Starting phenix.real_space_refine on Tue May 27 17:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.map" model { file = "/net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8imz_35577/05_2025/8imz_35577.cif" } resolution = 3.66 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= 0.024 sd= 0.168 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 19236 2.51 5 N 4941 2.21 5 O 5055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29409 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 9653 Classifications: {'peptide': 1223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 47, 'TRANS': 1175} Chain breaks: 14 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 235 Chain: "E" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 150 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 19} Restraints were copied for chains: C, B, D, F Time building chain proxies: 28.10, per 1000 atoms: 0.96 Number of scatterers: 29409 At special positions: 0 Unit cell: (186.735, 204.67, 154.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 5055 8.00 N 4941 7.00 C 19236 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: 7.25 Conformation dependent library (CDL) restraints added in 3.6 seconds 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7164 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 12 sheets defined 70.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 784 through 824 removed outlier: 4.159A pdb=" N ALA A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 832 " --> pdb=" O MET A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 858 removed outlier: 4.436A pdb=" N THR A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL A 862 " --> pdb=" O CYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 950 removed outlier: 3.680A pdb=" N ALA A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1006 removed outlier: 6.349A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1023 removed outlier: 4.171A pdb=" N HIS A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1053 removed outlier: 3.544A pdb=" N ILE A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A1031 " --> pdb=" O GLU A1027 " (cutoff:3.500A) Proline residue: A1034 - end of helix removed outlier: 3.584A pdb=" N CYS A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A1052 " --> pdb=" O TYR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1080 Processing helix chain 'A' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1159 Processing helix chain 'A' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL A1167 " --> pdb=" O TRP A1163 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU A1193 " --> pdb=" O PHE A1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1228 Processing helix chain 'A' and resid 1229 through 1232 Processing helix chain 'A' and resid 1244 through 1250 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.770A pdb=" N CYS A1286 " --> pdb=" O TRP A1282 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A1299 " --> pdb=" O ARG A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1365 removed outlier: 5.074A pdb=" N SER A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1321 " --> pdb=" O SER A1317 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1510 through 1546 removed outlier: 4.215A pdb=" N ASP A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A1540 " --> pdb=" O ALA A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1558 removed outlier: 3.967A pdb=" N VAL A1555 " --> pdb=" O VAL A1551 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A1556 " --> pdb=" O ARG A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1664 removed outlier: 4.035A pdb=" N ARG A1664 " --> pdb=" O GLU A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.623A pdb=" N GLN A1668 " --> pdb=" O ARG A1664 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A1669 " --> pdb=" O PHE A1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1664 through 1669' Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1686 through 1701 removed outlier: 3.806A pdb=" N TYR A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1707 Processing helix chain 'A' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A1744 " --> pdb=" O MET A1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A1749 " --> pdb=" O TYR A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1775 Processing helix chain 'A' and resid 1786 through 1803 Processing helix chain 'A' and resid 1958 through 1968 Processing helix chain 'A' and resid 1976 through 1997 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 4.110A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2069 removed outlier: 4.523A pdb=" N LEU A2065 " --> pdb=" O MET A2061 " (cutoff:3.500A) Proline residue: A2066 - end of helix Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU A2119 " --> pdb=" O ASN A2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A2120 " --> pdb=" O HIS A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 removed outlier: 3.702A pdb=" N LEU A2134 " --> pdb=" O PHE A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2184 through 2214 removed outlier: 3.806A pdb=" N ILE A2203 " --> pdb=" O LEU A2199 " (cutoff:3.500A) Proline residue: A2206 - end of helix removed outlier: 3.896A pdb=" N ARG A2214 " --> pdb=" O MET A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2262 Processing helix chain 'A' and resid 2266 through 2273 removed outlier: 4.232A pdb=" N MET A2270 " --> pdb=" O TYR A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2274 through 2276 No H-bonds generated for 'chain 'A' and resid 2274 through 2276' Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2326 through 2330 removed outlier: 3.829A pdb=" N LYS A2329 " --> pdb=" O ASP A2326 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2359 removed outlier: 3.769A pdb=" N GLN A2356 " --> pdb=" O ARG A2352 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A2359 " --> pdb=" O ALA A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2391 removed outlier: 3.732A pdb=" N LEU A2390 " --> pdb=" O VAL A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2466 through 2483 Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2519 through 2533 Processing helix chain 'A' and resid 2537 through 2542 Processing helix chain 'D' and resid 230 through 245 removed outlier: 3.594A pdb=" N LEU D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 244 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 245 " --> pdb=" O CYS D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.594A pdb=" N LEU E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS E 244 " --> pdb=" O CYS E 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 245 " --> pdb=" O CYS E 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 824 removed outlier: 5.423A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 815 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 816 " --> pdb=" O LEU C 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR C 817 " --> pdb=" O VAL C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU C 831 " --> pdb=" O VAL C 827 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 845 through 858 removed outlier: 4.436A pdb=" N THR C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 950 removed outlier: 3.680A pdb=" N ALA C 938 " --> pdb=" O LEU C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1006 removed outlier: 6.350A pdb=" N PHE C 986 " --> pdb=" O ILE C 982 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU C 991 " --> pdb=" O TYR C 987 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1023 removed outlier: 4.172A pdb=" N HIS C1013 " --> pdb=" O MET C1009 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1053 removed outlier: 3.544A pdb=" N ILE C1029 " --> pdb=" O ARG C1025 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C1031 " --> pdb=" O GLU C1027 " (cutoff:3.500A) Proline residue: C1034 - end of helix removed outlier: 3.584A pdb=" N CYS C1051 " --> pdb=" O GLN C1047 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C1052 " --> pdb=" O TYR C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1080 Processing helix chain 'C' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1159 Processing helix chain 'C' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL C1167 " --> pdb=" O TRP C1163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C1176 " --> pdb=" O ALA C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU C1193 " --> pdb=" O PHE C1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1228 Processing helix chain 'C' and resid 1229 through 1232 Processing helix chain 'C' and resid 1244 through 1250 Processing helix chain 'C' and resid 1282 through 1299 removed outlier: 3.771A pdb=" N CYS C1286 " --> pdb=" O TRP C1282 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C1287 " --> pdb=" O ASP C1283 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C1298 " --> pdb=" O ARG C1294 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C1299 " --> pdb=" O ARG C1295 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1365 removed outlier: 5.073A pdb=" N SER C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C1320 " --> pdb=" O ALA C1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C1321 " --> pdb=" O SER C1317 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C1365 " --> pdb=" O GLN C1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1408 Processing helix chain 'C' and resid 1510 through 1546 removed outlier: 4.215A pdb=" N ASP C1514 " --> pdb=" O GLN C1510 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C1540 " --> pdb=" O ALA C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1551 through 1558 removed outlier: 3.968A pdb=" N VAL C1555 " --> pdb=" O VAL C1551 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C1556 " --> pdb=" O ARG C1552 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1664 removed outlier: 4.034A pdb=" N ARG C1664 " --> pdb=" O GLU C1660 " (cutoff:3.500A) Processing helix chain 'C' and resid 1664 through 1669 removed outlier: 3.622A pdb=" N GLN C1668 " --> pdb=" O ARG C1664 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C1669 " --> pdb=" O PHE C1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1664 through 1669' Processing helix chain 'C' and resid 1672 through 1686 Processing helix chain 'C' and resid 1686 through 1701 removed outlier: 3.806A pdb=" N TYR C1692 " --> pdb=" O GLU C1688 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1707 Processing helix chain 'C' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C1744 " --> pdb=" O MET C1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C1749 " --> pdb=" O TYR C1745 " (cutoff:3.500A) Processing helix chain 'C' and resid 1771 through 1775 Processing helix chain 'C' and resid 1786 through 1803 Processing helix chain 'C' and resid 1958 through 1968 Processing helix chain 'C' and resid 1976 through 1997 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 4.109A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2069 removed outlier: 4.523A pdb=" N LEU C2065 " --> pdb=" O MET C2061 " (cutoff:3.500A) Proline residue: C2066 - end of helix Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU C2119 " --> pdb=" O ASN C2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C2120 " --> pdb=" O HIS C2116 " (cutoff:3.500A) Processing helix chain 'C' and resid 2130 through 2142 removed outlier: 3.701A pdb=" N LEU C2134 " --> pdb=" O PHE C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2184 through 2214 removed outlier: 3.804A pdb=" N ILE C2203 " --> pdb=" O LEU C2199 " (cutoff:3.500A) Proline residue: C2206 - end of helix removed outlier: 3.897A pdb=" N ARG C2214 " --> pdb=" O MET C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2252 through 2262 Processing helix chain 'C' and resid 2266 through 2273 removed outlier: 4.233A pdb=" N MET C2270 " --> pdb=" O TYR C2266 " (cutoff:3.500A) Processing helix chain 'C' and resid 2274 through 2276 No H-bonds generated for 'chain 'C' and resid 2274 through 2276' Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2326 through 2330 removed outlier: 3.830A pdb=" N LYS C2329 " --> pdb=" O ASP C2326 " (cutoff:3.500A) Processing helix chain 'C' and resid 2348 through 2359 removed outlier: 3.768A pdb=" N GLN C2356 " --> pdb=" O ARG C2352 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C2359 " --> pdb=" O ALA C2355 " (cutoff:3.500A) Processing helix chain 'C' and resid 2387 through 2391 removed outlier: 3.731A pdb=" N LEU C2390 " --> pdb=" O VAL C2387 " (cutoff:3.500A) Processing helix chain 'C' and resid 2466 through 2483 Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2519 through 2533 Processing helix chain 'C' and resid 2537 through 2542 Processing helix chain 'B' and resid 785 through 824 removed outlier: 5.423A pdb=" N PHE B 810 " --> pdb=" O GLU B 806 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 815 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR B 817 " --> pdb=" O VAL B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 840 removed outlier: 3.822A pdb=" N LEU B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 832 " --> pdb=" O MET B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 845 through 858 removed outlier: 4.437A pdb=" N THR B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 868 removed outlier: 3.880A pdb=" N VAL B 862 " --> pdb=" O CYS B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 950 removed outlier: 3.679A pdb=" N ALA B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 1006 removed outlier: 6.350A pdb=" N PHE B 986 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 991 " --> pdb=" O TYR B 987 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1023 removed outlier: 4.171A pdb=" N HIS B1013 " --> pdb=" O MET B1009 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1053 removed outlier: 3.543A pdb=" N ILE B1029 " --> pdb=" O ARG B1025 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B1031 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Proline residue: B1034 - end of helix removed outlier: 3.584A pdb=" N CYS B1051 " --> pdb=" O GLN B1047 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B1052 " --> pdb=" O TYR B1048 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1080 Processing helix chain 'B' and resid 1093 through 1114 removed outlier: 4.154A pdb=" N ASP B1097 " --> pdb=" O ASN B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1161 through 1176 removed outlier: 4.732A pdb=" N VAL B1167 " --> pdb=" O TRP B1163 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B1176 " --> pdb=" O ALA B1172 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1199 removed outlier: 3.571A pdb=" N LEU B1193 " --> pdb=" O PHE B1189 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B1196 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1228 Processing helix chain 'B' and resid 1229 through 1232 Processing helix chain 'B' and resid 1244 through 1250 Processing helix chain 'B' and resid 1282 through 1299 removed outlier: 3.770A pdb=" N CYS B1286 " --> pdb=" O TRP B1282 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1287 " --> pdb=" O ASP B1283 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B1298 " --> pdb=" O ARG B1294 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B1299 " --> pdb=" O ARG B1295 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1365 removed outlier: 5.073A pdb=" N SER B1317 " --> pdb=" O ALA B1313 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG B1318 " --> pdb=" O LEU B1314 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B1321 " --> pdb=" O SER B1317 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B1365 " --> pdb=" O GLN B1361 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1408 Processing helix chain 'B' and resid 1510 through 1546 removed outlier: 4.216A pdb=" N ASP B1514 " --> pdb=" O GLN B1510 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS B1526 " --> pdb=" O ALA B1522 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS B1527 " --> pdb=" O PHE B1523 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B1540 " --> pdb=" O ALA B1536 " (cutoff:3.500A) Processing helix chain 'B' and resid 1551 through 1558 removed outlier: 3.967A pdb=" N VAL B1555 " --> pdb=" O VAL B1551 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B1556 " --> pdb=" O ARG B1552 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1664 removed outlier: 4.034A pdb=" N ARG B1664 " --> pdb=" O GLU B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1669 removed outlier: 3.623A pdb=" N GLN B1668 " --> pdb=" O ARG B1664 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B1669 " --> pdb=" O PHE B1665 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1664 through 1669' Processing helix chain 'B' and resid 1672 through 1686 Processing helix chain 'B' and resid 1686 through 1701 removed outlier: 3.807A pdb=" N TYR B1692 " --> pdb=" O GLU B1688 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1707 Processing helix chain 'B' and resid 1708 through 1717 removed outlier: 3.730A pdb=" N VAL B1712 " --> pdb=" O LEU B1708 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B1713 " --> pdb=" O VAL B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1726 through 1749 removed outlier: 3.603A pdb=" N TRP B1730 " --> pdb=" O SER B1726 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B1744 " --> pdb=" O MET B1740 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B1749 " --> pdb=" O TYR B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1771 through 1775 Processing helix chain 'B' and resid 1786 through 1803 Processing helix chain 'B' and resid 1958 through 1968 Processing helix chain 'B' and resid 1976 through 1997 Processing helix chain 'B' and resid 2016 through 2041 removed outlier: 4.109A pdb=" N PHE B2022 " --> pdb=" O GLN B2018 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2069 removed outlier: 4.524A pdb=" N LEU B2065 " --> pdb=" O MET B2061 " (cutoff:3.500A) Proline residue: B2066 - end of helix Processing helix chain 'B' and resid 2076 through 2100 Processing helix chain 'B' and resid 2115 through 2128 removed outlier: 4.113A pdb=" N LEU B2119 " --> pdb=" O ASN B2115 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B2120 " --> pdb=" O HIS B2116 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2142 removed outlier: 3.702A pdb=" N LEU B2134 " --> pdb=" O PHE B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2148 through 2175 Processing helix chain 'B' and resid 2184 through 2214 removed outlier: 3.805A pdb=" N ILE B2203 " --> pdb=" O LEU B2199 " (cutoff:3.500A) Proline residue: B2206 - end of helix removed outlier: 3.897A pdb=" N ARG B2214 " --> pdb=" O MET B2210 " (cutoff:3.500A) Processing helix chain 'B' and resid 2252 through 2262 Processing helix chain 'B' and resid 2266 through 2273 removed outlier: 4.233A pdb=" N MET B2270 " --> pdb=" O TYR B2266 " (cutoff:3.500A) Processing helix chain 'B' and resid 2274 through 2276 No H-bonds generated for 'chain 'B' and resid 2274 through 2276' Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2326 through 2330 removed outlier: 3.829A pdb=" N LYS B2329 " --> pdb=" O ASP B2326 " (cutoff:3.500A) Processing helix chain 'B' and resid 2348 through 2359 removed outlier: 3.769A pdb=" N GLN B2356 " --> pdb=" O ARG B2352 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B2359 " --> pdb=" O ALA B2355 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2391 removed outlier: 3.731A pdb=" N LEU B2390 " --> pdb=" O VAL B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2466 through 2483 Processing helix chain 'B' and resid 2500 through 2516 Processing helix chain 'B' and resid 2519 through 2533 Processing helix chain 'B' and resid 2537 through 2542 Processing helix chain 'F' and resid 230 through 245 removed outlier: 3.595A pdb=" N LEU F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS F 244 " --> pdb=" O CYS F 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE F 245 " --> pdb=" O CYS F 241 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A2240 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A2228 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A2242 " --> pdb=" O VAL A2226 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A2226 " --> pdb=" O SER A2242 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A2338 " --> pdb=" O TRP A2321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A2240 " --> pdb=" O VAL A2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A2228 " --> pdb=" O THR A2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A2242 " --> pdb=" O VAL A2226 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A2226 " --> pdb=" O SER A2242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A2315 " --> pdb=" O LEU A2344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 6.465A pdb=" N ILE A2376 " --> pdb=" O PHE A2449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C2240 " --> pdb=" O VAL C2228 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C2228 " --> pdb=" O THR C2240 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C2242 " --> pdb=" O VAL C2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C2226 " --> pdb=" O SER C2242 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C2338 " --> pdb=" O TRP C2321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C2240 " --> pdb=" O VAL C2228 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C2228 " --> pdb=" O THR C2240 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C2242 " --> pdb=" O VAL C2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C2226 " --> pdb=" O SER C2242 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C2315 " --> pdb=" O LEU C2344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 6.465A pdb=" N ILE C2376 " --> pdb=" O PHE C2449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU B2230 " --> pdb=" O LEU B2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2240 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B2228 " --> pdb=" O THR B2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B2242 " --> pdb=" O VAL B2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B2226 " --> pdb=" O SER B2242 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B2338 " --> pdb=" O TRP B2321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 2237 through 2243 removed outlier: 6.760A pdb=" N LEU B2230 " --> pdb=" O LEU B2238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR B2240 " --> pdb=" O VAL B2228 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B2228 " --> pdb=" O THR B2240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER B2242 " --> pdb=" O VAL B2226 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B2226 " --> pdb=" O SER B2242 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B2315 " --> pdb=" O LEU B2344 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 6.466A pdb=" N ILE B2376 " --> pdb=" O PHE B2449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2366 through 2372 removed outlier: 5.216A pdb=" N VAL B2367 " --> pdb=" O ILE B2403 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B2403 " --> pdb=" O VAL B2367 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL B2401 " --> pdb=" O PRO B2369 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B2399 " --> pdb=" O LEU B2371 " (cutoff:3.500A) 1887 hydrogen bonds defined for protein. 5589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9220 1.34 - 1.46: 4772 1.46 - 1.57: 15831 1.57 - 1.69: 0 1.69 - 1.81: 261 Bond restraints: 30084 Sorted by residual: bond pdb=" CG GLU C2133 " pdb=" CD GLU C2133 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CG GLU B2133 " pdb=" CD GLU B2133 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CG GLU A2133 " pdb=" CD GLU A2133 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.17e+00 bond pdb=" C ASN B2221 " pdb=" N GLN B2222 " ideal model delta sigma weight residual 1.327 1.293 0.034 2.31e-02 1.87e+03 2.10e+00 bond pdb=" C ASN C2221 " pdb=" N GLN C2222 " ideal model delta sigma weight residual 1.327 1.294 0.033 2.31e-02 1.87e+03 2.07e+00 ... (remaining 30079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 39653 2.00 - 4.00: 989 4.00 - 6.01: 140 6.01 - 8.01: 27 8.01 - 10.01: 6 Bond angle restraints: 40815 Sorted by residual: angle pdb=" N PHE C1180 " pdb=" CA PHE C1180 " pdb=" C PHE C1180 " ideal model delta sigma weight residual 114.62 107.04 7.58 1.14e+00 7.69e-01 4.42e+01 angle pdb=" N PHE B1180 " pdb=" CA PHE B1180 " pdb=" C PHE B1180 " ideal model delta sigma weight residual 114.62 107.10 7.52 1.14e+00 7.69e-01 4.35e+01 angle pdb=" N PHE A1180 " pdb=" CA PHE A1180 " pdb=" C PHE A1180 " ideal model delta sigma weight residual 114.62 107.11 7.51 1.14e+00 7.69e-01 4.34e+01 angle pdb=" C PHE C1180 " pdb=" N GLY C1181 " pdb=" CA GLY C1181 " ideal model delta sigma weight residual 119.98 124.43 -4.45 1.11e+00 8.12e-01 1.61e+01 angle pdb=" C PHE A1180 " pdb=" N GLY A1181 " pdb=" CA GLY A1181 " ideal model delta sigma weight residual 119.98 124.42 -4.44 1.11e+00 8.12e-01 1.60e+01 ... (remaining 40810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16027 17.76 - 35.52: 1484 35.52 - 53.29: 225 53.29 - 71.05: 33 71.05 - 88.81: 33 Dihedral angle restraints: 17802 sinusoidal: 6822 harmonic: 10980 Sorted by residual: dihedral pdb=" CA PRO B2265 " pdb=" C PRO B2265 " pdb=" N TYR B2266 " pdb=" CA TYR B2266 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO C2265 " pdb=" C PRO C2265 " pdb=" N TYR C2266 " pdb=" CA TYR C2266 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO A2265 " pdb=" C PRO A2265 " pdb=" N TYR A2266 " pdb=" CA TYR A2266 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 17799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3478 0.049 - 0.097: 1014 0.097 - 0.146: 155 0.146 - 0.195: 24 0.195 - 0.243: 12 Chirality restraints: 4683 Sorted by residual: chirality pdb=" CB ILE C1179 " pdb=" CA ILE C1179 " pdb=" CG1 ILE C1179 " pdb=" CG2 ILE C1179 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A1179 " pdb=" CA ILE A1179 " pdb=" CG1 ILE A1179 " pdb=" CG2 ILE A1179 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B1179 " pdb=" CA ILE B1179 " pdb=" CG1 ILE B1179 " pdb=" CG2 ILE B1179 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4680 not shown) Planarity restraints: 5091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B2381 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B2382 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B2382 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B2382 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2381 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO A2382 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A2382 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A2382 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C2381 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO C2382 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C2382 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C2382 " -0.055 5.00e-02 4.00e+02 ... (remaining 5088 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 250 2.60 - 3.17: 26614 3.17 - 3.75: 45704 3.75 - 4.32: 58478 4.32 - 4.90: 95546 Nonbonded interactions: 226592 Sorted by model distance: nonbonded pdb=" NE ARG A1971 " pdb=" O ARG A2098 " model vdw 2.020 3.120 nonbonded pdb=" NE ARG C1971 " pdb=" O ARG C2098 " model vdw 2.021 3.120 nonbonded pdb=" NE ARG B1971 " pdb=" O ARG B2098 " model vdw 2.021 3.120 nonbonded pdb=" O MET B2270 " pdb=" OG SER B2274 " model vdw 2.073 3.040 nonbonded pdb=" O MET A2270 " pdb=" OG SER A2274 " model vdw 2.073 3.040 ... (remaining 226587 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 4.670 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.300 Process input model: 74.360 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 30084 Z= 0.285 Angle : 0.770 10.010 40815 Z= 0.423 Chirality : 0.046 0.243 4683 Planarity : 0.005 0.103 5091 Dihedral : 14.272 88.810 10638 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.02 (0.14), residues: 3636 helix: 1.07 (0.11), residues: 2328 sheet: -2.25 (0.29), residues: 246 loop : -1.75 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A2321 HIS 0.008 0.002 HIS B2116 PHE 0.019 0.002 PHE C2426 TYR 0.020 0.002 TYR A1803 ARG 0.012 0.001 ARG A2104 Details of bonding type rmsd hydrogen bonds : bond 0.13187 ( 1860) hydrogen bonds : angle 5.33072 ( 5589) covalent geometry : bond 0.00678 (30084) covalent geometry : angle 0.76984 (40815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2224 ILE cc_start: 0.8627 (tt) cc_final: 0.8384 (tp) REVERT: A 2270 MET cc_start: 0.5483 (tpt) cc_final: 0.5160 (tpt) REVERT: A 2372 PHE cc_start: 0.8508 (t80) cc_final: 0.7942 (t80) REVERT: A 2517 ARG cc_start: 0.7036 (mpt180) cc_final: 0.6206 (tmm160) REVERT: C 2270 MET cc_start: 0.5204 (tpt) cc_final: 0.4783 (tpt) REVERT: C 2372 PHE cc_start: 0.8637 (t80) cc_final: 0.8409 (t80) REVERT: C 2473 ILE cc_start: 0.8089 (tp) cc_final: 0.7838 (tp) REVERT: C 2517 ARG cc_start: 0.7232 (mpt180) cc_final: 0.6215 (tmm160) REVERT: B 2270 MET cc_start: 0.5113 (tpt) cc_final: 0.4868 (tpt) REVERT: B 2372 PHE cc_start: 0.8562 (t80) cc_final: 0.8099 (t80) REVERT: B 2517 ARG cc_start: 0.7006 (mpt180) cc_final: 0.6116 (tmm160) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.3907 time to fit residues: 244.6765 Evaluate side-chains 305 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 3.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 ASN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2364 GLN ** C1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2364 GLN ** B1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1225 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.171267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.153471 restraints weight = 54841.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.151774 restraints weight = 120994.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148911 restraints weight = 64604.454| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30084 Z= 0.161 Angle : 0.622 7.329 40815 Z= 0.317 Chirality : 0.041 0.177 4683 Planarity : 0.005 0.085 5091 Dihedral : 4.793 29.022 4026 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.40 % Allowed : 9.11 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3636 helix: 1.54 (0.11), residues: 2385 sheet: -1.88 (0.30), residues: 261 loop : -1.62 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C2140 HIS 0.006 0.001 HIS C2116 PHE 0.022 0.002 PHE C1794 TYR 0.019 0.001 TYR B1803 ARG 0.004 0.000 ARG B2534 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 1860) hydrogen bonds : angle 4.16880 ( 5589) covalent geometry : bond 0.00377 (30084) covalent geometry : angle 0.62158 (40815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 386 time to evaluate : 3.070 Fit side-chains revert: symmetry clash REVERT: A 2153 MET cc_start: 0.7819 (mtp) cc_final: 0.7557 (mtp) REVERT: A 2321 TRP cc_start: 0.8744 (p90) cc_final: 0.8430 (p90) REVERT: A 2517 ARG cc_start: 0.7137 (mpt180) cc_final: 0.6787 (tmm160) REVERT: C 1226 MET cc_start: 0.7685 (tpp) cc_final: 0.7472 (mmm) REVERT: C 2270 MET cc_start: 0.4158 (tpt) cc_final: 0.3708 (tpt) REVERT: C 2315 ILE cc_start: 0.8537 (tp) cc_final: 0.8323 (tp) REVERT: C 2321 TRP cc_start: 0.8579 (p90) cc_final: 0.8110 (p90) REVERT: C 2517 ARG cc_start: 0.7083 (mpt180) cc_final: 0.6484 (tmm160) REVERT: B 1349 MET cc_start: 0.8457 (tpp) cc_final: 0.8237 (mmm) REVERT: B 2034 ASP cc_start: 0.8336 (t0) cc_final: 0.7981 (t0) REVERT: B 2133 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: B 2270 MET cc_start: 0.4042 (tpt) cc_final: 0.3795 (tpt) REVERT: B 2321 TRP cc_start: 0.8591 (p90) cc_final: 0.8259 (p90) REVERT: B 2372 PHE cc_start: 0.8097 (t80) cc_final: 0.7745 (t80) REVERT: B 2517 ARG cc_start: 0.7030 (mpt180) cc_final: 0.6664 (tmm160) outliers start: 42 outliers final: 25 residues processed: 409 average time/residue: 0.3715 time to fit residues: 246.8511 Evaluate side-chains 367 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 341 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2432 ILE Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2227 THR Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2252 THR Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2464 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 118 optimal weight: 0.8980 chunk 319 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 355 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 345 optimal weight: 5.9990 chunk 326 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 150 optimal weight: 0.0270 chunk 231 optimal weight: 10.0000 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 HIS C1217 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 HIS B1217 ASN ** B1225 ASN ** 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 = 0.4366 r_free = 0.4366 target = 0.175430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.154909 restraints weight = 54620.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157099 restraints weight = 117715.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.157398 restraints weight = 54050.913| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30084 Z= 0.110 Angle : 0.548 12.179 40815 Z= 0.276 Chirality : 0.039 0.169 4683 Planarity : 0.004 0.070 5091 Dihedral : 4.349 27.501 4026 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.36 % Allowed : 13.09 % Favored : 85.54 % 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: 1.08 (0.14), residues: 3636 helix: 1.87 (0.11), residues: 2403 sheet: -1.44 (0.32), residues: 255 loop : -1.64 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C2140 HIS 0.004 0.001 HIS C2116 PHE 0.023 0.001 PHE B2426 TYR 0.016 0.001 TYR A1803 ARG 0.004 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 1860) hydrogen bonds : angle 3.82232 ( 5589) covalent geometry : bond 0.00237 (30084) covalent geometry : angle 0.54835 (40815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 396 time to evaluate : 3.151 Fit side-chains revert: symmetry clash REVERT: A 2321 TRP cc_start: 0.8671 (p90) cc_final: 0.8337 (p90) REVERT: A 2517 ARG cc_start: 0.7019 (mpt180) cc_final: 0.6709 (tmm160) REVERT: C 2270 MET cc_start: 0.3791 (tpt) cc_final: 0.3498 (tpt) REVERT: C 2321 TRP cc_start: 0.8535 (p90) cc_final: 0.8041 (p90) REVERT: C 2517 ARG cc_start: 0.6907 (mpt180) cc_final: 0.6539 (tmm160) REVERT: B 1722 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5446 (mm) REVERT: B 2034 ASP cc_start: 0.8303 (t0) cc_final: 0.8099 (t0) REVERT: B 2133 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6463 (mp0) REVERT: B 2270 MET cc_start: 0.3775 (tpt) cc_final: 0.3554 (tpt) REVERT: B 2321 TRP cc_start: 0.8443 (p90) cc_final: 0.7984 (p90) REVERT: B 2372 PHE cc_start: 0.7870 (t80) cc_final: 0.7659 (t80) outliers start: 41 outliers final: 21 residues processed: 419 average time/residue: 0.3883 time to fit residues: 263.0562 Evaluate side-chains 374 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 351 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1722 ILE Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2228 VAL Chi-restraints excluded: chain B residue 2428 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 28 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 334 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 239 optimal weight: 0.0980 chunk 325 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 HIS A2254 GLN A2322 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2322 ASN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1304 HIS B2245 GLN ** B2254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2322 ASN ** B2356 GLN ** 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 = 0.4294 r_free = 0.4294 target = 0.169535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.149022 restraints weight = 55567.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.147094 restraints weight = 84040.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145376 restraints weight = 75577.758| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30084 Z= 0.217 Angle : 0.638 8.958 40815 Z= 0.321 Chirality : 0.041 0.200 4683 Planarity : 0.005 0.059 5091 Dihedral : 4.487 31.566 4026 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.06 % Allowed : 16.09 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3636 helix: 1.69 (0.11), residues: 2406 sheet: -1.64 (0.30), residues: 279 loop : -1.66 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2142 HIS 0.007 0.001 HIS C2116 PHE 0.024 0.002 PHE B2426 TYR 0.016 0.002 TYR C2533 ARG 0.008 0.000 ARG C2407 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1860) hydrogen bonds : angle 3.92304 ( 5589) covalent geometry : bond 0.00527 (30084) covalent geometry : angle 0.63771 (40815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 358 time to evaluate : 3.485 Fit side-chains revert: symmetry clash REVERT: A 1226 MET cc_start: 0.7959 (tpp) cc_final: 0.7727 (mmm) REVERT: A 2042 THR cc_start: 0.8964 (p) cc_final: 0.8674 (p) REVERT: A 2517 ARG cc_start: 0.7021 (mpt180) cc_final: 0.6754 (tmm160) REVERT: C 2270 MET cc_start: 0.4100 (tpt) cc_final: 0.3805 (tpt) REVERT: C 2321 TRP cc_start: 0.8614 (p90) cc_final: 0.8091 (p90) REVERT: C 2426 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7693 (p90) REVERT: C 2509 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: C 2517 ARG cc_start: 0.6962 (mpt180) cc_final: 0.6673 (tmm160) REVERT: B 2133 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: B 2153 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: B 2270 MET cc_start: 0.3612 (tpt) cc_final: 0.3378 (tpt) REVERT: B 2321 TRP cc_start: 0.8638 (p90) cc_final: 0.8335 (p90) outliers start: 92 outliers final: 52 residues processed: 428 average time/residue: 0.3642 time to fit residues: 258.5018 Evaluate side-chains 396 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1304 HIS Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1741 VAL Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2426 PHE Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2467 VAL Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2509 ASP Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1219 THR Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2153 MET Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 247 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 GLN C1013 HIS ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2353 GLN B1013 HIS ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2245 GLN B2322 ASN B2356 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.173877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152260 restraints weight = 54661.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.154274 restraints weight = 119216.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.154986 restraints weight = 62465.377| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30084 Z= 0.115 Angle : 0.561 12.208 40815 Z= 0.279 Chirality : 0.038 0.180 4683 Planarity : 0.004 0.059 5091 Dihedral : 4.251 27.113 4026 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.59 % Allowed : 17.41 % Favored : 79.99 % 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: 1.09 (0.14), residues: 3636 helix: 1.89 (0.11), residues: 2421 sheet: -1.49 (0.31), residues: 279 loop : -1.70 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2142 HIS 0.020 0.001 HIS B1304 PHE 0.022 0.001 PHE B2426 TYR 0.012 0.001 TYR B1803 ARG 0.006 0.000 ARG C2407 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 1860) hydrogen bonds : angle 3.72496 ( 5589) covalent geometry : bond 0.00256 (30084) covalent geometry : angle 0.56053 (40815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 377 time to evaluate : 3.134 Fit side-chains revert: symmetry clash REVERT: A 1226 MET cc_start: 0.7918 (tpp) cc_final: 0.7684 (mmm) REVERT: A 2492 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9061 (tt) REVERT: A 2517 ARG cc_start: 0.7052 (mpt180) cc_final: 0.6818 (tmm160) REVERT: C 2270 MET cc_start: 0.4054 (tpt) cc_final: 0.3773 (tpt) REVERT: C 2321 TRP cc_start: 0.8553 (p90) cc_final: 0.8039 (p90) REVERT: C 2517 ARG cc_start: 0.6993 (mpt180) cc_final: 0.6619 (tmm160) REVERT: B 1349 MET cc_start: 0.8355 (mmm) cc_final: 0.7871 (mmp) REVERT: B 2034 ASP cc_start: 0.8372 (t0) cc_final: 0.7947 (t0) REVERT: B 2133 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: B 2321 TRP cc_start: 0.8577 (p90) cc_final: 0.7968 (p90) outliers start: 78 outliers final: 46 residues processed: 433 average time/residue: 0.3647 time to fit residues: 259.7980 Evaluate side-chains 407 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2492 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1304 HIS Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2399 LEU Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2228 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 283 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 285 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.173012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.154378 restraints weight = 55184.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153015 restraints weight = 119400.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.150299 restraints weight = 66663.509| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30084 Z= 0.122 Angle : 0.576 11.993 40815 Z= 0.283 Chirality : 0.039 0.265 4683 Planarity : 0.004 0.052 5091 Dihedral : 4.188 29.289 4026 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.06 % Allowed : 17.75 % Favored : 79.20 % 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: 1.20 (0.14), residues: 3636 helix: 1.98 (0.11), residues: 2421 sheet: -1.46 (0.31), residues: 279 loop : -1.68 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2321 HIS 0.003 0.001 HIS A2116 PHE 0.021 0.001 PHE B2426 TYR 0.011 0.001 TYR B1803 ARG 0.007 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 1860) hydrogen bonds : angle 3.65590 ( 5589) covalent geometry : bond 0.00276 (30084) covalent geometry : angle 0.57586 (40815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 366 time to evaluate : 3.060 Fit side-chains REVERT: A 1100 LEU cc_start: 0.8067 (tt) cc_final: 0.7478 (tp) REVERT: A 1226 MET cc_start: 0.8031 (tpp) cc_final: 0.7825 (mmm) REVERT: A 1342 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8251 (tp) REVERT: A 2492 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9094 (tt) REVERT: A 2517 ARG cc_start: 0.7084 (mpt180) cc_final: 0.6764 (tmm160) REVERT: C 1100 LEU cc_start: 0.8013 (tt) cc_final: 0.7393 (tp) REVERT: C 1226 MET cc_start: 0.7881 (mmm) cc_final: 0.7643 (mmm) REVERT: C 1342 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 2251 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: C 2270 MET cc_start: 0.4242 (tpt) cc_final: 0.4002 (tpt) REVERT: C 2321 TRP cc_start: 0.8520 (p90) cc_final: 0.8037 (p90) REVERT: C 2517 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6533 (tmm160) REVERT: B 1072 MET cc_start: 0.2698 (ptt) cc_final: 0.2484 (ttp) REVERT: B 1100 LEU cc_start: 0.8170 (tt) cc_final: 0.7596 (tp) REVERT: B 1342 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8245 (tp) REVERT: B 1349 MET cc_start: 0.8456 (mmm) cc_final: 0.8057 (mmp) REVERT: B 2034 ASP cc_start: 0.8308 (t0) cc_final: 0.7920 (t0) REVERT: B 2133 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6534 (mp0) outliers start: 92 outliers final: 56 residues processed: 438 average time/residue: 0.3582 time to fit residues: 258.0903 Evaluate side-chains 411 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2492 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1102 LEU Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2228 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 250 optimal weight: 40.0000 chunk 82 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 288 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 366 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 308 optimal weight: 0.6980 chunk 219 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 HIS ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.173758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152364 restraints weight = 55103.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154557 restraints weight = 122680.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.155074 restraints weight = 60578.438| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30084 Z= 0.116 Angle : 0.566 11.478 40815 Z= 0.280 Chirality : 0.039 0.249 4683 Planarity : 0.004 0.049 5091 Dihedral : 4.131 27.773 4026 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.96 % Allowed : 18.44 % Favored : 78.60 % 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: 1.31 (0.14), residues: 3636 helix: 2.05 (0.11), residues: 2421 sheet: -1.25 (0.32), residues: 258 loop : -1.66 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C2142 HIS 0.004 0.001 HIS A2116 PHE 0.048 0.001 PHE B1665 TYR 0.011 0.001 TYR B1803 ARG 0.008 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 1860) hydrogen bonds : angle 3.60468 ( 5589) covalent geometry : bond 0.00262 (30084) covalent geometry : angle 0.56639 (40815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 372 time to evaluate : 3.110 Fit side-chains revert: symmetry clash REVERT: A 1072 MET cc_start: 0.3727 (ptt) cc_final: 0.3170 (ttp) REVERT: A 1100 LEU cc_start: 0.7921 (tt) cc_final: 0.7357 (tp) REVERT: A 1226 MET cc_start: 0.8045 (tpp) cc_final: 0.7816 (mmm) REVERT: A 1342 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8233 (tp) REVERT: A 1782 TYR cc_start: 0.7382 (p90) cc_final: 0.6907 (p90) REVERT: A 1794 PHE cc_start: 0.7839 (m-80) cc_final: 0.7453 (m-80) REVERT: A 2492 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9078 (tt) REVERT: A 2517 ARG cc_start: 0.7113 (mpt180) cc_final: 0.6808 (tmm160) REVERT: C 1016 TRP cc_start: 0.6852 (t-100) cc_final: 0.6313 (t-100) REVERT: C 1100 LEU cc_start: 0.8013 (tt) cc_final: 0.7386 (tp) REVERT: C 1226 MET cc_start: 0.7888 (mmm) cc_final: 0.7664 (mmm) REVERT: C 1342 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8156 (tp) REVERT: C 2251 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: C 2270 MET cc_start: 0.4335 (tpt) cc_final: 0.4053 (tpt) REVERT: C 2321 TRP cc_start: 0.8482 (p90) cc_final: 0.7976 (p90) REVERT: C 2517 ARG cc_start: 0.6997 (mpt180) cc_final: 0.6548 (tmm160) REVERT: B 1072 MET cc_start: 0.2926 (ptt) cc_final: 0.2719 (ttp) REVERT: B 1100 LEU cc_start: 0.8175 (tt) cc_final: 0.7567 (tp) REVERT: B 1342 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8236 (tp) REVERT: B 1349 MET cc_start: 0.8443 (mmm) cc_final: 0.8036 (mmp) REVERT: B 2034 ASP cc_start: 0.8438 (t0) cc_final: 0.8052 (t0) REVERT: B 2133 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6603 (mp0) outliers start: 89 outliers final: 66 residues processed: 438 average time/residue: 0.3752 time to fit residues: 270.6303 Evaluate side-chains 425 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 353 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2039 LEU Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2492 ILE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1780 ASP Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2426 PHE Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1407 ILE Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1780 ASP Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 115 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 306 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 293 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2306 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2356 GLN B1013 HIS ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.173110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152458 restraints weight = 55378.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154603 restraints weight = 122288.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154933 restraints weight = 53537.561| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30084 Z= 0.128 Angle : 0.585 11.431 40815 Z= 0.287 Chirality : 0.039 0.220 4683 Planarity : 0.004 0.050 5091 Dihedral : 4.129 29.709 4026 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.89 % Allowed : 19.11 % Favored : 78.00 % 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: 1.29 (0.14), residues: 3636 helix: 2.04 (0.11), residues: 2427 sheet: -1.29 (0.32), residues: 258 loop : -1.70 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2321 HIS 0.003 0.001 HIS B2490 PHE 0.031 0.001 PHE B1665 TYR 0.011 0.001 TYR B1803 ARG 0.007 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 1860) hydrogen bonds : angle 3.59960 ( 5589) covalent geometry : bond 0.00297 (30084) covalent geometry : angle 0.58459 (40815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 367 time to evaluate : 3.199 Fit side-chains revert: symmetry clash REVERT: A 1072 MET cc_start: 0.3609 (ptt) cc_final: 0.3274 (ttp) REVERT: A 1100 LEU cc_start: 0.7975 (tt) cc_final: 0.7379 (tp) REVERT: A 1226 MET cc_start: 0.8056 (tpp) cc_final: 0.7841 (mmm) REVERT: A 1342 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 1782 TYR cc_start: 0.7320 (p90) cc_final: 0.6912 (p90) REVERT: A 1794 PHE cc_start: 0.7838 (m-80) cc_final: 0.7481 (m-80) REVERT: A 2251 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: A 2266 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: A 2492 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9097 (tt) REVERT: A 2517 ARG cc_start: 0.7127 (mpt180) cc_final: 0.6821 (tmm160) REVERT: C 1072 MET cc_start: 0.3189 (ptt) cc_final: 0.2717 (ttp) REVERT: C 1100 LEU cc_start: 0.8003 (tt) cc_final: 0.7367 (tp) REVERT: C 1215 LEU cc_start: 0.7851 (tt) cc_final: 0.7227 (mp) REVERT: C 1342 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8171 (tp) REVERT: C 2251 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: C 2270 MET cc_start: 0.4335 (tpt) cc_final: 0.3985 (tpt) REVERT: C 2321 TRP cc_start: 0.8446 (p90) cc_final: 0.7940 (p90) REVERT: C 2517 ARG cc_start: 0.6896 (mpt180) cc_final: 0.6523 (tmm160) REVERT: B 1100 LEU cc_start: 0.8178 (tt) cc_final: 0.7559 (tp) REVERT: B 1342 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8246 (tp) REVERT: B 2034 ASP cc_start: 0.8399 (t0) cc_final: 0.8033 (t0) REVERT: B 2133 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6669 (mp0) outliers start: 87 outliers final: 67 residues processed: 432 average time/residue: 0.3728 time to fit residues: 267.2548 Evaluate side-chains 428 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 353 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2254 GLN Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2492 ILE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1051 CYS Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2228 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 266 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 268 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 311 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1013 HIS ** B1225 ASN ** 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 = 0.4321 r_free = 0.4321 target = 0.171700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.151529 restraints weight = 55369.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.148323 restraints weight = 76785.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146154 restraints weight = 74171.816| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30084 Z= 0.165 Angle : 0.625 11.525 40815 Z= 0.306 Chirality : 0.040 0.210 4683 Planarity : 0.004 0.046 5091 Dihedral : 4.200 30.529 4026 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.16 % Allowed : 19.11 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.22 (0.14), residues: 3636 helix: 1.98 (0.11), residues: 2427 sheet: -1.37 (0.32), residues: 258 loop : -1.70 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2321 HIS 0.004 0.001 HIS B2490 PHE 0.027 0.001 PHE B1665 TYR 0.012 0.001 TYR C2533 ARG 0.008 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1860) hydrogen bonds : angle 3.66371 ( 5589) covalent geometry : bond 0.00395 (30084) covalent geometry : angle 0.62485 (40815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 361 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.7954 (tt) cc_final: 0.7352 (tp) REVERT: A 1342 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8281 (tp) REVERT: A 1782 TYR cc_start: 0.7325 (p90) cc_final: 0.6913 (p90) REVERT: A 2251 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: A 2266 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: A 2517 ARG cc_start: 0.7072 (mpt180) cc_final: 0.6739 (tmm160) REVERT: C 1016 TRP cc_start: 0.6945 (t-100) cc_final: 0.6414 (t-100) REVERT: C 1072 MET cc_start: 0.3321 (ptt) cc_final: 0.2956 (ttp) REVERT: C 1215 LEU cc_start: 0.7896 (tt) cc_final: 0.7222 (mp) REVERT: C 1342 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 2251 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: C 2266 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: C 2270 MET cc_start: 0.4020 (tpt) cc_final: 0.3656 (tpt) REVERT: C 2517 ARG cc_start: 0.6935 (mpt180) cc_final: 0.6718 (tmm160) REVERT: B 1016 TRP cc_start: 0.6850 (t-100) cc_final: 0.6382 (t-100) REVERT: B 1342 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 2034 ASP cc_start: 0.8609 (t0) cc_final: 0.8290 (t0) REVERT: B 2133 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6659 (mp0) outliers start: 95 outliers final: 73 residues processed: 436 average time/residue: 0.3494 time to fit residues: 253.8980 Evaluate side-chains 437 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 356 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2252 THR Chi-restraints excluded: chain A residue 2254 GLN Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1051 CYS Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2073 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2266 TYR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1780 ASP Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2297 SER Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2426 PHE Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 267 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 228 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 chunk 247 optimal weight: 0.2980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2356 GLN ** B1225 ASN ** 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 = 0.4320 r_free = 0.4320 target = 0.171679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.151221 restraints weight = 55404.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.153016 restraints weight = 132117.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153331 restraints weight = 63976.185| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30084 Z= 0.155 Angle : 0.621 11.239 40815 Z= 0.304 Chirality : 0.040 0.207 4683 Planarity : 0.004 0.045 5091 Dihedral : 4.203 30.847 4026 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.82 % Allowed : 19.57 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.19 (0.14), residues: 3636 helix: 1.94 (0.11), residues: 2436 sheet: -1.33 (0.32), residues: 258 loop : -1.70 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C2321 HIS 0.004 0.001 HIS B2490 PHE 0.026 0.001 PHE B1665 TYR 0.013 0.001 TYR B2256 ARG 0.008 0.000 ARG B1664 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1860) hydrogen bonds : angle 3.65669 ( 5589) covalent geometry : bond 0.00370 (30084) covalent geometry : angle 0.62091 (40815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 364 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.8016 (tt) cc_final: 0.7420 (tp) REVERT: A 1342 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8241 (tp) REVERT: A 1546 LEU cc_start: 0.7879 (mt) cc_final: 0.7579 (mt) REVERT: A 1782 TYR cc_start: 0.7383 (p90) cc_final: 0.7009 (p90) REVERT: A 2251 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: A 2266 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5533 (m-80) REVERT: A 2517 ARG cc_start: 0.7092 (mpt180) cc_final: 0.6863 (tmm160) REVERT: A 2539 MET cc_start: 0.8029 (ttp) cc_final: 0.7668 (ttp) REVERT: C 1016 TRP cc_start: 0.6946 (t-100) cc_final: 0.6419 (t-100) REVERT: C 1072 MET cc_start: 0.3351 (ptt) cc_final: 0.2954 (ttp) REVERT: C 1215 LEU cc_start: 0.7886 (tt) cc_final: 0.7222 (mp) REVERT: C 1342 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8163 (tp) REVERT: C 2251 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: C 2266 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5412 (m-80) REVERT: C 2270 MET cc_start: 0.4033 (tpt) cc_final: 0.3625 (tpt) REVERT: C 2517 ARG cc_start: 0.6989 (mpt180) cc_final: 0.6617 (tmm160) REVERT: B 1016 TRP cc_start: 0.6824 (t-100) cc_final: 0.6370 (t-100) REVERT: B 1342 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 1349 MET cc_start: 0.8691 (mmm) cc_final: 0.8197 (mmp) REVERT: B 2034 ASP cc_start: 0.8393 (t0) cc_final: 0.7972 (t0) REVERT: B 2133 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6720 (mp0) outliers start: 85 outliers final: 73 residues processed: 431 average time/residue: 0.3620 time to fit residues: 260.1325 Evaluate side-chains 433 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 352 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1961 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 2020 PHE Chi-restraints excluded: chain A residue 2078 VAL Chi-restraints excluded: chain A residue 2138 MET Chi-restraints excluded: chain A residue 2146 THR Chi-restraints excluded: chain A residue 2202 ILE Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2254 GLN Chi-restraints excluded: chain A residue 2266 TYR Chi-restraints excluded: chain A residue 2421 THR Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2428 GLU Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1051 CYS Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1281 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1988 ILE Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain C residue 2073 PHE Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2146 THR Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2266 TYR Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain B residue 1001 VAL Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1051 CYS Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1337 ILE Chi-restraints excluded: chain B residue 1342 LEU Chi-restraints excluded: chain B residue 1548 VAL Chi-restraints excluded: chain B residue 1648 LEU Chi-restraints excluded: chain B residue 1655 HIS Chi-restraints excluded: chain B residue 1780 ASP Chi-restraints excluded: chain B residue 1961 PHE Chi-restraints excluded: chain B residue 1985 ILE Chi-restraints excluded: chain B residue 1988 ILE Chi-restraints excluded: chain B residue 2020 PHE Chi-restraints excluded: chain B residue 2073 PHE Chi-restraints excluded: chain B residue 2078 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2133 GLU Chi-restraints excluded: chain B residue 2146 THR Chi-restraints excluded: chain B residue 2202 ILE Chi-restraints excluded: chain B residue 2216 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2297 SER Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2428 GLU Chi-restraints excluded: chain B residue 2432 ILE Chi-restraints excluded: chain B residue 2471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 139 optimal weight: 3.9990 chunk 320 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 215 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 HIS ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.173347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.154701 restraints weight = 55422.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155518 restraints weight = 119880.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154181 restraints weight = 55463.509| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30084 Z= 0.123 Angle : 0.602 11.222 40815 Z= 0.293 Chirality : 0.039 0.266 4683 Planarity : 0.004 0.047 5091 Dihedral : 4.127 29.474 4026 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.66 % Allowed : 19.97 % Favored : 77.37 % 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: 1.36 (0.14), residues: 3636 helix: 2.10 (0.11), residues: 2412 sheet: -1.27 (0.33), residues: 258 loop : -1.64 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C2321 HIS 0.003 0.001 HIS B2490 PHE 0.024 0.001 PHE B1665 TYR 0.017 0.001 TYR B2256 ARG 0.007 0.000 ARG C2104 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1860) hydrogen bonds : angle 3.58992 ( 5589) covalent geometry : bond 0.00285 (30084) covalent geometry : angle 0.60181 (40815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8790.72 seconds wall clock time: 154 minutes 51.65 seconds (9291.65 seconds total)