MET cc_start: 0.7167 (mmm) cc_final: 0.6746 (mpp) REVERT: A 2620 LEU cc_start: 0.8850 (pp) cc_final: 0.8598 (tt) REVERT: A 2696 VAL cc_start: 0.9149 (p) cc_final: 0.8609 (p) REVERT: A 2854 MET cc_start: 0.7911 (mtt) cc_final: 0.7408 (mtp) REVERT: A 2879 GLU cc_start: 0.8217 (pp20) cc_final: 0.7958 (pp20) REVERT: A 2990 MET cc_start: 0.8338 (tpt) cc_final: 0.7412 (mmm) REVERT: A 2992 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8601 (mmtm) REVERT: A 3001 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 3031 TRP cc_start: 0.9250 (m100) cc_final: 0.8825 (m100) REVERT: A 3047 MET cc_start: 0.8285 (mmt) cc_final: 0.7779 (mpp) REVERT: B 88 LEU cc_start: 0.8348 (mm) cc_final: 0.8060 (mm) REVERT: B 99 ARG cc_start: 0.7394 (ttm170) cc_final: 0.7005 (tpp-160) REVERT: B 279 LEU cc_start: 0.8739 (tp) cc_final: 0.8345 (tp) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.1378 time to fit residues: 96.5969 Evaluate side-chains 312 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 60 optimal weight: 0.0870 chunk 222 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 HIS A1309 GLN A1834 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3071 HIS ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100639 restraints weight = 42401.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101147 restraints weight = 36551.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101692 restraints weight = 27894.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102051 restraints weight = 25295.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102280 restraints weight = 22709.698| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20887 Z= 0.127 Angle : 0.666 10.791 28378 Z= 0.319 Chirality : 0.041 0.160 3395 Planarity : 0.005 0.069 3576 Dihedral : 4.815 39.084 2798 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.17), residues: 2575 helix: 1.00 (0.12), residues: 1861 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A2057 TYR 0.034 0.001 TYR A1768 PHE 0.045 0.002 PHE A 128 TRP 0.045 0.001 TRP A2454 HIS 0.010 0.001 HIS A1236 Details of bonding type rmsd covalent geometry : bond 0.00285 (20885) covalent geometry : angle 0.66573 (28374) SS BOND : bond 0.00726 ( 2) SS BOND : angle 2.28402 ( 4) hydrogen bonds : bond 0.03637 ( 1303) hydrogen bonds : angle 4.03409 ( 3870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5150 Ramachandran restraints generated. 2575 Oldfield, 0 Emsley, 2575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8711 (mmm) cc_final: 0.8219 (mmp) REVERT: A 145 GLU cc_start: 0.7973 (pp20) cc_final: 0.7724 (pp20) REVERT: A 224 LEU cc_start: 0.8900 (tp) cc_final: 0.8597 (tp) REVERT: A 269 SER cc_start: 0.8792 (m) cc_final: 0.8281 (p) REVERT: A 813 ASP cc_start: 0.6827 (t0) cc_final: 0.6208 (t0) REVERT: A 831 MET cc_start: 0.8042 (tpp) cc_final: 0.7614 (mmm) REVERT: A 886 LEU cc_start: 0.8012 (tp) cc_final: 0.7400 (tt) REVERT: A 1284 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8529 (mptt) REVERT: A 1356 MET cc_start: 0.6888 (tpt) cc_final: 0.6398 (tpp) REVERT: A 1528 ARG cc_start: 0.6585 (mmm-85) cc_final: 0.5998 (mmp80) REVERT: A 1563 GLN cc_start: 0.7819 (mt0) cc_final: 0.7524 (mp10) REVERT: A 1988 TYR cc_start: 0.6966 (m-10) cc_final: 0.6582 (m-10) REVERT: A 2024 MET cc_start: 0.8385 (ptp) cc_final: 0.8049 (ppp) REVERT: A 2447 TYR cc_start: 0.8675 (t80) cc_final: 0.8269 (t80) REVERT: A 2459 GLN cc_start: 0.7573 (mp10) cc_final: 0.7307 (mp10) REVERT: A 2696 VAL cc_start: 0.9048 (p) cc_final: 0.8437 (p) REVERT: A 2829 CYS cc_start: 0.6880 (p) cc_final: 0.6553 (p) REVERT: A 2879 GLU cc_start: 0.8162 (pp20) cc_final: 0.7876 (pp20) REVERT: A 2990 MET cc_start: 0.8145 (tpt) cc_final: 0.7226 (mmm) REVERT: A 2992 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8569 (mmtm) REVERT: A 3001 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 3031 TRP cc_start: 0.9129 (m100) cc_final: 0.8815 (m100) REVERT: A 3047 MET cc_start: 0.8278 (mmt) cc_final: 0.7824 (mpp) REVERT: B 68 TRP cc_start: 0.7263 (t-100) cc_final: 0.7026 (t-100) REVERT: B 88 LEU cc_start: 0.8350 (mm) cc_final: 0.8080 (mm) REVERT: B 99 ARG cc_start: 0.7379 (ttm170) cc_final: 0.7007 (tpp-160) REVERT: B 279 LEU cc_start: 0.8681 (tp) cc_final: 0.8316 (tp) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1385 time to fit residues: 98.6724 Evaluate side-chains 322 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6158 > 50: distance: 35 - 58: 4.151 distance: 38 - 43: 20.225 distance: 39 - 68: 19.634 distance: 43 - 44: 16.412 distance: 44 - 45: 39.333 distance: 44 - 47: 24.469 distance: 45 - 46: 16.658 distance: 45 - 51: 10.092 distance: 47 - 48: 17.328 distance: 47 - 49: 15.898 distance: 48 - 50: 26.360 distance: 51 - 52: 8.261 distance: 52 - 53: 5.810 distance: 52 - 55: 7.439 distance: 53 - 54: 13.760 distance: 53 - 58: 21.609 distance: 55 - 56: 11.140 distance: 55 - 57: 6.657 distance: 58 - 59: 9.246 distance: 59 - 60: 10.828 distance: 59 - 62: 21.196 distance: 60 - 61: 38.678 distance: 60 - 68: 11.693 distance: 62 - 63: 25.173 distance: 63 - 64: 43.912 distance: 63 - 65: 44.324 distance: 64 - 66: 39.689 distance: 65 - 67: 28.693 distance: 66 - 67: 42.027 distance: 68 - 69: 13.232 distance: 69 - 70: 15.314 distance: 69 - 72: 34.548 distance: 70 - 71: 24.504 distance: 70 - 76: 3.514 distance: 72 - 73: 19.226 distance: 73 - 74: 20.760 distance: 73 - 75: 13.954 distance: 77 - 78: 18.132 distance: 77 - 80: 6.973 distance: 78 - 79: 24.860 distance: 78 - 84: 22.638 distance: 80 - 81: 12.689 distance: 81 - 82: 28.200 distance: 81 - 83: 7.485 distance: 84 - 85: 14.779 distance: 85 - 86: 10.742 distance: 85 - 88: 11.194 distance: 86 - 87: 7.137 distance: 86 - 95: 10.868 distance: 88 - 89: 12.711 distance: 89 - 90: 27.260 distance: 89 - 91: 10.576 distance: 90 - 92: 7.036 distance: 91 - 93: 10.774 distance: 92 - 94: 13.314 distance: 93 - 94: 29.364 distance: 95 - 96: 10.227 distance: 96 - 97: 14.779 distance: 96 - 99: 19.214 distance: 97 - 98: 28.690 distance: 97 - 102: 10.886 distance: 99 - 100: 16.733 distance: 99 - 101: 12.778 distance: 102 - 103: 12.276 distance: 103 - 104: 11.790 distance: 103 - 106: 13.147 distance: 104 - 105: 9.445 distance: 106 - 107: 14.622 distance: 107 - 108: 15.875 distance: 107 - 109: 6.805 distance: 110 - 111: 12.999 distance: 111 - 112: 10.798 distance: 112 - 113: 12.708 distance: 112 - 114: 17.720 distance: 115 - 116: 9.868 distance: 115 - 118: 15.317 distance: 116 - 117: 4.645 distance: 118 - 119: 6.878 distance: 119 - 120: 12.071 distance: 120 - 121: 13.362 distance: 121 - 122: 51.917