Starting phenix.real_space_refine on Sat Jan 18 04:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.map" model { file = "/net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f45_50184/01_2025/9f45_50184.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 1.017 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 P 12 5.49 5 S 374 5.16 5 C 36206 2.51 5 N 9916 2.21 5 O 10340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 56848 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 17467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17467 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 17467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2192, 17467 Classifications: {'peptide': 2192} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 87, 'TRANS': 2104} Chain breaks: 20 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "D" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2456 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "E" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "F" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1052, 8385 Classifications: {'peptide': 1052} Link IDs: {'PTRANS': 56, 'TRANS': 995} Chain breaks: 5 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.25, per 1000 atoms: 0.41 Number of scatterers: 56848 At special positions: 0 Unit cell: (226.63, 310.47, 151.96, 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 374 16.00 P 12 15.00 O 10340 8.00 N 9916 7.00 C 36206 6.00 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=0, symmetry=0 Time building additional restraints: 10.96 Conformation dependent library (CDL) restraints added in 5.8 seconds 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13628 Finding SS restraints... Secondary structure from input PDB file: 342 helices and 38 sheets defined 65.5% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.73 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.633A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.081A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 156 removed outlier: 4.483A pdb=" N GLU A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 187 through 198 removed outlier: 3.764A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.551A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 259 through 276 removed outlier: 4.407A pdb=" N GLY A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.644A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 376 removed outlier: 3.551A pdb=" N ASP A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 404 Proline residue: A 397 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.580A pdb=" N HIS A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.519A pdb=" N VAL A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 499 through 512 removed outlier: 4.100A pdb=" N GLU A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix removed outlier: 4.047A pdb=" N GLY A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 528 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.038A pdb=" N PHE A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.548A pdb=" N ASP A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 645 through 666 Processing helix chain 'A' and resid 668 through 679 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 689 through 701 removed outlier: 4.064A pdb=" N ASN A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 718 Processing helix chain 'A' and resid 722 through 744 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 746 through 764 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.501A pdb=" N GLY A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 829 Processing helix chain 'A' and resid 836 through 852 Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'A' and resid 863 through 875 removed outlier: 3.597A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 892 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 942 through 960 Proline residue: A 948 - end of helix Processing helix chain 'A' and resid 963 through 983 removed outlier: 7.194A pdb=" N THR A 969 " --> pdb=" O SER A 965 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET A 970 " --> pdb=" O HIS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.861A pdb=" N VAL A 987 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1004 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1007 through 1024 removed outlier: 3.849A pdb=" N PHE A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1041 removed outlier: 4.383A pdb=" N ASP A1032 " --> pdb=" O ARG A1028 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU A1033 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1065 through 1069 removed outlier: 3.596A pdb=" N LYS A1068 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1084 removed outlier: 3.667A pdb=" N LEU A1074 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Proline residue: A1076 - end of helix Processing helix chain 'A' and resid 1087 through 1089 No H-bonds generated for 'chain 'A' and resid 1087 through 1089' Processing helix chain 'A' and resid 1090 through 1104 removed outlier: 3.995A pdb=" N GLY A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1108 Processing helix chain 'A' and resid 1110 through 1124 Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1128 through 1146 removed outlier: 3.668A pdb=" N GLU A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1145 " --> pdb=" O ARG A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1166 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1186 through 1190 removed outlier: 3.959A pdb=" N ILE A1190 " --> pdb=" O LYS A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1206 through 1219 Processing helix chain 'A' and resid 1262 through 1270 Processing helix chain 'A' and resid 1276 through 1295 Processing helix chain 'A' and resid 1297 through 1303 removed outlier: 3.765A pdb=" N CYS A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1310 Processing helix chain 'A' and resid 1310 through 1317 removed outlier: 3.673A pdb=" N ALA A1314 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1329 Processing helix chain 'A' and resid 1332 through 1347 Processing helix chain 'A' and resid 1350 through 1367 Processing helix chain 'A' and resid 1376 through 1378 No H-bonds generated for 'chain 'A' and resid 1376 through 1378' Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1392 through 1407 Processing helix chain 'A' and resid 1409 through 1423 Processing helix chain 'A' and resid 1425 through 1441 removed outlier: 3.604A pdb=" N GLY A1441 " --> pdb=" O MET A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.135A pdb=" N TYR A1450 " --> pdb=" O GLN A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1470 Processing helix chain 'A' and resid 1473 through 1488 Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1505 through 1524 removed outlier: 4.034A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1536 removed outlier: 3.567A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1554 Processing helix chain 'A' and resid 1556 through 1581 removed outlier: 4.498A pdb=" N ALA A1573 " --> pdb=" O ASP A1569 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A1581 " --> pdb=" O ALA A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1608 Processing helix chain 'A' and resid 1611 through 1626 Processing helix chain 'A' and resid 1629 through 1641 Processing helix chain 'A' and resid 1645 through 1648 Processing helix chain 'A' and resid 1649 through 1663 removed outlier: 3.973A pdb=" N TRP A1653 " --> pdb=" O ASP A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1693 through 1707 Processing helix chain 'A' and resid 1709 through 1732 Processing helix chain 'A' and resid 1737 through 1762 Processing helix chain 'A' and resid 1767 through 1783 removed outlier: 4.031A pdb=" N LYS A1771 " --> pdb=" O SER A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1813 removed outlier: 3.659A pdb=" N TRP A1790 " --> pdb=" O TRP A1786 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A1813 " --> pdb=" O GLN A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1896 removed outlier: 3.749A pdb=" N VAL A1882 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Proline residue: A1883 - end of helix Processing helix chain 'A' and resid 1899 through 1914 Processing helix chain 'A' and resid 1916 through 1930 Processing helix chain 'A' and resid 1932 through 1937 Processing helix chain 'A' and resid 1938 through 1945 removed outlier: 3.768A pdb=" N ARG A1945 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1967 removed outlier: 3.585A pdb=" N LEU A1956 " --> pdb=" O LEU A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1981 removed outlier: 4.893A pdb=" N TYR A1974 " --> pdb=" O GLN A1970 " (cutoff:3.500A) Proline residue: A1975 - end of helix removed outlier: 3.756A pdb=" N LYS A1981 " --> pdb=" O THR A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 2000 removed outlier: 3.540A pdb=" N HIS A1988 " --> pdb=" O THR A1984 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A2000 " --> pdb=" O LYS A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2004 through 2021 Processing helix chain 'A' and resid 2022 through 2041 Processing helix chain 'A' and resid 2043 through 2059 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2064 through 2092 removed outlier: 5.778A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2115 removed outlier: 3.909A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2116 through 2118 No H-bonds generated for 'chain 'A' and resid 2116 through 2118' Processing helix chain 'A' and resid 2123 through 2127 Processing helix chain 'A' and resid 2127 through 2133 removed outlier: 3.662A pdb=" N LEU A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2212 Processing helix chain 'A' and resid 2212 through 2219 Processing helix chain 'A' and resid 2246 through 2257 Processing helix chain 'A' and resid 2262 through 2272 Processing helix chain 'A' and resid 2274 through 2278 Processing helix chain 'A' and resid 2279 through 2293 Processing helix chain 'A' and resid 2297 through 2307 Processing helix chain 'A' and resid 2309 through 2335 Processing helix chain 'A' and resid 2363 through 2368 Processing helix chain 'A' and resid 2380 through 2387 Processing helix chain 'A' and resid 2394 through 2410 Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.604A pdb=" N PHE A2421 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2424 through 2427 Processing helix chain 'A' and resid 2428 through 2435 Processing helix chain 'A' and resid 2493 through 2510 Processing helix chain 'A' and resid 2520 through 2534 Processing helix chain 'A' and resid 2534 through 2540 removed outlier: 4.017A pdb=" N GLN A2540 " --> pdb=" O GLU A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2542 through 2546 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.637A pdb=" N LEU B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 83 through 98 Processing helix chain 'B' and resid 100 through 115 removed outlier: 4.130A pdb=" N ASN B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 138 through 156 removed outlier: 4.392A pdb=" N ALA B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 179 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.760A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.559A pdb=" N ALA B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 259 through 276 removed outlier: 4.405A pdb=" N GLY B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.708A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 376 removed outlier: 3.537A pdb=" N ASP B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 404 Proline residue: B 397 - end of helix Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.650A pdb=" N HIS B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.511A pdb=" N VAL B 450 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 499 through 512 removed outlier: 4.168A pdb=" N GLU B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix removed outlier: 3.995A pdb=" N GLY B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 531 through 549 removed outlier: 4.282A pdb=" N HIS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 592 removed outlier: 4.133A pdb=" N PHE B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.569A pdb=" N ASP B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Processing helix chain 'B' and resid 645 through 666 Processing helix chain 'B' and resid 668 through 679 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 689 through 701 removed outlier: 4.100A pdb=" N ASN B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 718 Processing helix chain 'B' and resid 722 through 744 Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 746 through 764 Processing helix chain 'B' and resid 764 through 769 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 792 through 810 Processing helix chain 'B' and resid 816 through 829 Processing helix chain 'B' and resid 836 through 852 Processing helix chain 'B' and resid 855 through 861 Processing helix chain 'B' and resid 863 through 875 removed outlier: 3.581A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS B 873 " --> pdb=" O LEU B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 892 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 942 through 960 Proline residue: B 948 - end of helix Processing helix chain 'B' and resid 963 through 983 removed outlier: 7.211A pdb=" N THR B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N MET B 970 " --> pdb=" O HIS B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 988 removed outlier: 3.872A pdb=" N VAL B 987 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1004 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1007 through 1024 removed outlier: 3.804A pdb=" N PHE B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1042 removed outlier: 4.420A pdb=" N ASP B1032 " --> pdb=" O ARG B1028 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU B1033 " --> pdb=" O PRO B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1064 Processing helix chain 'B' and resid 1066 through 1084 removed outlier: 4.329A pdb=" N TYR B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) Proline residue: B1072 - end of helix Proline residue: B1076 - end of helix Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'B' and resid 1090 through 1104 removed outlier: 3.952A pdb=" N GLY B1104 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1108 Processing helix chain 'B' and resid 1110 through 1124 Proline residue: B1116 - end of helix Processing helix chain 'B' and resid 1128 through 1146 removed outlier: 3.635A pdb=" N GLU B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1166 Proline residue: B1158 - end of helix Processing helix chain 'B' and resid 1169 through 1185 Processing helix chain 'B' and resid 1186 through 1190 removed outlier: 4.054A pdb=" N ILE B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1203 Processing helix chain 'B' and resid 1206 through 1219 Processing helix chain 'B' and resid 1262 through 1270 Processing helix chain 'B' and resid 1276 through 1295 Processing helix chain 'B' and resid 1297 through 1302 Processing helix chain 'B' and resid 1303 through 1310 Processing helix chain 'B' and resid 1310 through 1317 removed outlier: 3.642A pdb=" N ALA B1314 " --> pdb=" O TYR B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1329 Processing helix chain 'B' and resid 1332 through 1347 Processing helix chain 'B' and resid 1350 through 1367 Processing helix chain 'B' and resid 1376 through 1378 No H-bonds generated for 'chain 'B' and resid 1376 through 1378' Processing helix chain 'B' and resid 1379 through 1390 Processing helix chain 'B' and resid 1392 through 1407 Processing helix chain 'B' and resid 1409 through 1423 Processing helix chain 'B' and resid 1425 through 1441 removed outlier: 3.583A pdb=" N GLY B1441 " --> pdb=" O MET B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1454 removed outlier: 4.089A pdb=" N TYR B1450 " --> pdb=" O GLN B1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1470 Processing helix chain 'B' and resid 1473 through 1488 Processing helix chain 'B' and resid 1489 through 1500 Processing helix chain 'B' and resid 1505 through 1524 removed outlier: 4.040A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1525 through 1536 removed outlier: 3.682A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1554 Processing helix chain 'B' and resid 1556 through 1581 removed outlier: 4.548A pdb=" N ALA B1573 " --> pdb=" O ASP B1569 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B1581 " --> pdb=" O ALA B1577 " (cutoff:3.500A) Processing helix chain 'B' and resid 1586 through 1608 Processing helix chain 'B' and resid 1611 through 1626 Processing helix chain 'B' and resid 1629 through 1641 Processing helix chain 'B' and resid 1645 through 1648 Processing helix chain 'B' and resid 1649 through 1663 removed outlier: 3.981A pdb=" N TRP B1653 " --> pdb=" O ASP B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1665 through 1678 Processing helix chain 'B' and resid 1693 through 1707 Processing helix chain 'B' and resid 1709 through 1732 Processing helix chain 'B' and resid 1737 through 1762 Processing helix chain 'B' and resid 1767 through 1783 removed outlier: 4.000A pdb=" N LYS B1771 " --> pdb=" O SER B1767 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1812 removed outlier: 3.550A pdb=" N TRP B1790 " --> pdb=" O TRP B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1868 through 1896 removed outlier: 3.769A pdb=" N VAL B1882 " --> pdb=" O LEU B1878 " (cutoff:3.500A) Proline residue: B1883 - end of helix Processing helix chain 'B' and resid 1899 through 1914 Processing helix chain 'B' and resid 1916 through 1930 Processing helix chain 'B' and resid 1931 through 1937 removed outlier: 3.685A pdb=" N THR B1934 " --> pdb=" O GLN B1931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1945 removed outlier: 3.784A pdb=" N ARG B1945 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1967 removed outlier: 3.632A pdb=" N LEU B1956 " --> pdb=" O LEU B1952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1971 Processing helix chain 'B' and resid 1972 through 1981 removed outlier: 3.648A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 2000 removed outlier: 3.542A pdb=" N HIS B1988 " --> pdb=" O THR B1984 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B1997 " --> pdb=" O LYS B1993 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B2000 " --> pdb=" O LYS B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2004 through 2021 Processing helix chain 'B' and resid 2022 through 2041 Processing helix chain 'B' and resid 2043 through 2061 Proline residue: B2053 - end of helix removed outlier: 3.692A pdb=" N ARG B2060 " --> pdb=" O ALA B2056 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B2061 " --> pdb=" O MET B2057 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2092 removed outlier: 5.797A pdb=" N ARG B2076 " --> pdb=" O GLN B2072 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASP B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2118 removed outlier: 3.844A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Proline residue: B2116 - end of helix Processing helix chain 'B' and resid 2123 through 2127 Processing helix chain 'B' and resid 2127 through 2133 removed outlier: 3.608A pdb=" N LEU B2131 " --> pdb=" O SER B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2212 Processing helix chain 'B' and resid 2212 through 2219 Processing helix chain 'B' and resid 2246 through 2257 Processing helix chain 'B' and resid 2262 through 2272 Processing helix chain 'B' and resid 2274 through 2278 Processing helix chain 'B' and resid 2279 through 2293 Processing helix chain 'B' and resid 2297 through 2307 Processing helix chain 'B' and resid 2309 through 2335 Processing helix chain 'B' and resid 2363 through 2368 Processing helix chain 'B' and resid 2380 through 2387 Processing helix chain 'B' and resid 2394 through 2410 Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.641A pdb=" N PHE B2421 " --> pdb=" O VAL B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2424 through 2427 Processing helix chain 'B' and resid 2428 through 2435 Processing helix chain 'B' and resid 2493 through 2510 Processing helix chain 'B' and resid 2520 through 2534 Processing helix chain 'B' and resid 2534 through 2539 Processing helix chain 'B' and resid 2542 through 2546 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.573A pdb=" N ASP E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 94 through 114 removed outlier: 3.828A pdb=" N TRP E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 141 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'E' and resid 198 through 219 removed outlier: 3.592A pdb=" N ILE E 202 " --> pdb=" O ASN E 198 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL E 219 " --> pdb=" O GLN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 280 through 287 removed outlier: 6.173A pdb=" N CYS E 283 " --> pdb=" O MET E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 307 through 328 Processing helix chain 'E' and resid 329 through 338 Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.843A pdb=" N LEU E 352 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER E 359 " --> pdb=" O ARG E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 391 removed outlier: 3.591A pdb=" N ALA E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 407 through 423 removed outlier: 3.617A pdb=" N MET E 422 " --> pdb=" O VAL E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.797A pdb=" N LEU E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER E 442 " --> pdb=" O GLN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 458 Processing helix chain 'E' and resid 460 through 471 removed outlier: 3.526A pdb=" N GLY E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 486 through 502 removed outlier: 4.781A pdb=" N LEU E 490 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 513 removed outlier: 4.396A pdb=" N ASP E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 514 through 523 Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 557 through 565 Processing helix chain 'E' and resid 570 through 585 removed outlier: 3.588A pdb=" N TRP E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'E' and resid 599 through 605 Processing helix chain 'E' and resid 606 through 610 Processing helix chain 'E' and resid 612 through 629 removed outlier: 3.826A pdb=" N ASN E 629 " --> pdb=" O THR E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 650 removed outlier: 3.844A pdb=" N GLN E 650 " --> pdb=" O MET E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 653 No H-bonds generated for 'chain 'E' and resid 651 through 653' Processing helix chain 'E' and resid 656 through 674 Processing helix chain 'E' and resid 674 through 685 removed outlier: 3.567A pdb=" N PHE E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 820 Processing helix chain 'E' and resid 823 through 839 removed outlier: 3.539A pdb=" N ALA E 838 " --> pdb=" O LEU E 834 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 839 " --> pdb=" O ASN E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 950 through 954 Processing helix chain 'E' and resid 958 through 969 removed outlier: 3.881A pdb=" N TYR E 966 " --> pdb=" O TRP E 962 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE E 967 " --> pdb=" O SER E 963 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA E 968 " --> pdb=" O ALA E 964 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 1008 Processing helix chain 'F' and resid 19 through 25 removed outlier: 3.603A pdb=" N ASP F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 94 through 114 removed outlier: 3.749A pdb=" N TRP F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 141 Processing helix chain 'F' and resid 179 through 186 Processing helix chain 'F' and resid 198 through 219 removed outlier: 3.582A pdb=" N ILE F 202 " --> pdb=" O ASN F 198 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 269 Processing helix chain 'F' and resid 269 through 279 Processing helix chain 'F' and resid 280 through 287 removed outlier: 6.168A pdb=" N CYS F 283 " --> pdb=" O MET F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 307 through 328 Processing helix chain 'F' and resid 329 through 338 removed outlier: 3.503A pdb=" N ARG F 338 " --> pdb=" O GLN F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 removed outlier: 3.861A pdb=" N LEU F 352 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER F 359 " --> pdb=" O ARG F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 391 removed outlier: 3.599A pdb=" N ALA F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 398 Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.634A pdb=" N MET F 422 " --> pdb=" O VAL F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 442 removed outlier: 3.860A pdb=" N LEU F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER F 442 " --> pdb=" O GLN F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 458 Processing helix chain 'F' and resid 460 through 471 removed outlier: 3.536A pdb=" N GLY F 471 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 480 through 482 No H-bonds generated for 'chain 'F' and resid 480 through 482' Processing helix chain 'F' and resid 486 through 502 removed outlier: 4.739A pdb=" N LEU F 490 " --> pdb=" O GLU F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 513 removed outlier: 4.514A pdb=" N ASP F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 523 Processing helix chain 'F' and resid 528 through 543 Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 557 through 565 Processing helix chain 'F' and resid 570 through 585 removed outlier: 3.616A pdb=" N TRP F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'F' and resid 599 through 605 Processing helix chain 'F' and resid 606 through 610 Processing helix chain 'F' and resid 612 through 629 removed outlier: 3.689A pdb=" N ASN F 629 " --> pdb=" O THR F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 650 removed outlier: 3.758A pdb=" N GLN F 650 " --> pdb=" O MET F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 653 No H-bonds generated for 'chain 'F' and resid 651 through 653' Processing helix chain 'F' and resid 656 through 674 Processing helix chain 'F' and resid 674 through 686 removed outlier: 3.537A pdb=" N PHE F 685 " --> pdb=" O VAL F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 820 Processing helix chain 'F' and resid 823 through 839 removed outlier: 3.550A pdb=" N TYR F 839 " --> pdb=" O ASN F 835 " (cutoff:3.500A) Processing helix chain 'F' and resid 950 through 954 Processing helix chain 'F' and resid 958 through 969 removed outlier: 3.944A pdb=" N TYR F 966 " --> pdb=" O TRP F 962 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE F 967 " --> pdb=" O SER F 963 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 968 " --> pdb=" O ALA F 964 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id=AA2, first strand: chain 'A' and resid 2153 through 2156 removed outlier: 6.707A pdb=" N MET A2175 " --> pdb=" O GLN A2154 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE A2156 " --> pdb=" O THR A2173 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A2173 " --> pdb=" O ILE A2156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id=AA4, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id=AA5, first strand: chain 'B' and resid 2153 through 2156 removed outlier: 6.752A pdb=" N MET B2175 " --> pdb=" O GLN B2154 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE B2156 " --> pdb=" O THR B2173 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR B2173 " --> pdb=" O ILE B2156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.901A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 15 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 14 " --> pdb=" O ASN C 321 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA C 18 " --> pdb=" O CYS C 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.772A pdb=" N ILE C 79 " --> pdb=" O MET C 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 178 removed outlier: 7.059A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE C 178 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N TYR C 184 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 214 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.752A pdb=" N THR C 256 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 277 through 278 removed outlier: 6.619A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 36 through 39 removed outlier: 4.019A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 18 " --> pdb=" O CYS D 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.744A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 91 removed outlier: 6.793A pdb=" N GLY D 103 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 91 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY D 104 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D 123 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 136 Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 178 removed outlier: 3.597A pdb=" N SER D 175 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR D 214 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN D 198 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 223 through 228 removed outlier: 3.847A pdb=" N GLN D 225 " --> pdb=" O CYS D 238 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 239 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR D 256 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 278 removed outlier: 6.510A pdb=" N CYS D 298 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE D 304 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 118 through 123 removed outlier: 6.830A pdb=" N SER E 59 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N HIS E 149 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA E 61 " --> pdb=" O HIS E 149 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN E 151 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL E 63 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 163 through 167 Processing sheet with id=AC5, first strand: chain 'E' and resid 1015 through 1021 removed outlier: 3.969A pdb=" N ASP E1015 " --> pdb=" O SER E1329 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER E1329 " --> pdb=" O ASP E1015 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E1327 " --> pdb=" O ILE E1017 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU E1019 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E1325 " --> pdb=" O LEU E1019 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER E1326 " --> pdb=" O VAL E1318 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E1318 " --> pdb=" O SER E1326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS E1306 " --> pdb=" O GLY E1319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1028 through 1031 removed outlier: 3.713A pdb=" N VAL E1028 " --> pdb=" O ALA E1041 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E1048 " --> pdb=" O ASP E1058 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP E1058 " --> pdb=" O PHE E1048 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 1084 through 1087 removed outlier: 6.770A pdb=" N ILE E1093 " --> pdb=" O ALA E1111 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA E1111 " --> pdb=" O ILE E1093 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL E1095 " --> pdb=" O VAL E1109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1128 through 1129 removed outlier: 5.827A pdb=" N VAL E1147 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP E1160 " --> pdb=" O VAL E1147 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E1149 " --> pdb=" O VAL E1158 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET E1156 " --> pdb=" O ASP E1151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 1169 through 1173 removed outlier: 3.743A pdb=" N SER E1171 " --> pdb=" O GLY E1184 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E1190 " --> pdb=" O THR E1206 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR E1206 " --> pdb=" O ILE E1190 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL E1192 " --> pdb=" O VAL E1204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 1214 through 1219 removed outlier: 7.138A pdb=" N VAL E1230 " --> pdb=" O VAL E1215 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA E1217 " --> pdb=" O VAL E1228 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL E1228 " --> pdb=" O ALA E1217 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER E1231 " --> pdb=" O ASP E1235 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP E1235 " --> pdb=" O SER E1231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E1248 " --> pdb=" O ILE E1238 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 1259 through 1261 Processing sheet with id=AD3, first strand: chain 'F' and resid 118 through 123 removed outlier: 6.846A pdb=" N SER F 59 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N HIS F 149 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 61 " --> pdb=" O HIS F 149 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN F 151 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F 63 " --> pdb=" O ASN F 151 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 163 through 167 Processing sheet with id=AD5, first strand: chain 'F' and resid 1015 through 1021 removed outlier: 4.067A pdb=" N ASP F1015 " --> pdb=" O SER F1329 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER F1329 " --> pdb=" O ASP F1015 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL F1327 " --> pdb=" O ILE F1017 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU F1019 " --> pdb=" O ILE F1325 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F1325 " --> pdb=" O LEU F1019 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER F1326 " --> pdb=" O VAL F1318 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS F1306 " --> pdb=" O GLY F1319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 1028 through 1031 removed outlier: 3.701A pdb=" N VAL F1028 " --> pdb=" O ALA F1041 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE F1048 " --> pdb=" O ASP F1058 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP F1058 " --> pdb=" O PHE F1048 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 1070 through 1076 removed outlier: 3.709A pdb=" N ALA F1072 " --> pdb=" O ALA F1087 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA F1087 " --> pdb=" O ALA F1072 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA F1092 " --> pdb=" O THR F1088 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE F1093 " --> pdb=" O ALA F1111 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA F1111 " --> pdb=" O ILE F1093 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F1095 " --> pdb=" O VAL F1109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 1127 through 1129 removed outlier: 5.337A pdb=" N GLY F1142 " --> pdb=" O ILE F1146 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F1146 " --> pdb=" O GLY F1142 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL F1147 " --> pdb=" O ASP F1160 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP F1160 " --> pdb=" O VAL F1147 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F1149 " --> pdb=" O VAL F1158 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F1156 " --> pdb=" O ASP F1151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 1172 through 1173 removed outlier: 7.125A pdb=" N ILE F1190 " --> pdb=" O THR F1206 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR F1206 " --> pdb=" O ILE F1190 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F1192 " --> pdb=" O VAL F1204 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 1214 through 1219 removed outlier: 7.136A pdb=" N VAL F1230 " --> pdb=" O VAL F1215 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ALA F1217 " --> pdb=" O VAL F1228 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL F1228 " --> pdb=" O ALA F1217 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER F1231 " --> pdb=" O ASP F1235 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP F1235 " --> pdb=" O SER F1231 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN F1248 " --> pdb=" O ILE F1238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 1259 through 1261 removed outlier: 6.710A pdb=" N ASN F1281 " --> pdb=" O LEU F1286 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU F1286 " --> pdb=" O ASN F1281 " (cutoff:3.500A) 3421 hydrogen bonds defined for protein. 10020 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: 28.06 Time building geometry restraints manager: 13.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 18716 1.35 - 1.47: 13078 1.47 - 1.59: 25650 1.59 - 1.70: 12 1.70 - 1.82: 604 Bond restraints: 58060 Sorted by residual: bond pdb=" O12 IHP B2601 " pdb=" P2 IHP B2601 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O12 IHP A2601 " pdb=" P2 IHP A2601 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" O14 IHP A2601 " pdb=" P4 IHP A2601 " ideal model delta sigma weight residual 1.671 1.600 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O14 IHP B2601 " pdb=" P4 IHP B2601 " ideal model delta sigma weight residual 1.671 1.601 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O15 IHP B2601 " pdb=" P5 IHP B2601 " ideal model delta sigma weight residual 1.675 1.620 0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 58055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 77417 1.49 - 2.99: 1057 2.99 - 4.48: 196 4.48 - 5.98: 102 5.98 - 7.47: 6 Bond angle restraints: 78778 Sorted by residual: angle pdb=" C CYS F 81 " pdb=" CA CYS F 81 " pdb=" CB CYS F 81 " ideal model delta sigma weight residual 115.79 110.23 5.56 1.19e+00 7.06e-01 2.19e+01 angle pdb=" C CYS E 81 " pdb=" CA CYS E 81 " pdb=" CB CYS E 81 " ideal model delta sigma weight residual 115.79 110.28 5.51 1.19e+00 7.06e-01 2.14e+01 angle pdb=" C THR A1881 " pdb=" N VAL A1882 " pdb=" CA VAL A1882 " ideal model delta sigma weight residual 120.33 122.78 -2.45 8.00e-01 1.56e+00 9.38e+00 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.53e+00 angle pdb=" C TYR B1310 " pdb=" N ASN B1311 " pdb=" CA ASN B1311 " ideal model delta sigma weight residual 119.78 123.37 -3.59 1.24e+00 6.50e-01 8.38e+00 ... (remaining 78773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 32997 17.75 - 35.50: 1651 35.50 - 53.25: 355 53.25 - 71.01: 59 71.01 - 88.76: 28 Dihedral angle restraints: 35090 sinusoidal: 14186 harmonic: 20904 Sorted by residual: dihedral pdb=" CA LYS A1024 " pdb=" C LYS A1024 " pdb=" N SER A1025 " pdb=" CA SER A1025 " ideal model delta harmonic sigma weight residual 180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN A1330 " pdb=" C ASN A1330 " pdb=" N GLU A1331 " pdb=" CA GLU A1331 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA MET A1512 " pdb=" C MET A1512 " pdb=" N ALA A1513 " pdb=" CA ALA A1513 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 35087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 8193 0.066 - 0.133: 739 0.133 - 0.199: 8 0.199 - 0.266: 2 0.266 - 0.332: 2 Chirality restraints: 8944 Sorted by residual: chirality pdb=" C1 IHP B2601 " pdb=" C2 IHP B2601 " pdb=" C6 IHP B2601 " pdb=" O11 IHP B2601 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C1 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C6 IHP A2601 " pdb=" O11 IHP A2601 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3 IHP A2601 " pdb=" C2 IHP A2601 " pdb=" C4 IHP A2601 " pdb=" O13 IHP A2601 " both_signs ideal model delta sigma weight residual False -2.34 -2.60 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 8941 not shown) Planarity restraints: 10028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1116 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO A1117 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1117 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1117 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1116 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO B1117 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B1117 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B1117 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 464 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO B 465 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 465 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 465 " 0.030 5.00e-02 4.00e+02 ... (remaining 10025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1061 2.70 - 3.25: 58273 3.25 - 3.80: 94436 3.80 - 4.35: 118537 4.35 - 4.90: 196237 Nonbonded interactions: 468544 Sorted by model distance: nonbonded pdb=" OH TYR A2332 " pdb=" OD2 ASP A2512 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR B2332 " pdb=" OD2 ASP B2512 " model vdw 2.147 3.040 nonbonded pdb=" O VAL A 661 " pdb=" OG1 THR A 665 " model vdw 2.149 3.040 nonbonded pdb=" OD2 ASP C 147 " pdb=" OG SER C 149 " model vdw 2.155 3.040 nonbonded pdb=" O VAL B 661 " pdb=" OG1 THR B 665 " model vdw 2.189 3.040 ... (remaining 468539 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 10.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.670 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 105.410 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.003 0.080 58060 Z= 0.171 Angle : 0.501 7.474 78778 Z= 0.271 Chirality : 0.038 0.332 8944 Planarity : 0.004 0.066 10028 Dihedral : 11.494 88.757 21462 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.01 % Allowed : 5.61 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.10), residues: 7024 helix: 2.63 (0.08), residues: 4242 sheet: -0.66 (0.21), residues: 688 loop : -0.20 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 816 HIS 0.005 0.001 HIS E 531 PHE 0.025 0.001 PHE B 610 TYR 0.011 0.001 TYR A2542 ARG 0.004 0.000 ARG A2381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 759 time to evaluate : 4.937 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: 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 277 MET cc_start: -0.0901 (ttt) cc_final: -0.1230 (mmm) REVERT: A 693 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9393 (mp) REVERT: A 756 MET cc_start: 0.9519 (mmm) cc_final: 0.9181 (mmt) REVERT: A 780 ILE cc_start: 0.9600 (mm) cc_final: 0.9317 (mt) REVERT: A 805 LEU cc_start: 0.9730 (tp) cc_final: 0.9435 (tt) REVERT: A 824 ILE cc_start: 0.9762 (mt) cc_final: 0.9471 (tp) REVERT: A 843 THR cc_start: 0.9463 (t) cc_final: 0.9238 (p) REVERT: A 1031 MET cc_start: 0.9362 (tpt) cc_final: 0.8315 (tpp) REVERT: A 1038 MET cc_start: 0.8815 (mtp) cc_final: 0.8523 (mtp) REVERT: A 1140 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.9032 (t0) REVERT: A 1174 MET cc_start: 0.8666 (tpp) cc_final: 0.8216 (tpp) REVERT: A 1177 LEU cc_start: 0.9524 (tp) cc_final: 0.8936 (tp) REVERT: A 1209 TYR cc_start: 0.8612 (t80) cc_final: 0.8369 (t80) REVERT: A 1214 CYS cc_start: 0.9408 (t) cc_final: 0.8855 (p) REVERT: A 1284 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9319 (pp) REVERT: A 1477 MET cc_start: 0.8539 (tmm) cc_final: 0.7115 (tmm) REVERT: A 1481 MET cc_start: 0.8912 (mtm) cc_final: 0.7865 (mtp) REVERT: A 1621 GLU cc_start: 0.9013 (tt0) cc_final: 0.8507 (tm-30) REVERT: A 1796 MET cc_start: 0.8885 (tpt) cc_final: 0.8628 (tpp) REVERT: A 1912 ASP cc_start: 0.8245 (m-30) cc_final: 0.7891 (t70) REVERT: A 2010 MET cc_start: 0.8662 (mmt) cc_final: 0.8286 (mmm) REVERT: A 2011 MET cc_start: 0.8935 (ppp) cc_final: 0.8682 (ppp) REVERT: A 2047 MET cc_start: 0.8038 (tmm) cc_final: 0.7835 (tmm) REVERT: A 2382 MET cc_start: 0.8864 (tpp) cc_final: 0.8306 (tpp) REVERT: B 123 MET cc_start: -0.1351 (mtt) cc_final: -0.1699 (tpp) REVERT: B 125 MET cc_start: 0.5057 (ttm) cc_final: 0.4643 (ptm) REVERT: B 586 LEU cc_start: 0.7457 (mt) cc_final: 0.7245 (mt) REVERT: B 737 ILE cc_start: 0.9709 (mt) cc_final: 0.9344 (tt) REVERT: B 808 VAL cc_start: 0.9471 (t) cc_final: 0.9000 (p) REVERT: B 827 MET cc_start: 0.9387 (ptp) cc_final: 0.8875 (tmm) REVERT: B 955 LEU cc_start: 0.9666 (mt) cc_final: 0.9091 (mp) REVERT: B 984 LEU cc_start: 0.8781 (pt) cc_final: 0.8459 (mm) REVERT: B 1074 LEU cc_start: 0.9572 (mt) cc_final: 0.9296 (mt) REVERT: B 1075 ILE cc_start: 0.9657 (mt) cc_final: 0.9379 (mm) REVERT: B 1140 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8583 (t0) REVERT: B 1364 MET cc_start: 0.9347 (mmm) cc_final: 0.8977 (mmm) REVERT: B 1434 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8407 (tp30) REVERT: B 1477 MET cc_start: 0.8917 (tmm) cc_final: 0.8444 (tmm) REVERT: B 1481 MET cc_start: 0.9070 (mtm) cc_final: 0.8203 (mtt) REVERT: B 1515 MET cc_start: 0.9006 (mtt) cc_final: 0.8769 (mtm) REVERT: B 1578 MET cc_start: 0.9061 (mmp) cc_final: 0.8784 (mmp) REVERT: B 1590 MET cc_start: 0.9331 (mmm) cc_final: 0.8629 (mmm) REVERT: B 1624 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: B 1673 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9143 (mt) REVERT: B 2010 MET cc_start: 0.8402 (mmt) cc_final: 0.8024 (mmm) REVERT: B 2382 MET cc_start: 0.8338 (tpp) cc_final: 0.8088 (tpp) REVERT: B 2400 CYS cc_start: 0.8806 (m) cc_final: 0.8600 (m) REVERT: C 255 MET cc_start: 0.7733 (ptp) cc_final: 0.7145 (ppp) REVERT: C 305 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8422 (mmmm) REVERT: D 86 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8734 (mtpt) REVERT: D 93 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.5430 (m-10) REVERT: D 100 MET cc_start: 0.8883 (ttp) cc_final: 0.8465 (ttp) REVERT: D 255 MET cc_start: 0.8733 (ptp) cc_final: 0.8111 (ppp) REVERT: D 274 TRP cc_start: 0.5671 (OUTLIER) cc_final: 0.5038 (p90) REVERT: D 284 TYR cc_start: 0.8283 (m-80) cc_final: 0.7171 (m-80) REVERT: E 30 PHE cc_start: 0.6547 (m-10) cc_final: 0.6305 (m-10) REVERT: E 40 GLU cc_start: 0.9099 (pt0) cc_final: 0.8891 (pp20) REVERT: E 186 MET cc_start: 0.9006 (tpt) cc_final: 0.8310 (tpp) REVERT: E 547 HIS cc_start: 0.9352 (m-70) cc_final: 0.8980 (t-90) REVERT: E 1011 THR cc_start: 0.4238 (OUTLIER) cc_final: 0.4024 (m) REVERT: E 1013 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7464 (tt) REVERT: E 1243 MET cc_start: 0.6125 (mtp) cc_final: 0.5830 (ttm) REVERT: E 1274 ASN cc_start: 0.8734 (m-40) cc_final: 0.8491 (t0) REVERT: F 93 MET cc_start: 0.8416 (ptp) cc_final: 0.8145 (ptp) REVERT: F 128 ASP cc_start: 0.9467 (m-30) cc_final: 0.9070 (p0) REVERT: F 188 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7328 (t) REVERT: F 336 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9228 (mp) REVERT: F 417 GLN cc_start: 0.9520 (tt0) cc_final: 0.9157 (tm-30) REVERT: F 534 MET cc_start: 0.8868 (mtm) cc_final: 0.8393 (mmm) REVERT: F 635 ASP cc_start: 0.9299 (m-30) cc_final: 0.9013 (t0) REVERT: F 1156 MET cc_start: 0.7307 (mtt) cc_final: 0.6876 (mtm) REVERT: G 400 VAL cc_start: 0.7266 (t) cc_final: 0.7047 (p) outliers start: 124 outliers final: 23 residues processed: 858 average time/residue: 0.5481 time to fit residues: 792.4444 Evaluate side-chains 497 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 462 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1624 GLN Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1973 ILE Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain B residue 605 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1555 ASP Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1673 LEU Chi-restraints excluded: chain B residue 1930 ILE Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 1011 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 1323 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 3.9990 chunk 538 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 363 optimal weight: 0.5980 chunk 287 optimal weight: 0.9980 chunk 556 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 338 optimal weight: 0.7980 chunk 414 optimal weight: 0.0770 chunk 644 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 HIS A 418 ASN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2055 HIS ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 HIS B 689 GLN ** B 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1997 ASN B2028 HIS ** B2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2194 GLN B2515 HIS C 251 ASN D 132 ASN E 107 GLN E 121 GLN E 149 HIS ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 544 ASN E 550 GLN E 642 HIS ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1248 ASN ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.068465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.047419 restraints weight = 368664.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.048607 restraints weight = 222883.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.049237 restraints weight = 155040.390| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 58060 Z= 0.193 Angle : 0.590 10.955 78778 Z= 0.296 Chirality : 0.041 0.279 8944 Planarity : 0.004 0.059 10028 Dihedral : 4.914 73.201 7854 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.90 % Allowed : 9.77 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.10), residues: 7024 helix: 2.32 (0.08), residues: 4294 sheet: -0.63 (0.21), residues: 650 loop : -0.20 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 593 HIS 0.014 0.001 HIS B 968 PHE 0.026 0.001 PHE B2070 TYR 0.017 0.001 TYR E1067 ARG 0.010 0.000 ARG B 882 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 488 time to evaluate : 4.934 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: 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 125 MET cc_start: 0.0412 (ttm) cc_final: 0.0069 (ptp) REVERT: A 277 MET cc_start: -0.0505 (ttt) cc_final: -0.0731 (mmm) REVERT: A 488 MET cc_start: 0.4227 (mpp) cc_final: 0.3864 (mpp) REVERT: A 542 MET cc_start: 0.7979 (ptt) cc_final: 0.7743 (ptt) REVERT: A 693 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9376 (mp) REVERT: A 756 MET cc_start: 0.9468 (mmm) cc_final: 0.9121 (mmt) REVERT: A 805 LEU cc_start: 0.9642 (tp) cc_final: 0.9425 (tt) REVERT: A 824 ILE cc_start: 0.9642 (mt) cc_final: 0.9393 (tp) REVERT: A 825 MET cc_start: 0.9049 (mtm) cc_final: 0.8819 (mtt) REVERT: A 1018 MET cc_start: 0.9103 (mtm) cc_final: 0.8858 (ptp) REVERT: A 1038 MET cc_start: 0.8699 (mtp) cc_final: 0.8417 (mtp) REVERT: A 1174 MET cc_start: 0.8498 (tpp) cc_final: 0.8017 (tpp) REVERT: A 1177 LEU cc_start: 0.9588 (tp) cc_final: 0.8708 (tp) REVERT: A 1313 MET cc_start: 0.8879 (tpp) cc_final: 0.8490 (tpp) REVERT: A 1477 MET cc_start: 0.8757 (tmm) cc_final: 0.8289 (tpp) REVERT: A 1481 MET cc_start: 0.8896 (mtm) cc_final: 0.8374 (mtp) REVERT: A 1484 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9135 (mm) REVERT: A 1590 MET cc_start: 0.9316 (mmm) cc_final: 0.8620 (mmm) REVERT: A 1621 GLU cc_start: 0.8853 (tt0) cc_final: 0.8434 (tm-30) REVERT: A 1638 MET cc_start: 0.8568 (tpp) cc_final: 0.8331 (tpp) REVERT: A 1704 MET cc_start: 0.9103 (ttm) cc_final: 0.8863 (tmm) REVERT: A 1747 MET cc_start: 0.8632 (mtp) cc_final: 0.8264 (ptp) REVERT: A 1796 MET cc_start: 0.8886 (tpt) cc_final: 0.8647 (tpp) REVERT: A 1912 ASP cc_start: 0.8114 (m-30) cc_final: 0.7841 (t70) REVERT: A 2010 MET cc_start: 0.8546 (mmt) cc_final: 0.8314 (mmm) REVERT: A 2175 MET cc_start: 0.8623 (tpp) cc_final: 0.8052 (tpp) REVERT: A 2382 MET cc_start: 0.8833 (tpp) cc_final: 0.8182 (tpp) REVERT: A 2404 MET cc_start: 0.9321 (mmm) cc_final: 0.8705 (tpp) REVERT: B 123 MET cc_start: -0.1570 (mtt) cc_final: -0.1874 (tpp) REVERT: B 125 MET cc_start: 0.5053 (ttm) cc_final: 0.4700 (ptm) REVERT: B 781 LEU cc_start: 0.9554 (mt) cc_final: 0.9284 (pp) REVERT: B 864 LEU cc_start: 0.9391 (tt) cc_final: 0.9180 (tp) REVERT: B 955 LEU cc_start: 0.9585 (mt) cc_final: 0.9177 (mp) REVERT: B 994 MET cc_start: 0.8779 (mmm) cc_final: 0.8447 (mmm) REVERT: B 1079 LEU cc_start: 0.9424 (mt) cc_final: 0.9094 (mm) REVERT: B 1140 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8554 (t0) REVERT: B 1364 MET cc_start: 0.9131 (mmm) cc_final: 0.8816 (mmm) REVERT: B 1434 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8439 (tp30) REVERT: B 1477 MET cc_start: 0.9174 (tmm) cc_final: 0.8804 (tmm) REVERT: B 1481 MET cc_start: 0.9159 (mtm) cc_final: 0.8450 (mtt) REVERT: B 1512 MET cc_start: 0.8266 (mmm) cc_final: 0.7991 (mmm) REVERT: B 1529 MET cc_start: 0.9313 (tpp) cc_final: 0.9100 (tpp) REVERT: B 1590 MET cc_start: 0.9245 (mmm) cc_final: 0.8660 (mmm) REVERT: B 1595 MET cc_start: 0.8820 (mmm) cc_final: 0.8524 (tpp) REVERT: B 1624 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: B 1638 MET cc_start: 0.8458 (tpp) cc_final: 0.8185 (tpp) REVERT: B 1701 MET cc_start: 0.8918 (mtp) cc_final: 0.8676 (mtp) REVERT: B 1964 ILE cc_start: 0.9046 (mm) cc_final: 0.8646 (pt) REVERT: B 2010 MET cc_start: 0.8336 (mmt) cc_final: 0.7947 (mmm) REVERT: B 2199 MET cc_start: 0.9109 (tpp) cc_final: 0.8516 (mmt) REVERT: B 2285 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: B 2382 MET cc_start: 0.8309 (tpp) cc_final: 0.8029 (tpp) REVERT: B 2415 MET cc_start: 0.7937 (tpp) cc_final: 0.7216 (tpp) REVERT: C 185 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6463 (tmm) REVERT: C 255 MET cc_start: 0.7473 (ptp) cc_final: 0.7015 (ppp) REVERT: D 86 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8661 (mtpp) REVERT: D 255 MET cc_start: 0.8629 (ptp) cc_final: 0.8091 (ppp) REVERT: D 274 TRP cc_start: 0.6402 (OUTLIER) cc_final: 0.5304 (p90) REVERT: D 284 TYR cc_start: 0.7917 (m-80) cc_final: 0.7638 (m-10) REVERT: E 186 MET cc_start: 0.8949 (tpt) cc_final: 0.8537 (tpp) REVERT: E 413 LEU cc_start: 0.9490 (tp) cc_final: 0.9160 (tp) REVERT: E 527 MET cc_start: 0.4378 (mtp) cc_final: 0.4135 (mtt) REVERT: E 534 MET cc_start: 0.8756 (mtp) cc_final: 0.8536 (ptp) REVERT: E 547 HIS cc_start: 0.9348 (m-70) cc_final: 0.8989 (t-90) REVERT: E 658 MET cc_start: 0.8521 (ptp) cc_final: 0.7894 (ppp) REVERT: E 1013 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7470 (tt) REVERT: E 1243 MET cc_start: 0.6460 (mtp) cc_final: 0.6235 (ttm) REVERT: E 1274 ASN cc_start: 0.8728 (m-40) cc_final: 0.8502 (t0) REVERT: F 31 MET cc_start: 0.7895 (mmm) cc_final: 0.7289 (mtp) REVERT: F 55 MET cc_start: 0.8665 (mmm) cc_final: 0.8414 (mmp) REVERT: F 93 MET cc_start: 0.8337 (ptp) cc_final: 0.8083 (ptt) REVERT: F 128 ASP cc_start: 0.9353 (m-30) cc_final: 0.9010 (p0) REVERT: F 186 MET cc_start: 0.8925 (tpp) cc_final: 0.8523 (tpp) REVERT: F 188 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7335 (t) REVERT: F 417 GLN cc_start: 0.9429 (tt0) cc_final: 0.9138 (tm-30) REVERT: F 534 MET cc_start: 0.8956 (mtm) cc_final: 0.8743 (mmm) REVERT: F 635 ASP cc_start: 0.9305 (m-30) cc_final: 0.8963 (t0) REVERT: F 662 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8388 (tp30) REVERT: F 1108 MET cc_start: 0.6733 (tmm) cc_final: 0.6497 (tmm) REVERT: F 1127 MET cc_start: 0.6286 (tpp) cc_final: 0.6045 (tpp) REVERT: F 1156 MET cc_start: 0.7235 (mtt) cc_final: 0.6834 (mtm) REVERT: F 1197 MET cc_start: 0.8893 (ptp) cc_final: 0.8334 (ptp) REVERT: G 403 MET cc_start: 0.3015 (tmm) cc_final: 0.1484 (tpp) REVERT: H 403 MET cc_start: 0.5311 (ttt) cc_final: 0.4670 (tpp) outliers start: 117 outliers final: 35 residues processed: 577 average time/residue: 0.5479 time to fit residues: 544.0615 Evaluate side-chains 452 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 408 time to evaluate : 4.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 2057 MET Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1730 HIS Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 484 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 559 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 375 optimal weight: 3.9990 chunk 431 optimal weight: 0.0370 chunk 323 optimal weight: 5.9990 chunk 229 optimal weight: 0.4980 chunk 0 optimal weight: 50.0000 chunk 302 optimal weight: 0.9980 chunk 550 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN A 650 GLN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 ASN A 937 ASN A 940 ASN ** A1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1803 HIS ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2292 ASN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 HIS B 763 ASN B 968 HIS B2055 HIS B2114 GLN ** B2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 251 ASN D 225 GLN E 281 GLN ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 HIS F 417 GLN F 513 ASN ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 642 HIS ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.067851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.046652 restraints weight = 371834.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.047432 restraints weight = 226903.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.048261 restraints weight = 156399.699| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58060 Z= 0.178 Angle : 0.566 12.808 78778 Z= 0.281 Chirality : 0.040 0.339 8944 Planarity : 0.004 0.056 10028 Dihedral : 4.568 67.335 7822 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.67 % Allowed : 10.51 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.10), residues: 7024 helix: 2.22 (0.08), residues: 4310 sheet: -0.67 (0.21), residues: 652 loop : -0.23 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP E 593 HIS 0.019 0.001 HIS A1730 PHE 0.024 0.001 PHE B 610 TYR 0.018 0.001 TYR C 284 ARG 0.008 0.000 ARG E 988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 435 time to evaluate : 4.967 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: 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 542 MET cc_start: 0.7916 (ptt) cc_final: 0.7589 (ptt) REVERT: A 693 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9358 (mp) REVERT: A 756 MET cc_start: 0.9439 (mmm) cc_final: 0.9120 (mmt) REVERT: A 824 ILE cc_start: 0.9663 (mt) cc_final: 0.9423 (tp) REVERT: A 825 MET cc_start: 0.8937 (mtm) cc_final: 0.8644 (mtt) REVERT: A 1018 MET cc_start: 0.9048 (mtm) cc_final: 0.8798 (ptp) REVERT: A 1031 MET cc_start: 0.8928 (tpp) cc_final: 0.8028 (tpp) REVERT: A 1038 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8115 (ptp) REVERT: A 1140 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.9031 (t0) REVERT: A 1154 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8256 (ttm-80) REVERT: A 1177 LEU cc_start: 0.9649 (tp) cc_final: 0.9421 (tp) REVERT: A 1313 MET cc_start: 0.8811 (tpp) cc_final: 0.8320 (tpp) REVERT: A 1477 MET cc_start: 0.8934 (tmm) cc_final: 0.8658 (tpp) REVERT: A 1481 MET cc_start: 0.8822 (mtm) cc_final: 0.8601 (mtp) REVERT: A 1484 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 1512 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8374 (mmm) REVERT: A 1590 MET cc_start: 0.9126 (mmm) cc_final: 0.8609 (mmm) REVERT: A 1621 GLU cc_start: 0.8781 (tt0) cc_final: 0.8417 (tm-30) REVERT: A 1638 MET cc_start: 0.8502 (tpp) cc_final: 0.8191 (tpp) REVERT: A 1747 MET cc_start: 0.8606 (mtp) cc_final: 0.8153 (ptp) REVERT: A 1773 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8303 (mt) REVERT: A 1796 MET cc_start: 0.8798 (tpt) cc_final: 0.8565 (tpp) REVERT: A 1912 ASP cc_start: 0.8124 (m-30) cc_final: 0.7865 (t70) REVERT: A 1988 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.8172 (p-80) REVERT: A 2010 MET cc_start: 0.8480 (mmt) cc_final: 0.8221 (tpt) REVERT: A 2011 MET cc_start: 0.8627 (ppp) cc_final: 0.8418 (ppp) REVERT: A 2089 MET cc_start: 0.7679 (ptt) cc_final: 0.7464 (ppp) REVERT: A 2175 MET cc_start: 0.8812 (tpp) cc_final: 0.8256 (tpp) REVERT: A 2329 MET cc_start: 0.8611 (mmm) cc_final: 0.8238 (mmt) REVERT: A 2382 MET cc_start: 0.8828 (tpp) cc_final: 0.8123 (tpp) REVERT: A 2387 MET cc_start: 0.8524 (mtm) cc_final: 0.8274 (ttm) REVERT: A 2404 MET cc_start: 0.9235 (mmm) cc_final: 0.8640 (tpp) REVERT: B 123 MET cc_start: -0.1572 (mtt) cc_final: -0.1830 (tpp) REVERT: B 125 MET cc_start: 0.4788 (ttm) cc_final: 0.4496 (ptm) REVERT: B 645 SER cc_start: 0.1513 (OUTLIER) cc_final: 0.0929 (m) REVERT: B 781 LEU cc_start: 0.9582 (mt) cc_final: 0.9308 (pp) REVERT: B 1140 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8515 (t0) REVERT: B 1364 MET cc_start: 0.9066 (mmm) cc_final: 0.8812 (mmm) REVERT: B 1434 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7853 (tp30) REVERT: B 1477 MET cc_start: 0.9046 (tmm) cc_final: 0.8559 (tmm) REVERT: B 1481 MET cc_start: 0.8975 (mtm) cc_final: 0.7728 (mtt) REVERT: B 1515 MET cc_start: 0.8734 (mtm) cc_final: 0.8387 (mtm) REVERT: B 1529 MET cc_start: 0.9234 (tpp) cc_final: 0.8979 (tpp) REVERT: B 1590 MET cc_start: 0.9151 (mmm) cc_final: 0.8726 (mmm) REVERT: B 1624 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: B 1638 MET cc_start: 0.8408 (tpp) cc_final: 0.7963 (tpp) REVERT: B 1724 MET cc_start: 0.8805 (mmm) cc_final: 0.8499 (tpp) REVERT: B 1799 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 1988 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8058 (p-80) REVERT: B 2010 MET cc_start: 0.8238 (mmt) cc_final: 0.7816 (tpp) REVERT: B 2201 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9493 (tt) REVERT: B 2285 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: B 2366 MET cc_start: 0.7860 (mtp) cc_final: 0.7533 (mtt) REVERT: B 2382 MET cc_start: 0.8268 (tpp) cc_final: 0.8007 (tpp) REVERT: B 2415 MET cc_start: 0.8044 (tpp) cc_final: 0.7454 (tpp) REVERT: C 56 MET cc_start: 0.8740 (pmm) cc_final: 0.8424 (pmm) REVERT: C 185 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6302 (tmm) REVERT: C 255 MET cc_start: 0.7293 (ptp) cc_final: 0.6853 (ppp) REVERT: C 305 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8610 (mmmm) REVERT: D 233 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8704 (p) REVERT: D 255 MET cc_start: 0.8591 (ptp) cc_final: 0.7989 (ppp) REVERT: D 274 TRP cc_start: 0.6610 (OUTLIER) cc_final: 0.5548 (p90) REVERT: D 284 TYR cc_start: 0.7886 (m-80) cc_final: 0.7593 (m-10) REVERT: E 186 MET cc_start: 0.8908 (tpt) cc_final: 0.8498 (tpp) REVERT: E 413 LEU cc_start: 0.9459 (tp) cc_final: 0.9171 (tp) REVERT: E 547 HIS cc_start: 0.9303 (m-70) cc_final: 0.8895 (t-90) REVERT: E 658 MET cc_start: 0.8672 (ptp) cc_final: 0.7966 (ppp) REVERT: E 1013 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7825 (tt) REVERT: E 1161 ILE cc_start: 0.1092 (OUTLIER) cc_final: 0.0870 (pt) REVERT: E 1243 MET cc_start: 0.6721 (mtp) cc_final: 0.6320 (ttm) REVERT: E 1274 ASN cc_start: 0.8761 (m-40) cc_final: 0.8540 (t0) REVERT: F 31 MET cc_start: 0.8032 (mmm) cc_final: 0.7762 (mmm) REVERT: F 93 MET cc_start: 0.8323 (ptp) cc_final: 0.7927 (ptp) REVERT: F 128 ASP cc_start: 0.9328 (m-30) cc_final: 0.8992 (p0) REVERT: F 188 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7373 (t) REVERT: F 417 GLN cc_start: 0.9331 (tt0) cc_final: 0.9049 (tm-30) REVERT: F 534 MET cc_start: 0.8978 (mtm) cc_final: 0.8750 (mmm) REVERT: F 635 ASP cc_start: 0.9295 (m-30) cc_final: 0.8969 (t0) REVERT: F 662 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8434 (tp30) REVERT: F 979 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.5974 (p0) REVERT: F 1073 MET cc_start: 0.7941 (mmm) cc_final: 0.7641 (mmm) REVERT: F 1156 MET cc_start: 0.7723 (mtt) cc_final: 0.7312 (mtm) REVERT: G 403 MET cc_start: 0.2774 (OUTLIER) cc_final: 0.1849 (tpp) REVERT: H 403 MET cc_start: 0.5193 (ttt) cc_final: 0.4632 (tpp) outliers start: 103 outliers final: 46 residues processed: 514 average time/residue: 0.5472 time to fit residues: 488.8744 Evaluate side-chains 466 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 397 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1154 ARG Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1730 HIS Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2201 LEU Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2500 ILE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1228 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 311 optimal weight: 3.9990 chunk 386 optimal weight: 0.6980 chunk 337 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 60.0000 chunk 646 optimal weight: 3.9990 chunk 660 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 115 optimal weight: 0.0060 chunk 86 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 418 ASN ** B1206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1624 GLN ** B2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1288 ASN F 550 GLN ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.067534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.045948 restraints weight = 367737.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.047265 restraints weight = 214118.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.048182 restraints weight = 149104.054| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 58060 Z= 0.167 Angle : 0.561 17.386 78778 Z= 0.276 Chirality : 0.040 0.239 8944 Planarity : 0.004 0.056 10028 Dihedral : 4.523 68.359 7817 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 11.05 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.10), residues: 7024 helix: 2.22 (0.08), residues: 4316 sheet: -0.83 (0.20), residues: 638 loop : -0.27 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 593 HIS 0.015 0.001 HIS B1084 PHE 0.026 0.001 PHE G 401 TYR 0.014 0.001 TYR B1310 ARG 0.006 0.000 ARG F 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 420 time to evaluate : 4.905 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: 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 277 MET cc_start: 0.1796 (mmm) cc_final: 0.1496 (mmm) REVERT: A 542 MET cc_start: 0.8047 (ptt) cc_final: 0.7710 (ptt) REVERT: A 756 MET cc_start: 0.9356 (mmm) cc_final: 0.9017 (mmt) REVERT: A 824 ILE cc_start: 0.9636 (mt) cc_final: 0.9431 (tp) REVERT: A 825 MET cc_start: 0.8827 (mtm) cc_final: 0.8627 (mtm) REVERT: A 1018 MET cc_start: 0.9068 (mtm) cc_final: 0.8844 (ptp) REVERT: A 1031 MET cc_start: 0.8905 (tpp) cc_final: 0.8686 (tpp) REVERT: A 1038 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8119 (ptp) REVERT: A 1140 ASP cc_start: 0.9288 (OUTLIER) cc_final: 0.9024 (t0) REVERT: A 1154 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8260 (ttm-80) REVERT: A 1477 MET cc_start: 0.8897 (tmm) cc_final: 0.8617 (tpp) REVERT: A 1478 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9269 (mt) REVERT: A 1481 MET cc_start: 0.8852 (mtm) cc_final: 0.8328 (mtp) REVERT: A 1484 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 1529 MET cc_start: 0.9192 (tpp) cc_final: 0.8976 (tpp) REVERT: A 1590 MET cc_start: 0.9072 (mmm) cc_final: 0.8630 (mmm) REVERT: A 1621 GLU cc_start: 0.8749 (tt0) cc_final: 0.8395 (tm-30) REVERT: A 1638 MET cc_start: 0.8449 (tpp) cc_final: 0.8188 (tpp) REVERT: A 1747 MET cc_start: 0.8617 (mtp) cc_final: 0.8126 (ptp) REVERT: A 1773 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 1796 MET cc_start: 0.8779 (tpt) cc_final: 0.8550 (tpp) REVERT: A 1988 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8144 (p-80) REVERT: A 2010 MET cc_start: 0.8526 (mmt) cc_final: 0.8284 (tpt) REVERT: A 2175 MET cc_start: 0.8886 (tpp) cc_final: 0.8397 (tpp) REVERT: A 2382 MET cc_start: 0.8883 (tpp) cc_final: 0.8253 (tpp) REVERT: A 2387 MET cc_start: 0.8489 (mtm) cc_final: 0.8265 (ttm) REVERT: A 2404 MET cc_start: 0.9244 (mmm) cc_final: 0.9004 (tpp) REVERT: B 123 MET cc_start: -0.1053 (mtt) cc_final: -0.1429 (tpp) REVERT: B 125 MET cc_start: 0.5252 (ttm) cc_final: 0.4969 (ptm) REVERT: B 660 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9248 (mp) REVERT: B 727 MET cc_start: 0.8973 (mmp) cc_final: 0.8715 (mmp) REVERT: B 781 LEU cc_start: 0.9573 (mt) cc_final: 0.9330 (pp) REVERT: B 994 MET cc_start: 0.8718 (mmm) cc_final: 0.7775 (tpp) REVERT: B 1091 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9264 (tp) REVERT: B 1364 MET cc_start: 0.8981 (mmm) cc_final: 0.8704 (mmm) REVERT: B 1477 MET cc_start: 0.9120 (tmm) cc_final: 0.8906 (tmm) REVERT: B 1481 MET cc_start: 0.9001 (mtm) cc_final: 0.8586 (mtt) REVERT: B 1512 MET cc_start: 0.8164 (mmm) cc_final: 0.7945 (mmm) REVERT: B 1515 MET cc_start: 0.8643 (mtm) cc_final: 0.8173 (mtm) REVERT: B 1529 MET cc_start: 0.9183 (tpp) cc_final: 0.8921 (tpp) REVERT: B 1578 MET cc_start: 0.8883 (mmp) cc_final: 0.8483 (mmm) REVERT: B 1590 MET cc_start: 0.9128 (mmm) cc_final: 0.8781 (mmm) REVERT: B 1638 MET cc_start: 0.8427 (tpp) cc_final: 0.7962 (tpp) REVERT: B 1704 MET cc_start: 0.8844 (ptt) cc_final: 0.8570 (ppp) REVERT: B 1799 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: B 1964 ILE cc_start: 0.9070 (mm) cc_final: 0.8683 (pt) REVERT: B 1988 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8122 (p-80) REVERT: B 2010 MET cc_start: 0.8280 (mmt) cc_final: 0.7849 (tpt) REVERT: B 2285 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: B 2327 MET cc_start: 0.9255 (mmm) cc_final: 0.8914 (tmm) REVERT: B 2366 MET cc_start: 0.7771 (mtp) cc_final: 0.7486 (mtt) REVERT: B 2415 MET cc_start: 0.8068 (tpp) cc_final: 0.7481 (tpp) REVERT: C 100 MET cc_start: 0.8812 (ptm) cc_final: 0.8524 (ptp) REVERT: C 185 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6345 (tmm) REVERT: C 255 MET cc_start: 0.7377 (ptp) cc_final: 0.7104 (ppp) REVERT: D 233 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8649 (p) REVERT: D 255 MET cc_start: 0.8576 (ptp) cc_final: 0.8032 (ppp) REVERT: D 274 TRP cc_start: 0.6898 (OUTLIER) cc_final: 0.5981 (p90) REVERT: D 284 TYR cc_start: 0.7931 (m-80) cc_final: 0.7621 (m-10) REVERT: E 40 GLU cc_start: 0.9195 (pt0) cc_final: 0.8764 (pp20) REVERT: E 186 MET cc_start: 0.8907 (tpt) cc_final: 0.8498 (tpp) REVERT: E 237 MET cc_start: 0.8060 (mtt) cc_final: 0.7305 (mmt) REVERT: E 413 LEU cc_start: 0.9466 (tp) cc_final: 0.9172 (tp) REVERT: E 527 MET cc_start: 0.3920 (mtp) cc_final: 0.3624 (mtt) REVERT: E 534 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8251 (ptp) REVERT: E 547 HIS cc_start: 0.9336 (m-70) cc_final: 0.8967 (t-90) REVERT: E 658 MET cc_start: 0.8681 (ptp) cc_final: 0.7983 (ppp) REVERT: E 1013 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8101 (tt) REVERT: E 1127 MET cc_start: 0.6023 (tpp) cc_final: 0.5815 (tpt) REVERT: E 1161 ILE cc_start: 0.1754 (OUTLIER) cc_final: 0.1503 (pt) REVERT: E 1243 MET cc_start: 0.6865 (mtp) cc_final: 0.6430 (ttm) REVERT: E 1274 ASN cc_start: 0.8752 (m-40) cc_final: 0.8526 (t0) REVERT: F 31 MET cc_start: 0.8057 (mmm) cc_final: 0.7783 (mmm) REVERT: F 93 MET cc_start: 0.8265 (ptp) cc_final: 0.7906 (ptp) REVERT: F 128 ASP cc_start: 0.9330 (m-30) cc_final: 0.8970 (p0) REVERT: F 188 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7331 (t) REVERT: F 417 GLN cc_start: 0.9309 (tt0) cc_final: 0.9006 (tm-30) REVERT: F 635 ASP cc_start: 0.9300 (m-30) cc_final: 0.8973 (t0) REVERT: F 662 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8396 (tp30) REVERT: F 979 ASP cc_start: 0.6003 (OUTLIER) cc_final: 0.5722 (p0) REVERT: F 1156 MET cc_start: 0.7759 (mtt) cc_final: 0.7346 (mtm) REVERT: F 1316 LEU cc_start: 0.9268 (mt) cc_final: 0.8819 (mt) REVERT: G 403 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.1957 (tpp) REVERT: H 403 MET cc_start: 0.5575 (ttt) cc_final: 0.4867 (tpp) outliers start: 114 outliers final: 59 residues processed: 505 average time/residue: 0.5384 time to fit residues: 471.3492 Evaluate side-chains 466 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 386 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1154 ARG Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1730 HIS Chi-restraints excluded: chain B residue 1799 GLU Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1228 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 438 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 517 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 604 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 439 optimal weight: 3.9990 chunk 357 optimal weight: 0.7980 chunk 665 optimal weight: 3.9990 chunk 648 optimal weight: 1.9990 chunk 475 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2233 ASN ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 ASN B 967 HIS ** B1206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1310 HIS F 531 HIS ** F 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.066243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.044231 restraints weight = 368873.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.045430 restraints weight = 212376.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.046257 restraints weight = 146866.812| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 58060 Z= 0.194 Angle : 0.578 14.366 78778 Z= 0.285 Chirality : 0.040 0.276 8944 Planarity : 0.004 0.055 10028 Dihedral : 4.486 67.751 7811 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.24 % Allowed : 11.62 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.10), residues: 7024 helix: 2.21 (0.08), residues: 4320 sheet: -0.80 (0.21), residues: 622 loop : -0.24 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP E 593 HIS 0.013 0.001 HIS B1084 PHE 0.032 0.001 PHE G 401 TYR 0.014 0.001 TYR E1075 ARG 0.008 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 393 time to evaluate : 5.026 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.1741 (mmm) cc_final: 0.1466 (mmm) REVERT: A 542 MET cc_start: 0.8187 (ptt) cc_final: 0.7826 (ptt) REVERT: A 756 MET cc_start: 0.9459 (mmm) cc_final: 0.9042 (mmt) REVERT: A 824 ILE cc_start: 0.9694 (mt) cc_final: 0.9454 (tp) REVERT: A 825 MET cc_start: 0.9067 (mtm) cc_final: 0.8802 (mtm) REVERT: A 1018 MET cc_start: 0.9297 (mtm) cc_final: 0.9028 (ptp) REVERT: A 1038 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8402 (ptp) REVERT: A 1140 ASP cc_start: 0.9441 (OUTLIER) cc_final: 0.9061 (t0) REVERT: A 1154 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8295 (ttm-80) REVERT: A 1313 MET cc_start: 0.8996 (tpp) cc_final: 0.8747 (tpp) REVERT: A 1477 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8781 (tpp) REVERT: A 1478 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9230 (mm) REVERT: A 1481 MET cc_start: 0.9067 (mtm) cc_final: 0.8356 (mtp) REVERT: A 1484 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9195 (mm) REVERT: A 1512 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8654 (mtm) REVERT: A 1529 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9068 (tpp) REVERT: A 1581 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: A 1590 MET cc_start: 0.9343 (mmm) cc_final: 0.8895 (mmm) REVERT: A 1595 MET cc_start: 0.9391 (mmm) cc_final: 0.9125 (mmt) REVERT: A 1621 GLU cc_start: 0.9036 (tt0) cc_final: 0.8546 (tm-30) REVERT: A 1638 MET cc_start: 0.8617 (tpp) cc_final: 0.8254 (tpp) REVERT: A 1701 MET cc_start: 0.8943 (ttp) cc_final: 0.8728 (ptp) REVERT: A 1717 MET cc_start: 0.9011 (tpp) cc_final: 0.8727 (tpt) REVERT: A 1747 MET cc_start: 0.8821 (mtp) cc_final: 0.8274 (ptp) REVERT: A 1773 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8370 (mt) REVERT: A 1796 MET cc_start: 0.9095 (tpt) cc_final: 0.8870 (tpp) REVERT: A 1988 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8338 (p-80) REVERT: A 2010 MET cc_start: 0.8639 (mmt) cc_final: 0.8371 (tpt) REVERT: A 2089 MET cc_start: 0.8635 (ppp) cc_final: 0.8398 (ppp) REVERT: A 2175 MET cc_start: 0.8803 (tpp) cc_final: 0.8280 (tpp) REVERT: A 2271 MET cc_start: 0.8982 (ttp) cc_final: 0.8777 (mtp) REVERT: A 2382 MET cc_start: 0.9115 (tpp) cc_final: 0.8474 (tpp) REVERT: A 2387 MET cc_start: 0.8813 (mtm) cc_final: 0.8581 (ttm) REVERT: A 2404 MET cc_start: 0.9443 (mmm) cc_final: 0.9166 (tpp) REVERT: B 123 MET cc_start: -0.0905 (mtt) cc_final: -0.1236 (tpp) REVERT: B 125 MET cc_start: 0.5260 (ttm) cc_final: 0.4981 (ptm) REVERT: B 727 MET cc_start: 0.9202 (mmp) cc_final: 0.8842 (mmp) REVERT: B 781 LEU cc_start: 0.9641 (mt) cc_final: 0.9421 (pp) REVERT: B 827 MET cc_start: 0.9338 (tmm) cc_final: 0.9003 (tmm) REVERT: B 970 MET cc_start: 0.8420 (ptp) cc_final: 0.8102 (ptp) REVERT: B 1091 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9376 (tp) REVERT: B 1140 ASP cc_start: 0.9316 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 1364 MET cc_start: 0.9364 (mmm) cc_final: 0.8999 (mmm) REVERT: B 1477 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8169 (tmm) REVERT: B 1481 MET cc_start: 0.9160 (mtm) cc_final: 0.7741 (mtm) REVERT: B 1512 MET cc_start: 0.8427 (mmm) cc_final: 0.8040 (mmm) REVERT: B 1515 MET cc_start: 0.8866 (mtm) cc_final: 0.8348 (mtm) REVERT: B 1529 MET cc_start: 0.9410 (tpp) cc_final: 0.9127 (tpp) REVERT: B 1590 MET cc_start: 0.9404 (mmm) cc_final: 0.9019 (mmm) REVERT: B 1595 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8625 (mmt) REVERT: B 1638 MET cc_start: 0.8638 (tpp) cc_final: 0.8084 (tpp) REVERT: B 1704 MET cc_start: 0.9239 (ptt) cc_final: 0.8738 (ppp) REVERT: B 1964 ILE cc_start: 0.9261 (mm) cc_final: 0.8855 (pt) REVERT: B 1988 HIS cc_start: 0.9037 (OUTLIER) cc_final: 0.8247 (p-80) REVERT: B 2010 MET cc_start: 0.8499 (mmt) cc_final: 0.8105 (tpp) REVERT: B 2175 MET cc_start: 0.8467 (tpp) cc_final: 0.8239 (tpp) REVERT: B 2285 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8137 (tp30) REVERT: B 2327 MET cc_start: 0.9406 (mmm) cc_final: 0.9080 (tmm) REVERT: B 2366 MET cc_start: 0.8225 (mtp) cc_final: 0.7994 (mtt) REVERT: B 2382 MET cc_start: 0.8258 (tpp) cc_final: 0.7981 (tpp) REVERT: B 2415 MET cc_start: 0.8134 (tpp) cc_final: 0.7472 (tpp) REVERT: C 56 MET cc_start: 0.8031 (pmm) cc_final: 0.7664 (pmm) REVERT: C 100 MET cc_start: 0.8998 (ptm) cc_final: 0.8666 (ptp) REVERT: C 185 MET cc_start: 0.6647 (tmm) cc_final: 0.6321 (tmm) REVERT: C 255 MET cc_start: 0.7796 (ptp) cc_final: 0.7267 (ppp) REVERT: D 233 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8690 (p) REVERT: D 255 MET cc_start: 0.8753 (ptp) cc_final: 0.8159 (ppp) REVERT: D 274 TRP cc_start: 0.7008 (OUTLIER) cc_final: 0.6341 (p90) REVERT: D 284 TYR cc_start: 0.8147 (m-80) cc_final: 0.7667 (m-10) REVERT: E 40 GLU cc_start: 0.9232 (pt0) cc_final: 0.8792 (pp20) REVERT: E 55 MET cc_start: 0.7757 (tpp) cc_final: 0.7374 (tmm) REVERT: E 186 MET cc_start: 0.8993 (tpt) cc_final: 0.8561 (tpp) REVERT: E 237 MET cc_start: 0.8259 (mtt) cc_final: 0.7469 (mmt) REVERT: E 413 LEU cc_start: 0.9548 (tp) cc_final: 0.9188 (tp) REVERT: E 534 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8136 (ptp) REVERT: E 547 HIS cc_start: 0.9310 (m-70) cc_final: 0.8953 (t-90) REVERT: E 658 MET cc_start: 0.8740 (ptp) cc_final: 0.8243 (ppp) REVERT: E 1013 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7999 (tt) REVERT: E 1074 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: E 1085 LEU cc_start: 0.8724 (tp) cc_final: 0.8491 (tp) REVERT: E 1138 LEU cc_start: 0.8936 (tp) cc_final: 0.8078 (pp) REVERT: E 1161 ILE cc_start: 0.1641 (OUTLIER) cc_final: 0.0913 (mp) REVERT: E 1243 MET cc_start: 0.6693 (mtp) cc_final: 0.6282 (ttm) REVERT: E 1274 ASN cc_start: 0.8661 (m-40) cc_final: 0.8408 (t0) REVERT: F 31 MET cc_start: 0.8076 (mmm) cc_final: 0.7795 (mmm) REVERT: F 93 MET cc_start: 0.8502 (ptp) cc_final: 0.8104 (ptp) REVERT: F 128 ASP cc_start: 0.9456 (m-30) cc_final: 0.9073 (p0) REVERT: F 188 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7199 (t) REVERT: F 417 GLN cc_start: 0.9518 (tt0) cc_final: 0.9251 (tm-30) REVERT: F 635 ASP cc_start: 0.9324 (m-30) cc_final: 0.9050 (t0) REVERT: F 662 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8419 (tp30) REVERT: F 979 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.5936 (p0) REVERT: F 1127 MET cc_start: 0.6646 (tpp) cc_final: 0.6328 (tpp) REVERT: F 1156 MET cc_start: 0.7842 (mtt) cc_final: 0.7557 (mtm) REVERT: F 1316 LEU cc_start: 0.9304 (mt) cc_final: 0.8865 (mt) REVERT: G 403 MET cc_start: 0.3232 (OUTLIER) cc_final: 0.2228 (tpp) REVERT: H 403 MET cc_start: 0.5749 (ttt) cc_final: 0.4976 (tpp) outliers start: 138 outliers final: 72 residues processed: 499 average time/residue: 0.5410 time to fit residues: 470.6663 Evaluate side-chains 469 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 371 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1154 ARG Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1477 MET Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1581 GLU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1199 LEU Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1595 MET Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1730 HIS Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2198 VAL Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2508 LEU Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 479 LEU Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1074 GLU Chi-restraints excluded: chain E residue 1161 ILE Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1228 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain G residue 403 MET Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 598 optimal weight: 5.9990 chunk 403 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 547 optimal weight: 6.9990 chunk 447 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 446 optimal weight: 5.9990 chunk 407 optimal weight: 0.9990 chunk 607 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN A1106 ASN A1454 HIS A1541 HIS A1647 HIS A1958 HIS ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 ASN B1106 ASN ** B1206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1207 GLN B1470 ASN B1730 HIS B1758 GLN B1803 HIS B2161 GLN ** B2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2401 HIS ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 140 ASN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN F1177 HIS ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.062392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.040663 restraints weight = 380360.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.042409 restraints weight = 227987.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.042426 restraints weight = 147529.956| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 58060 Z= 0.395 Angle : 0.726 11.307 78778 Z= 0.367 Chirality : 0.043 0.298 8944 Planarity : 0.005 0.105 10028 Dihedral : 4.902 70.123 7811 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.35 % Allowed : 12.85 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.10), residues: 7024 helix: 1.83 (0.08), residues: 4316 sheet: -0.86 (0.21), residues: 622 loop : -0.39 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 593 HIS 0.025 0.002 HIS F1177 PHE 0.034 0.002 PHE B1720 TYR 0.016 0.002 TYR A1110 ARG 0.008 0.001 ARG F1242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 365 time to evaluate : 4.963 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: A 277 MET cc_start: 0.0937 (mmm) cc_final: 0.0648 (mmm) REVERT: A 390 MET cc_start: 0.8326 (ppp) cc_final: 0.7521 (ttm) REVERT: A 542 MET cc_start: 0.8474 (ptt) cc_final: 0.8102 (ptt) REVERT: A 756 MET cc_start: 0.9541 (mmm) cc_final: 0.9122 (mmt) REVERT: A 825 MET cc_start: 0.9088 (mtm) cc_final: 0.8787 (mtm) REVERT: A 1018 MET cc_start: 0.9380 (mtm) cc_final: 0.9117 (mtp) REVERT: A 1031 MET cc_start: 0.9321 (tpp) cc_final: 0.8426 (tpp) REVERT: A 1140 ASP cc_start: 0.9483 (OUTLIER) cc_final: 0.9027 (t70) REVERT: A 1481 MET cc_start: 0.9145 (mtm) cc_final: 0.8512 (mtp) REVERT: A 1484 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9120 (mm) REVERT: A 1512 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8698 (mtm) REVERT: A 1529 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9163 (tpp) REVERT: A 1590 MET cc_start: 0.9420 (mmm) cc_final: 0.9026 (mmm) REVERT: A 1621 GLU cc_start: 0.9107 (tt0) cc_final: 0.8648 (tm-30) REVERT: A 1638 MET cc_start: 0.8654 (tpp) cc_final: 0.8141 (tpp) REVERT: A 1747 MET cc_start: 0.8853 (mtp) cc_final: 0.8342 (ptp) REVERT: A 1988 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8338 (p-80) REVERT: A 2010 MET cc_start: 0.8765 (mmt) cc_final: 0.8415 (tpt) REVERT: A 2089 MET cc_start: 0.8706 (ppp) cc_final: 0.8438 (ppp) REVERT: A 2175 MET cc_start: 0.8752 (tpp) cc_final: 0.8278 (tpp) REVERT: A 2366 MET cc_start: 0.9169 (mmm) cc_final: 0.8881 (mmm) REVERT: A 2382 MET cc_start: 0.9219 (tpp) cc_final: 0.8360 (tpp) REVERT: B 123 MET cc_start: -0.1244 (mtt) cc_final: -0.1454 (tpp) REVERT: B 125 MET cc_start: 0.4065 (ttm) cc_final: 0.3790 (ptm) REVERT: B 727 MET cc_start: 0.9243 (mmp) cc_final: 0.8963 (mmp) REVERT: B 827 MET cc_start: 0.9351 (tmm) cc_final: 0.8932 (tmm) REVERT: B 970 MET cc_start: 0.8609 (ptp) cc_final: 0.8272 (ptp) REVERT: B 1031 MET cc_start: 0.9238 (tpp) cc_final: 0.8740 (tpp) REVERT: B 1091 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9487 (tp) REVERT: B 1111 LEU cc_start: 0.9316 (tp) cc_final: 0.9066 (tp) REVERT: B 1140 ASP cc_start: 0.9372 (OUTLIER) cc_final: 0.8606 (t0) REVERT: B 1364 MET cc_start: 0.9410 (mmm) cc_final: 0.8989 (mmm) REVERT: B 1477 MET cc_start: 0.9118 (tmm) cc_final: 0.7900 (tmm) REVERT: B 1481 MET cc_start: 0.9046 (mtm) cc_final: 0.7563 (mtm) REVERT: B 1512 MET cc_start: 0.8701 (mmm) cc_final: 0.8348 (mmm) REVERT: B 1515 MET cc_start: 0.8946 (mtm) cc_final: 0.8544 (mtm) REVERT: B 1529 MET cc_start: 0.9468 (tpp) cc_final: 0.9179 (tpp) REVERT: B 1590 MET cc_start: 0.9506 (mmm) cc_final: 0.9075 (mmm) REVERT: B 1624 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: B 1638 MET cc_start: 0.8644 (tpp) cc_final: 0.8080 (tpp) REVERT: B 1704 MET cc_start: 0.9392 (ptt) cc_final: 0.8792 (ppp) REVERT: B 2010 MET cc_start: 0.8658 (mmt) cc_final: 0.8189 (tpt) REVERT: B 2175 MET cc_start: 0.8708 (tpp) cc_final: 0.8439 (tpp) REVERT: B 2199 MET cc_start: 0.9301 (tpp) cc_final: 0.9063 (tpp) REVERT: B 2327 MET cc_start: 0.9416 (mmm) cc_final: 0.9041 (tmm) REVERT: B 2382 MET cc_start: 0.8386 (tpp) cc_final: 0.7987 (tpp) REVERT: B 2415 MET cc_start: 0.8570 (tpp) cc_final: 0.7921 (tpp) REVERT: C 100 MET cc_start: 0.9094 (ptm) cc_final: 0.8818 (ptp) REVERT: C 185 MET cc_start: 0.7578 (tmm) cc_final: 0.7201 (tmm) REVERT: C 255 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7539 (ppp) REVERT: C 297 TRP cc_start: 0.9076 (OUTLIER) cc_final: 0.8784 (m100) REVERT: D 86 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8715 (mppt) REVERT: D 233 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (p) REVERT: D 255 MET cc_start: 0.8843 (ptp) cc_final: 0.8203 (tmm) REVERT: D 284 TYR cc_start: 0.8447 (m-80) cc_final: 0.8206 (m-10) REVERT: E 31 MET cc_start: 0.9483 (tmm) cc_final: 0.9154 (ttp) REVERT: E 40 GLU cc_start: 0.9383 (pt0) cc_final: 0.8915 (pp20) REVERT: E 237 MET cc_start: 0.8380 (mtt) cc_final: 0.7703 (mmt) REVERT: E 378 MET cc_start: 0.9406 (mmm) cc_final: 0.9004 (mtp) REVERT: E 413 LEU cc_start: 0.9574 (tp) cc_final: 0.9171 (tp) REVERT: E 527 MET cc_start: 0.2998 (mtt) cc_final: 0.2615 (mtt) REVERT: E 534 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8121 (ptp) REVERT: E 547 HIS cc_start: 0.9259 (m-70) cc_final: 0.8892 (t-90) REVERT: E 658 MET cc_start: 0.8883 (ptp) cc_final: 0.8013 (ppp) REVERT: E 1013 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8012 (tt) REVERT: E 1022 ASN cc_start: 0.6604 (OUTLIER) cc_final: 0.4562 (t0) REVERT: E 1208 ARG cc_start: 0.9267 (mtt180) cc_final: 0.9009 (mpp80) REVERT: E 1243 MET cc_start: 0.6870 (mtp) cc_final: 0.6576 (ttm) REVERT: E 1274 ASN cc_start: 0.8730 (m-40) cc_final: 0.8475 (t0) REVERT: F 31 MET cc_start: 0.7864 (mmm) cc_final: 0.7592 (mmm) REVERT: F 55 MET cc_start: 0.9159 (mmp) cc_final: 0.8926 (mmm) REVERT: F 93 MET cc_start: 0.8825 (ptp) cc_final: 0.8614 (ptp) REVERT: F 128 ASP cc_start: 0.9491 (m-30) cc_final: 0.9102 (p0) REVERT: F 188 SER cc_start: 0.7436 (OUTLIER) cc_final: 0.7089 (t) REVERT: F 216 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8651 (pt0) REVERT: F 417 GLN cc_start: 0.9579 (tt0) cc_final: 0.9365 (tm-30) REVERT: F 479 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8605 (mm) REVERT: F 635 ASP cc_start: 0.9359 (m-30) cc_final: 0.9040 (t0) REVERT: F 662 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8324 (tp30) REVERT: F 979 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.5944 (p0) REVERT: F 1028 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.6991 (m) REVERT: F 1108 MET cc_start: 0.6945 (tpp) cc_final: 0.6721 (tpp) REVERT: F 1156 MET cc_start: 0.7801 (mtt) cc_final: 0.7519 (mtp) REVERT: G 403 MET cc_start: 0.3583 (tmm) cc_final: 0.1896 (tpp) REVERT: H 403 MET cc_start: 0.6008 (ttt) cc_final: 0.5370 (tpp) outliers start: 145 outliers final: 82 residues processed: 479 average time/residue: 0.5413 time to fit residues: 455.3776 Evaluate side-chains 448 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 347 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2379 LEU Chi-restraints excluded: chain A residue 2392 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1599 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1730 HIS Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 2153 ILE Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2198 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2500 ILE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1012 ARG Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1172 LEU Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 188 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1028 VAL Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 453 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 339 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 151 optimal weight: 0.0980 chunk 208 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 310 optimal weight: 0.7980 chunk 703 optimal weight: 7.9990 chunk 386 optimal weight: 0.0570 chunk 598 optimal weight: 9.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 ASN A1106 ASN A2003 ASN ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 ASN B2003 ASN ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS E 140 ASN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.064478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042552 restraints weight = 375372.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.043634 restraints weight = 212948.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.044478 restraints weight = 143792.754| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 58060 Z= 0.165 Angle : 0.616 13.619 78778 Z= 0.301 Chirality : 0.041 0.492 8944 Planarity : 0.004 0.055 10028 Dihedral : 4.643 72.647 7809 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 1.70 % Allowed : 13.79 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.10), residues: 7024 helix: 2.02 (0.08), residues: 4332 sheet: -0.92 (0.21), residues: 640 loop : -0.32 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 593 HIS 0.014 0.001 HIS B1084 PHE 0.022 0.001 PHE A 610 TYR 0.029 0.001 TYR A 522 ARG 0.007 0.000 ARG E 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 371 time to evaluate : 4.912 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: A 277 MET cc_start: 0.1209 (mmm) cc_final: 0.0929 (mmm) REVERT: A 390 MET cc_start: 0.8179 (ppp) cc_final: 0.7402 (ttm) REVERT: A 542 MET cc_start: 0.8403 (ptt) cc_final: 0.8101 (ptt) REVERT: A 756 MET cc_start: 0.9541 (mmm) cc_final: 0.9188 (mmt) REVERT: A 825 MET cc_start: 0.9133 (mtm) cc_final: 0.8777 (mtm) REVERT: A 1004 CYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 1018 MET cc_start: 0.9387 (mtm) cc_final: 0.9017 (ptp) REVERT: A 1038 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8664 (ptp) REVERT: A 1140 ASP cc_start: 0.9460 (OUTLIER) cc_final: 0.8995 (t0) REVERT: A 1364 MET cc_start: 0.8758 (tpp) cc_final: 0.8430 (tpp) REVERT: A 1478 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9395 (mm) REVERT: A 1481 MET cc_start: 0.9119 (mtm) cc_final: 0.8490 (mtp) REVERT: A 1484 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 1512 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8677 (mtm) REVERT: A 1529 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9157 (tpp) REVERT: A 1590 MET cc_start: 0.9433 (mmm) cc_final: 0.9124 (mmm) REVERT: A 1595 MET cc_start: 0.9408 (mmm) cc_final: 0.9201 (mmt) REVERT: A 1621 GLU cc_start: 0.9117 (tt0) cc_final: 0.8581 (tm-30) REVERT: A 1638 MET cc_start: 0.8747 (tpp) cc_final: 0.8247 (tpp) REVERT: A 1701 MET cc_start: 0.9368 (ttp) cc_final: 0.7729 (ttm) REVERT: A 1717 MET cc_start: 0.9044 (tpp) cc_final: 0.8735 (tpt) REVERT: A 1747 MET cc_start: 0.8909 (mtp) cc_final: 0.8319 (ptp) REVERT: A 1879 MET cc_start: 0.8506 (tmm) cc_final: 0.8228 (ppp) REVERT: A 1988 HIS cc_start: 0.9145 (OUTLIER) cc_final: 0.8452 (p-80) REVERT: A 2010 MET cc_start: 0.8806 (mmt) cc_final: 0.8516 (tpt) REVERT: A 2089 MET cc_start: 0.8733 (ppp) cc_final: 0.8487 (ppp) REVERT: A 2175 MET cc_start: 0.8728 (tpp) cc_final: 0.8203 (tpp) REVERT: A 2329 MET cc_start: 0.8949 (mmm) cc_final: 0.8633 (mmm) REVERT: A 2382 MET cc_start: 0.9219 (tpp) cc_final: 0.8677 (tpp) REVERT: A 2387 MET cc_start: 0.8893 (mtm) cc_final: 0.8671 (ttm) REVERT: B 123 MET cc_start: -0.0957 (mtt) cc_final: -0.1177 (tpp) REVERT: B 125 MET cc_start: 0.4242 (ttm) cc_final: 0.3961 (ptm) REVERT: B 727 MET cc_start: 0.9206 (mmp) cc_final: 0.8900 (mmp) REVERT: B 781 LEU cc_start: 0.9625 (mt) cc_final: 0.9396 (pp) REVERT: B 813 MET cc_start: 0.8955 (ptp) cc_final: 0.8532 (pmm) REVERT: B 827 MET cc_start: 0.9395 (tmm) cc_final: 0.8962 (tmm) REVERT: B 883 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8231 (tp30) REVERT: B 970 MET cc_start: 0.8626 (ptp) cc_final: 0.8320 (ptp) REVERT: B 994 MET cc_start: 0.9143 (tpp) cc_final: 0.8926 (mmm) REVERT: B 1018 MET cc_start: 0.9028 (tpp) cc_final: 0.8602 (tpp) REVERT: B 1031 MET cc_start: 0.9127 (tpp) cc_final: 0.8892 (tpp) REVERT: B 1044 MET cc_start: 0.8071 (tpp) cc_final: 0.7764 (tpp) REVERT: B 1091 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9451 (tp) REVERT: B 1140 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.8627 (t0) REVERT: B 1364 MET cc_start: 0.9495 (mmm) cc_final: 0.9073 (mmm) REVERT: B 1403 GLU cc_start: 0.9169 (tt0) cc_final: 0.8800 (pt0) REVERT: B 1477 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7884 (tmm) REVERT: B 1481 MET cc_start: 0.9099 (mtm) cc_final: 0.7558 (mtm) REVERT: B 1512 MET cc_start: 0.8365 (mmm) cc_final: 0.8015 (mmm) REVERT: B 1515 MET cc_start: 0.8953 (mtm) cc_final: 0.8545 (mtm) REVERT: B 1529 MET cc_start: 0.9376 (tpp) cc_final: 0.9092 (tmm) REVERT: B 1590 MET cc_start: 0.9415 (mmm) cc_final: 0.9157 (mmm) REVERT: B 1624 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8594 (mp10) REVERT: B 1638 MET cc_start: 0.8825 (tpp) cc_final: 0.8268 (tpp) REVERT: B 1704 MET cc_start: 0.9394 (ptt) cc_final: 0.8760 (ppp) REVERT: B 1988 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8490 (p-80) REVERT: B 2010 MET cc_start: 0.8630 (mmt) cc_final: 0.8155 (tpt) REVERT: B 2175 MET cc_start: 0.8612 (tpp) cc_final: 0.8392 (tpp) REVERT: B 2199 MET cc_start: 0.9269 (tpp) cc_final: 0.8714 (mmt) REVERT: B 2285 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: B 2327 MET cc_start: 0.9260 (mmm) cc_final: 0.8916 (tmm) REVERT: B 2382 MET cc_start: 0.8342 (tpp) cc_final: 0.8000 (tpp) REVERT: B 2415 MET cc_start: 0.8537 (tpp) cc_final: 0.7835 (tpp) REVERT: C 56 MET cc_start: 0.8615 (pmm) cc_final: 0.8406 (pmm) REVERT: C 100 MET cc_start: 0.9060 (ptm) cc_final: 0.8706 (ptp) REVERT: C 185 MET cc_start: 0.7425 (tmm) cc_final: 0.7083 (tmm) REVERT: C 255 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7270 (ppp) REVERT: D 86 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8744 (mppt) REVERT: D 233 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8764 (p) REVERT: D 255 MET cc_start: 0.8683 (ptp) cc_final: 0.8117 (tmm) REVERT: D 284 TYR cc_start: 0.8379 (m-80) cc_final: 0.8146 (m-10) REVERT: E 31 MET cc_start: 0.9471 (tmm) cc_final: 0.9150 (ttp) REVERT: E 51 MET cc_start: 0.6585 (mmt) cc_final: 0.5929 (mmt) REVERT: E 237 MET cc_start: 0.8204 (mtt) cc_final: 0.7441 (mmt) REVERT: E 413 LEU cc_start: 0.9556 (tp) cc_final: 0.9163 (tp) REVERT: E 527 MET cc_start: 0.2365 (mtt) cc_final: 0.2007 (mtt) REVERT: E 534 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8157 (ptp) REVERT: E 547 HIS cc_start: 0.9259 (m-70) cc_final: 0.8957 (t-90) REVERT: E 658 MET cc_start: 0.8828 (ptp) cc_final: 0.7879 (ppp) REVERT: E 1013 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8078 (tt) REVERT: E 1022 ASN cc_start: 0.6546 (OUTLIER) cc_final: 0.6311 (m110) REVERT: E 1108 MET cc_start: 0.6849 (tmm) cc_final: 0.6452 (tmm) REVERT: E 1138 LEU cc_start: 0.8905 (tp) cc_final: 0.8033 (pp) REVERT: E 1208 ARG cc_start: 0.9222 (mtt180) cc_final: 0.8949 (mpp80) REVERT: E 1243 MET cc_start: 0.6850 (mtp) cc_final: 0.6612 (ttm) REVERT: E 1274 ASN cc_start: 0.8712 (m-40) cc_final: 0.8467 (t0) REVERT: F 31 MET cc_start: 0.7970 (mmm) cc_final: 0.7675 (mmm) REVERT: F 55 MET cc_start: 0.9125 (mmp) cc_final: 0.8922 (mmp) REVERT: F 93 MET cc_start: 0.8765 (ptp) cc_final: 0.8463 (ptp) REVERT: F 128 ASP cc_start: 0.9479 (m-30) cc_final: 0.9090 (p0) REVERT: F 417 GLN cc_start: 0.9653 (tt0) cc_final: 0.9335 (tm-30) REVERT: F 479 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8505 (mm) REVERT: F 635 ASP cc_start: 0.9353 (m-30) cc_final: 0.9039 (t0) REVERT: F 646 MET cc_start: 0.8489 (mmp) cc_final: 0.8128 (mmt) REVERT: F 662 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8423 (tp30) REVERT: F 979 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5731 (p0) REVERT: F 1156 MET cc_start: 0.7909 (mtt) cc_final: 0.7595 (mtm) REVERT: F 1197 MET cc_start: 0.9035 (pmm) cc_final: 0.8793 (pmm) REVERT: G 403 MET cc_start: 0.3133 (tmm) cc_final: 0.2095 (tpp) REVERT: H 403 MET cc_start: 0.5985 (ttt) cc_final: 0.5372 (tpp) outliers start: 105 outliers final: 58 residues processed: 453 average time/residue: 0.5210 time to fit residues: 414.5067 Evaluate side-chains 431 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 352 time to evaluate : 4.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2003 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1470 ASN Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 171 optimal weight: 0.9990 chunk 483 optimal weight: 4.9990 chunk 455 optimal weight: 5.9990 chunk 627 optimal weight: 0.0670 chunk 223 optimal weight: 20.0000 chunk 682 optimal weight: 4.9990 chunk 707 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 456 optimal weight: 0.7980 chunk 575 optimal weight: 9.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2003 ASN ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.063349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.041457 restraints weight = 373356.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042403 restraints weight = 213213.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.043215 restraints weight = 146433.409| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 58060 Z= 0.224 Angle : 0.629 15.352 78778 Z= 0.307 Chirality : 0.041 0.397 8944 Planarity : 0.004 0.055 10028 Dihedral : 4.619 74.824 7808 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 1.67 % Allowed : 14.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.10), residues: 7024 helix: 2.08 (0.08), residues: 4330 sheet: -0.92 (0.20), residues: 664 loop : -0.28 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 593 HIS 0.014 0.001 HIS B1084 PHE 0.023 0.001 PHE B 610 TYR 0.015 0.001 TYR F1207 ARG 0.006 0.000 ARG F 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 358 time to evaluate : 5.000 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: A 277 MET cc_start: 0.1614 (mmm) cc_final: 0.1352 (mmm) REVERT: A 390 MET cc_start: 0.8170 (ppp) cc_final: 0.7427 (ttm) REVERT: A 542 MET cc_start: 0.8417 (ptt) cc_final: 0.8097 (ptt) REVERT: A 721 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8061 (ptp) REVERT: A 825 MET cc_start: 0.9177 (mtm) cc_final: 0.8812 (mtm) REVERT: A 934 MET cc_start: 0.9077 (ppp) cc_final: 0.8442 (ppp) REVERT: A 1004 CYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8734 (m) REVERT: A 1018 MET cc_start: 0.9420 (mtm) cc_final: 0.9019 (ptp) REVERT: A 1038 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8793 (ptp) REVERT: A 1140 ASP cc_start: 0.9496 (OUTLIER) cc_final: 0.9079 (t0) REVERT: A 1364 MET cc_start: 0.8770 (tpp) cc_final: 0.8382 (tpp) REVERT: A 1478 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9434 (mm) REVERT: A 1481 MET cc_start: 0.9145 (mtm) cc_final: 0.8469 (mtp) REVERT: A 1484 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 1512 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8643 (mtm) REVERT: A 1529 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9187 (tpp) REVERT: A 1621 GLU cc_start: 0.9155 (tt0) cc_final: 0.8564 (tp30) REVERT: A 1638 MET cc_start: 0.8770 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1701 MET cc_start: 0.9422 (ttp) cc_final: 0.7947 (ttm) REVERT: A 1717 MET cc_start: 0.9104 (tpp) cc_final: 0.8859 (tpt) REVERT: A 1747 MET cc_start: 0.8987 (mtp) cc_final: 0.8405 (ptp) REVERT: A 1988 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8437 (p-80) REVERT: A 2010 MET cc_start: 0.8857 (mmt) cc_final: 0.8500 (tpt) REVERT: A 2089 MET cc_start: 0.8808 (ppp) cc_final: 0.8550 (ppp) REVERT: A 2175 MET cc_start: 0.8738 (tpp) cc_final: 0.8222 (tpp) REVERT: A 2271 MET cc_start: 0.9057 (ttp) cc_final: 0.8811 (mtp) REVERT: A 2366 MET cc_start: 0.9206 (mmm) cc_final: 0.8818 (mmm) REVERT: A 2382 MET cc_start: 0.9261 (tpp) cc_final: 0.8601 (tpp) REVERT: A 2387 MET cc_start: 0.8924 (mtm) cc_final: 0.8707 (ttm) REVERT: A 2404 MET cc_start: 0.9575 (tpt) cc_final: 0.9190 (tpp) REVERT: B 123 MET cc_start: -0.0657 (mtt) cc_final: -0.0943 (tpp) REVERT: B 125 MET cc_start: 0.4374 (ttm) cc_final: 0.4096 (ptm) REVERT: B 693 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9486 (mt) REVERT: B 721 MET cc_start: 0.8712 (pmm) cc_final: 0.8495 (pmm) REVERT: B 727 MET cc_start: 0.9255 (mmp) cc_final: 0.8965 (mmp) REVERT: B 781 LEU cc_start: 0.9640 (mt) cc_final: 0.9365 (pp) REVERT: B 813 MET cc_start: 0.8983 (ptp) cc_final: 0.8508 (pmm) REVERT: B 827 MET cc_start: 0.9430 (tmm) cc_final: 0.8943 (tmm) REVERT: B 883 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8096 (tp30) REVERT: B 970 MET cc_start: 0.8665 (ptp) cc_final: 0.8344 (ptp) REVERT: B 994 MET cc_start: 0.9186 (tpp) cc_final: 0.8979 (mmm) REVERT: B 1018 MET cc_start: 0.9120 (tpp) cc_final: 0.8907 (tpp) REVERT: B 1031 MET cc_start: 0.9229 (tpp) cc_final: 0.9000 (tpp) REVERT: B 1075 ILE cc_start: 0.9834 (OUTLIER) cc_final: 0.9621 (mm) REVERT: B 1140 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8575 (t70) REVERT: B 1364 MET cc_start: 0.9527 (mmm) cc_final: 0.9101 (mmm) REVERT: B 1403 GLU cc_start: 0.9165 (tt0) cc_final: 0.8802 (pt0) REVERT: B 1477 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: B 1481 MET cc_start: 0.9088 (mtm) cc_final: 0.7375 (mtm) REVERT: B 1515 MET cc_start: 0.8960 (mtm) cc_final: 0.8543 (mtm) REVERT: B 1529 MET cc_start: 0.9451 (tpp) cc_final: 0.9130 (tmm) REVERT: B 1590 MET cc_start: 0.9471 (mmm) cc_final: 0.9149 (mmm) REVERT: B 1638 MET cc_start: 0.8864 (tpp) cc_final: 0.8343 (tpp) REVERT: B 1704 MET cc_start: 0.9432 (ptt) cc_final: 0.8793 (ppp) REVERT: B 2010 MET cc_start: 0.8647 (mmt) cc_final: 0.8163 (tpt) REVERT: B 2175 MET cc_start: 0.8652 (tpp) cc_final: 0.8406 (tpp) REVERT: B 2285 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: B 2327 MET cc_start: 0.9284 (mmm) cc_final: 0.8972 (tmm) REVERT: B 2382 MET cc_start: 0.8354 (tpp) cc_final: 0.8040 (tpp) REVERT: B 2415 MET cc_start: 0.8543 (tpp) cc_final: 0.7858 (tpp) REVERT: C 100 MET cc_start: 0.9104 (ptm) cc_final: 0.8777 (ptp) REVERT: C 185 MET cc_start: 0.7594 (tmm) cc_final: 0.7237 (tmm) REVERT: C 255 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7406 (ppp) REVERT: C 274 TRP cc_start: 0.7704 (OUTLIER) cc_final: 0.7050 (p90) REVERT: D 86 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8790 (mmmm) REVERT: D 233 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8868 (p) REVERT: D 255 MET cc_start: 0.8792 (ptp) cc_final: 0.8195 (tmm) REVERT: D 284 TYR cc_start: 0.8531 (m-80) cc_final: 0.8096 (m-10) REVERT: E 31 MET cc_start: 0.9470 (tmm) cc_final: 0.9125 (ttp) REVERT: E 51 MET cc_start: 0.6634 (mmt) cc_final: 0.5971 (mmt) REVERT: E 55 MET cc_start: 0.7992 (tpp) cc_final: 0.7583 (tmm) REVERT: E 148 PHE cc_start: 0.9148 (t80) cc_final: 0.8884 (t80) REVERT: E 237 MET cc_start: 0.8360 (mtt) cc_final: 0.7674 (mmt) REVERT: E 413 LEU cc_start: 0.9567 (tp) cc_final: 0.9175 (tp) REVERT: E 527 MET cc_start: 0.2934 (mtt) cc_final: 0.2424 (mtt) REVERT: E 534 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8366 (ptp) REVERT: E 547 HIS cc_start: 0.9229 (m-70) cc_final: 0.8893 (t-90) REVERT: E 658 MET cc_start: 0.8818 (ptp) cc_final: 0.7868 (ppp) REVERT: E 1013 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8074 (tt) REVERT: E 1022 ASN cc_start: 0.6583 (OUTLIER) cc_final: 0.6330 (m110) REVERT: E 1108 MET cc_start: 0.6976 (tmm) cc_final: 0.6574 (tmm) REVERT: E 1138 LEU cc_start: 0.9074 (tp) cc_final: 0.8287 (pp) REVERT: E 1208 ARG cc_start: 0.9197 (mtt180) cc_final: 0.8960 (mpp80) REVERT: E 1243 MET cc_start: 0.6853 (mtp) cc_final: 0.6645 (ttm) REVERT: E 1274 ASN cc_start: 0.8711 (m-40) cc_final: 0.8464 (t0) REVERT: F 31 MET cc_start: 0.7969 (mmm) cc_final: 0.7684 (mmm) REVERT: F 55 MET cc_start: 0.9202 (mmp) cc_final: 0.8972 (mmp) REVERT: F 93 MET cc_start: 0.8817 (ptp) cc_final: 0.8592 (ptp) REVERT: F 128 ASP cc_start: 0.9511 (m-30) cc_final: 0.9127 (p0) REVERT: F 417 GLN cc_start: 0.9668 (tt0) cc_final: 0.9342 (tm-30) REVERT: F 479 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8549 (mm) REVERT: F 534 MET cc_start: 0.9196 (mmt) cc_final: 0.8825 (mmm) REVERT: F 635 ASP cc_start: 0.9353 (m-30) cc_final: 0.9036 (t0) REVERT: F 662 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8426 (tp30) REVERT: F 979 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5695 (p0) REVERT: F 1073 MET cc_start: 0.7719 (mmm) cc_final: 0.6937 (mmm) REVERT: F 1156 MET cc_start: 0.7962 (mtt) cc_final: 0.7701 (mtp) REVERT: F 1197 MET cc_start: 0.9018 (pmm) cc_final: 0.8763 (pmm) REVERT: G 403 MET cc_start: 0.3351 (tmm) cc_final: 0.2264 (tpp) REVERT: H 403 MET cc_start: 0.5988 (ttt) cc_final: 0.5316 (tpp) outliers start: 103 outliers final: 65 residues processed: 440 average time/residue: 0.5264 time to fit residues: 406.3263 Evaluate side-chains 434 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 347 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2333 ILE Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1470 ASN Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 2003 ASN Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2392 LEU Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 971 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 472 optimal weight: 0.0370 chunk 303 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 394 optimal weight: 0.5980 chunk 619 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 360 optimal weight: 0.0040 chunk 656 optimal weight: 3.9990 chunk 629 optimal weight: 0.8980 chunk 391 optimal weight: 0.9990 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1898 ASN B2003 ASN ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 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 = 0.3799 r_free = 0.3799 target = 0.064139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.042270 restraints weight = 373981.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.043250 restraints weight = 211067.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.044136 restraints weight = 143858.660| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 58060 Z= 0.165 Angle : 0.628 15.603 78778 Z= 0.304 Chirality : 0.041 0.376 8944 Planarity : 0.004 0.054 10028 Dihedral : 4.569 79.174 7808 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.82 % Favored : 97.17 % Rotamer: Outliers : 1.52 % Allowed : 14.44 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.10), residues: 7024 helix: 2.07 (0.08), residues: 4334 sheet: -0.98 (0.20), residues: 632 loop : -0.27 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP E 593 HIS 0.013 0.001 HIS B1084 PHE 0.022 0.001 PHE B 610 TYR 0.023 0.001 TYR A 522 ARG 0.005 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 353 time to evaluate : 5.174 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: A 277 MET cc_start: 0.1354 (mmm) cc_final: 0.1074 (mmm) REVERT: A 390 MET cc_start: 0.8205 (ppp) cc_final: 0.7878 (ptp) REVERT: A 542 MET cc_start: 0.8401 (ptt) cc_final: 0.8091 (ptt) REVERT: A 548 MET cc_start: 0.8816 (mtp) cc_final: 0.8540 (mmm) REVERT: A 721 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8083 (ptp) REVERT: A 756 MET cc_start: 0.9485 (tpp) cc_final: 0.9047 (mmt) REVERT: A 825 MET cc_start: 0.9071 (mtm) cc_final: 0.8718 (mtm) REVERT: A 934 MET cc_start: 0.9075 (ppp) cc_final: 0.8496 (ppp) REVERT: A 1004 CYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8719 (m) REVERT: A 1018 MET cc_start: 0.9333 (mtm) cc_final: 0.8939 (ptp) REVERT: A 1038 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8637 (ptp) REVERT: A 1140 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9044 (t0) REVERT: A 1364 MET cc_start: 0.8695 (tpp) cc_final: 0.8274 (tpp) REVERT: A 1478 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9471 (mm) REVERT: A 1481 MET cc_start: 0.9136 (mtm) cc_final: 0.8581 (mtp) REVERT: A 1484 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9129 (mm) REVERT: A 1512 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: A 1529 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9103 (tpp) REVERT: A 1590 MET cc_start: 0.9248 (mmm) cc_final: 0.9004 (ttm) REVERT: A 1621 GLU cc_start: 0.9046 (tt0) cc_final: 0.8474 (tp30) REVERT: A 1638 MET cc_start: 0.8748 (tpp) cc_final: 0.8213 (tpp) REVERT: A 1701 MET cc_start: 0.9335 (ttp) cc_final: 0.7746 (ttm) REVERT: A 1717 MET cc_start: 0.9010 (tpp) cc_final: 0.8761 (tpt) REVERT: A 1747 MET cc_start: 0.8883 (mtp) cc_final: 0.8332 (ptp) REVERT: A 1988 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8415 (p-80) REVERT: A 2010 MET cc_start: 0.8831 (mmt) cc_final: 0.8501 (tpt) REVERT: A 2089 MET cc_start: 0.8789 (ppp) cc_final: 0.8542 (ppp) REVERT: A 2175 MET cc_start: 0.8779 (tpp) cc_final: 0.8267 (tpp) REVERT: A 2382 MET cc_start: 0.9195 (tpp) cc_final: 0.8612 (tpp) REVERT: A 2404 MET cc_start: 0.9473 (tpt) cc_final: 0.8810 (tmm) REVERT: A 2415 MET cc_start: 0.8919 (tpp) cc_final: 0.8622 (mmt) REVERT: B 125 MET cc_start: 0.4311 (ttm) cc_final: 0.4036 (ptm) REVERT: B 721 MET cc_start: 0.8651 (pmm) cc_final: 0.8398 (pmm) REVERT: B 727 MET cc_start: 0.9145 (mmp) cc_final: 0.8882 (mmp) REVERT: B 756 MET cc_start: 0.9030 (mmm) cc_final: 0.8786 (tpp) REVERT: B 781 LEU cc_start: 0.9617 (mt) cc_final: 0.9340 (pp) REVERT: B 813 MET cc_start: 0.8723 (ptp) cc_final: 0.8373 (pmm) REVERT: B 827 MET cc_start: 0.9399 (tmm) cc_final: 0.8833 (tmm) REVERT: B 883 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8109 (tp30) REVERT: B 970 MET cc_start: 0.8624 (ptp) cc_final: 0.8295 (ptp) REVERT: B 1018 MET cc_start: 0.9071 (tpp) cc_final: 0.8868 (tpp) REVERT: B 1031 MET cc_start: 0.9086 (tpp) cc_final: 0.8828 (tpp) REVERT: B 1044 MET cc_start: 0.7916 (tpp) cc_final: 0.7592 (tpp) REVERT: B 1074 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9445 (tp) REVERT: B 1140 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.8582 (t70) REVERT: B 1364 MET cc_start: 0.9443 (mmm) cc_final: 0.9038 (mmm) REVERT: B 1403 GLU cc_start: 0.9086 (tt0) cc_final: 0.8749 (pt0) REVERT: B 1477 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7883 (tmm) REVERT: B 1481 MET cc_start: 0.8930 (mtm) cc_final: 0.7627 (mtm) REVERT: B 1512 MET cc_start: 0.8347 (mmm) cc_final: 0.7690 (mmm) REVERT: B 1515 MET cc_start: 0.8914 (mtm) cc_final: 0.8519 (mtm) REVERT: B 1529 MET cc_start: 0.9308 (tpp) cc_final: 0.9066 (tmm) REVERT: B 1590 MET cc_start: 0.9346 (mmm) cc_final: 0.9143 (mmm) REVERT: B 1638 MET cc_start: 0.8865 (tpp) cc_final: 0.8291 (tpp) REVERT: B 1704 MET cc_start: 0.9399 (ptt) cc_final: 0.8778 (ppp) REVERT: B 1988 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8504 (p-80) REVERT: B 2010 MET cc_start: 0.8588 (mmt) cc_final: 0.8096 (tpp) REVERT: B 2175 MET cc_start: 0.8670 (tpp) cc_final: 0.8461 (tpp) REVERT: B 2285 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: B 2327 MET cc_start: 0.9155 (mmm) cc_final: 0.8849 (tmm) REVERT: B 2382 MET cc_start: 0.8327 (tpp) cc_final: 0.8029 (tpp) REVERT: B 2415 MET cc_start: 0.8543 (tpp) cc_final: 0.7843 (tpp) REVERT: C 100 MET cc_start: 0.8996 (ptm) cc_final: 0.8691 (ptp) REVERT: C 185 MET cc_start: 0.7549 (tmm) cc_final: 0.7214 (tmm) REVERT: C 255 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7213 (ppp) REVERT: C 274 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.7173 (p90) REVERT: D 56 MET cc_start: 0.5873 (tmm) cc_final: 0.5334 (tmm) REVERT: D 86 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8829 (mmmm) REVERT: D 233 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8817 (p) REVERT: D 255 MET cc_start: 0.8674 (ptp) cc_final: 0.8141 (tmm) REVERT: D 284 TYR cc_start: 0.8382 (m-80) cc_final: 0.7965 (m-10) REVERT: E 31 MET cc_start: 0.9478 (tmm) cc_final: 0.9118 (ttp) REVERT: E 51 MET cc_start: 0.6682 (mmt) cc_final: 0.6069 (mmt) REVERT: E 55 MET cc_start: 0.7890 (tpp) cc_final: 0.7436 (tmm) REVERT: E 148 PHE cc_start: 0.9147 (t80) cc_final: 0.8873 (t80) REVERT: E 237 MET cc_start: 0.8328 (mtt) cc_final: 0.7472 (pmm) REVERT: E 254 MET cc_start: 0.8489 (mmp) cc_final: 0.7579 (ttm) REVERT: E 375 MET cc_start: 0.9512 (pmm) cc_final: 0.9301 (pmm) REVERT: E 413 LEU cc_start: 0.9530 (tp) cc_final: 0.9140 (tp) REVERT: E 527 MET cc_start: 0.2730 (mtt) cc_final: 0.2214 (mtt) REVERT: E 534 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8194 (ptp) REVERT: E 658 MET cc_start: 0.8882 (ptp) cc_final: 0.7960 (ppp) REVERT: E 1013 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8065 (tt) REVERT: E 1022 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6387 (m110) REVERT: E 1108 MET cc_start: 0.6930 (tmm) cc_final: 0.6370 (tmm) REVERT: E 1138 LEU cc_start: 0.9044 (tp) cc_final: 0.8208 (pp) REVERT: E 1208 ARG cc_start: 0.9216 (mtt180) cc_final: 0.8944 (mpp80) REVERT: E 1243 MET cc_start: 0.6835 (mtp) cc_final: 0.6492 (ttm) REVERT: E 1274 ASN cc_start: 0.8722 (m-40) cc_final: 0.8476 (t0) REVERT: F 31 MET cc_start: 0.7969 (mmm) cc_final: 0.7668 (mmm) REVERT: F 55 MET cc_start: 0.9182 (mmp) cc_final: 0.8816 (mmp) REVERT: F 93 MET cc_start: 0.8827 (ptp) cc_final: 0.8513 (ptp) REVERT: F 128 ASP cc_start: 0.9467 (m-30) cc_final: 0.9084 (p0) REVERT: F 417 GLN cc_start: 0.9605 (tt0) cc_final: 0.9299 (tm-30) REVERT: F 479 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8555 (mm) REVERT: F 635 ASP cc_start: 0.9341 (m-30) cc_final: 0.9065 (t0) REVERT: F 662 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8433 (tp30) REVERT: F 1073 MET cc_start: 0.7677 (mmm) cc_final: 0.6934 (mmm) REVERT: F 1156 MET cc_start: 0.7952 (mtt) cc_final: 0.7650 (mtm) REVERT: F 1197 MET cc_start: 0.8986 (pmm) cc_final: 0.8707 (pmm) REVERT: G 403 MET cc_start: 0.3191 (tmm) cc_final: 0.2161 (tpp) REVERT: H 403 MET cc_start: 0.5960 (ttt) cc_final: 0.5357 (tpp) outliers start: 94 outliers final: 62 residues processed: 426 average time/residue: 0.5195 time to fit residues: 388.8516 Evaluate side-chains 427 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 344 time to evaluate : 5.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1038 MET Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1483 CYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 1988 HIS Chi-restraints excluded: chain B residue 2111 ILE Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2392 LEU Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1182 VAL Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 971 VAL Chi-restraints excluded: chain F residue 1182 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 193 optimal weight: 0.9990 chunk 499 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 575 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 390 optimal weight: 0.9980 chunk 635 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1310 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.063697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.041928 restraints weight = 372477.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.042966 restraints weight = 212032.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.043628 restraints weight = 145351.016| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 58060 Z= 0.185 Angle : 0.630 14.944 78778 Z= 0.306 Chirality : 0.041 0.368 8944 Planarity : 0.004 0.054 10028 Dihedral : 4.554 82.235 7808 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 1.36 % Allowed : 14.65 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.10), residues: 7024 helix: 2.10 (0.08), residues: 4322 sheet: -0.97 (0.20), residues: 646 loop : -0.26 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 593 HIS 0.014 0.001 HIS B1084 PHE 0.023 0.001 PHE B 610 TYR 0.026 0.001 TYR A 522 ARG 0.005 0.000 ARG A2197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14048 Ramachandran restraints generated. 7024 Oldfield, 0 Emsley, 7024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 351 time to evaluate : 4.963 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: A 277 MET cc_start: 0.1661 (mmm) cc_final: 0.1420 (mmm) REVERT: A 390 MET cc_start: 0.8197 (ppp) cc_final: 0.7898 (ptp) REVERT: A 542 MET cc_start: 0.8418 (ptt) cc_final: 0.8107 (ptt) REVERT: A 548 MET cc_start: 0.8698 (mtp) cc_final: 0.8454 (mmm) REVERT: A 756 MET cc_start: 0.9555 (tpp) cc_final: 0.9109 (mmt) REVERT: A 825 MET cc_start: 0.9160 (mtm) cc_final: 0.8763 (mtm) REVERT: A 934 MET cc_start: 0.9049 (ppp) cc_final: 0.8415 (ppp) REVERT: A 1004 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8759 (m) REVERT: A 1018 MET cc_start: 0.9395 (mtm) cc_final: 0.8983 (ptp) REVERT: A 1031 MET cc_start: 0.9318 (tpp) cc_final: 0.8420 (tpp) REVERT: A 1140 ASP cc_start: 0.9472 (OUTLIER) cc_final: 0.9023 (t0) REVERT: A 1364 MET cc_start: 0.8769 (tpp) cc_final: 0.8341 (tpp) REVERT: A 1481 MET cc_start: 0.9187 (mtm) cc_final: 0.8803 (mtp) REVERT: A 1484 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9109 (mm) REVERT: A 1512 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: A 1529 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9174 (tpp) REVERT: A 1590 MET cc_start: 0.9318 (mmm) cc_final: 0.9053 (ttm) REVERT: A 1621 GLU cc_start: 0.9153 (tt0) cc_final: 0.8539 (tp30) REVERT: A 1638 MET cc_start: 0.8848 (tpp) cc_final: 0.8438 (tpp) REVERT: A 1701 MET cc_start: 0.9423 (ttp) cc_final: 0.7898 (ttm) REVERT: A 1717 MET cc_start: 0.9122 (tpp) cc_final: 0.8793 (tpt) REVERT: A 1747 MET cc_start: 0.8993 (mtp) cc_final: 0.8441 (ptp) REVERT: A 1988 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8482 (p-80) REVERT: A 2010 MET cc_start: 0.8906 (mmt) cc_final: 0.8564 (tpt) REVERT: A 2089 MET cc_start: 0.8837 (ppp) cc_final: 0.8583 (ppp) REVERT: A 2175 MET cc_start: 0.8767 (tpp) cc_final: 0.8161 (tpp) REVERT: A 2366 MET cc_start: 0.9237 (mmm) cc_final: 0.8973 (mmm) REVERT: A 2382 MET cc_start: 0.9277 (tpp) cc_final: 0.8612 (tpp) REVERT: A 2404 MET cc_start: 0.9560 (tpt) cc_final: 0.8856 (tmm) REVERT: A 2415 MET cc_start: 0.8969 (tpp) cc_final: 0.8679 (mmt) REVERT: B 721 MET cc_start: 0.8695 (pmm) cc_final: 0.8449 (pmm) REVERT: B 727 MET cc_start: 0.9243 (mmp) cc_final: 0.8943 (mmp) REVERT: B 781 LEU cc_start: 0.9635 (mt) cc_final: 0.9368 (pp) REVERT: B 813 MET cc_start: 0.8699 (ptp) cc_final: 0.8431 (pmm) REVERT: B 827 MET cc_start: 0.9458 (tmm) cc_final: 0.8932 (tmm) REVERT: B 883 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8157 (tp30) REVERT: B 970 MET cc_start: 0.8647 (ptp) cc_final: 0.8307 (ptp) REVERT: B 990 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9381 (mm) REVERT: B 994 MET cc_start: 0.9334 (mmm) cc_final: 0.8489 (tpp) REVERT: B 1018 MET cc_start: 0.9155 (tpp) cc_final: 0.8947 (tpp) REVERT: B 1031 MET cc_start: 0.9225 (tpp) cc_final: 0.8976 (tpp) REVERT: B 1044 MET cc_start: 0.7986 (tpp) cc_final: 0.7648 (tpp) REVERT: B 1140 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.8571 (t70) REVERT: B 1364 MET cc_start: 0.9513 (mmm) cc_final: 0.9093 (mmm) REVERT: B 1403 GLU cc_start: 0.9191 (tt0) cc_final: 0.8827 (pt0) REVERT: B 1477 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.7995 (tmm) REVERT: B 1481 MET cc_start: 0.9066 (mtm) cc_final: 0.7711 (mtm) REVERT: B 1512 MET cc_start: 0.8505 (mmm) cc_final: 0.7808 (mmm) REVERT: B 1515 MET cc_start: 0.8975 (mtm) cc_final: 0.8571 (mtm) REVERT: B 1529 MET cc_start: 0.9382 (tpp) cc_final: 0.9103 (tpp) REVERT: B 1590 MET cc_start: 0.9449 (mmm) cc_final: 0.9150 (mmm) REVERT: B 1638 MET cc_start: 0.8899 (tpp) cc_final: 0.8297 (tpp) REVERT: B 1704 MET cc_start: 0.9441 (ptt) cc_final: 0.8787 (ppp) REVERT: B 1747 MET cc_start: 0.8974 (mmt) cc_final: 0.8724 (mmt) REVERT: B 2010 MET cc_start: 0.8687 (mmt) cc_final: 0.8171 (tpp) REVERT: B 2199 MET cc_start: 0.9321 (mmt) cc_final: 0.8993 (mmt) REVERT: B 2285 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8373 (tp30) REVERT: B 2327 MET cc_start: 0.9212 (mmm) cc_final: 0.8887 (tmm) REVERT: B 2382 MET cc_start: 0.8361 (tpp) cc_final: 0.8057 (tpp) REVERT: B 2415 MET cc_start: 0.8511 (tpp) cc_final: 0.7776 (tpp) REVERT: B 2540 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7315 (mp-120) REVERT: C 100 MET cc_start: 0.9076 (ptm) cc_final: 0.8778 (ptp) REVERT: C 185 MET cc_start: 0.7601 (tmm) cc_final: 0.7249 (tmm) REVERT: C 255 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7417 (ppp) REVERT: C 274 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7272 (p90) REVERT: D 56 MET cc_start: 0.6280 (tmm) cc_final: 0.5604 (tmm) REVERT: D 86 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8804 (mmmm) REVERT: D 233 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8880 (p) REVERT: D 255 MET cc_start: 0.8758 (ptp) cc_final: 0.8216 (tmm) REVERT: D 284 TYR cc_start: 0.8491 (m-80) cc_final: 0.8044 (m-10) REVERT: E 31 MET cc_start: 0.9446 (tmm) cc_final: 0.9098 (ttp) REVERT: E 51 MET cc_start: 0.6728 (mmt) cc_final: 0.6143 (mmt) REVERT: E 55 MET cc_start: 0.8039 (tpp) cc_final: 0.7684 (tmm) REVERT: E 148 PHE cc_start: 0.9148 (t80) cc_final: 0.8841 (t80) REVERT: E 237 MET cc_start: 0.8409 (mtt) cc_final: 0.7569 (pmm) REVERT: E 254 MET cc_start: 0.8596 (mmp) cc_final: 0.7359 (tpp) REVERT: E 375 MET cc_start: 0.9493 (pmm) cc_final: 0.9246 (pmm) REVERT: E 413 LEU cc_start: 0.9544 (tp) cc_final: 0.9145 (tp) REVERT: E 527 MET cc_start: 0.2725 (mtt) cc_final: 0.2225 (mtt) REVERT: E 534 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8401 (ptp) REVERT: E 658 MET cc_start: 0.8953 (ptp) cc_final: 0.8122 (ppp) REVERT: E 1013 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7951 (tt) REVERT: E 1022 ASN cc_start: 0.6770 (OUTLIER) cc_final: 0.6504 (m110) REVERT: E 1108 MET cc_start: 0.6980 (tmm) cc_final: 0.6732 (tmm) REVERT: E 1138 LEU cc_start: 0.9044 (tp) cc_final: 0.8277 (pp) REVERT: E 1208 ARG cc_start: 0.9186 (mtt180) cc_final: 0.8953 (mpp80) REVERT: E 1243 MET cc_start: 0.6900 (mtp) cc_final: 0.6624 (ttm) REVERT: E 1274 ASN cc_start: 0.8708 (m-40) cc_final: 0.8459 (t0) REVERT: F 31 MET cc_start: 0.7937 (mmm) cc_final: 0.7663 (mmm) REVERT: F 55 MET cc_start: 0.9199 (mmp) cc_final: 0.8822 (mmp) REVERT: F 93 MET cc_start: 0.8871 (ptp) cc_final: 0.8611 (ptp) REVERT: F 128 ASP cc_start: 0.9502 (m-30) cc_final: 0.9112 (p0) REVERT: F 417 GLN cc_start: 0.9653 (tt0) cc_final: 0.9304 (tm-30) REVERT: F 534 MET cc_start: 0.9012 (tpp) cc_final: 0.8654 (tpp) REVERT: F 635 ASP cc_start: 0.9367 (m-30) cc_final: 0.9057 (t0) REVERT: F 646 MET cc_start: 0.8296 (mmp) cc_final: 0.7926 (mmt) REVERT: F 647 MET cc_start: 0.5387 (ptm) cc_final: 0.5004 (ppp) REVERT: F 662 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8414 (tp30) REVERT: F 1073 MET cc_start: 0.7411 (mmm) cc_final: 0.6772 (mmm) REVERT: F 1156 MET cc_start: 0.7930 (mtt) cc_final: 0.7699 (mtp) REVERT: F 1197 MET cc_start: 0.8977 (pmm) cc_final: 0.8717 (pmm) REVERT: G 403 MET cc_start: 0.3290 (tmm) cc_final: 0.2248 (tpp) REVERT: H 403 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5373 (tpp) outliers start: 84 outliers final: 60 residues processed: 412 average time/residue: 0.5208 time to fit residues: 376.9074 Evaluate side-chains 422 residues out of total 6270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 344 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 615 HIS Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1004 CYS Chi-restraints excluded: chain A residue 1140 ASP Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1512 MET Chi-restraints excluded: chain A residue 1529 MET Chi-restraints excluded: chain A residue 1773 LEU Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 1988 HIS Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2240 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain B residue 609 HIS Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1140 ASP Chi-restraints excluded: chain B residue 1277 LYS Chi-restraints excluded: chain B residue 1437 MET Chi-restraints excluded: chain B residue 1477 MET Chi-restraints excluded: chain B residue 1483 CYS Chi-restraints excluded: chain B residue 1484 LEU Chi-restraints excluded: chain B residue 1624 GLN Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1885 VAL Chi-restraints excluded: chain B residue 1984 THR Chi-restraints excluded: chain B residue 2172 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2285 GLU Chi-restraints excluded: chain B residue 2392 LEU Chi-restraints excluded: chain B residue 2421 PHE Chi-restraints excluded: chain B residue 2540 GLN Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 274 TRP Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 534 MET Chi-restraints excluded: chain E residue 593 TRP Chi-restraints excluded: chain E residue 652 VAL Chi-restraints excluded: chain E residue 979 ASP Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1022 ASN Chi-restraints excluded: chain E residue 1028 VAL Chi-restraints excluded: chain E residue 1257 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 422 MET Chi-restraints excluded: chain F residue 445 HIS Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 526 TYR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain F residue 671 VAL Chi-restraints excluded: chain F residue 971 VAL Chi-restraints excluded: chain F residue 1254 LYS Chi-restraints excluded: chain F residue 1323 TYR Chi-restraints excluded: chain F residue 1330 VAL Chi-restraints excluded: chain H residue 403 MET Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 615 optimal weight: 0.7980 chunk 287 optimal weight: 0.9980 chunk 225 optimal weight: 20.0000 chunk 633 optimal weight: 1.9990 chunk 676 optimal weight: 0.9980 chunk 501 optimal weight: 0.0060 chunk 541 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 703 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1808 ASN ** B2189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN E1312 HIS ** F1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.063710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.041856 restraints weight = 376403.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.042764 restraints weight = 214385.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.043565 restraints weight = 147245.450| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 58060 Z= 0.181 Angle : 0.635 14.806 78778 Z= 0.306 Chirality : 0.041 0.355 8944 Planarity : 0.004 0.054 10028 Dihedral : 4.539 83.586 7808 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 1.35 % Allowed : 14.67 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.10), residues: 7024 helix: 2.06 (0.08), residues: 4336 sheet: -0.80 (0.20), residues: 642 loop : -0.26 (0.15), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 593 HIS 0.014 0.001 HIS B1084 PHE 0.022 0.001 PHE B 610 TYR 0.026 0.001 TYR A 522 ARG 0.005 0.000 ARG A1482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19431.64 seconds wall clock time: 337 minutes 16.47 seconds (20236.47 seconds total)