Starting phenix.real_space_refine on Mon Aug 25 17:47:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8imz_35577/08_2025/8imz_35577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8imz_35577/08_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_35577/08_2025/8imz_35577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8imz_35577/08_2025/8imz_35577.map" model { file = "/net/cci-nas-00/data/ceres_data/8imz_35577/08_2025/8imz_35577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8imz_35577/08_2025/8imz_35577.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.024 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'PHE:plan': 6, 'ARG:plan': 9, 'GLN:plan1': 7, 'GLU:plan': 7, 'HIS:plan': 4, 'TYR:plan': 6, 'TRP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 235 Chain: "D" 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, E, F Time building chain proxies: 10.95, per 1000 atoms: 0.37 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.16 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: 5.32 Time building geometry restraints manager: 3.13 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 29.360 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- 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 : 12.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (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 ARG 0.012 0.001 ARG A2104 TYR 0.020 0.002 TYR A1803 PHE 0.019 0.002 PHE C2426 TRP 0.015 0.002 TRP A2321 HIS 0.008 0.002 HIS B2116 Details of bonding type rmsd covalent geometry : bond 0.00678 (30084) covalent geometry : angle 0.76984 (40815) hydrogen bonds : bond 0.13187 ( 1860) hydrogen bonds : angle 5.33072 ( 5589) *********************** 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 : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2224 ILE cc_start: 0.8627 (tt) cc_final: 0.8388 (tp) REVERT: A 2270 MET cc_start: 0.5483 (tpt) cc_final: 0.5159 (tpt) REVERT: A 2372 PHE cc_start: 0.8508 (t80) cc_final: 0.7944 (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: 0.8411 (t80) REVERT: C 2473 ILE cc_start: 0.8089 (tp) cc_final: 0.7839 (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: 0.4869 (tpt) REVERT: B 2372 PHE cc_start: 0.8562 (t80) cc_final: 0.8100 (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: 0.1691 time to fit residues: 106.5297 Evaluate side-chains 304 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 120.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** A2116 HIS A2364 GLN C1217 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN C2364 GLN B1217 ASN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2116 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.153139 restraints weight = 55317.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.155076 restraints weight = 119705.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.154549 restraints weight = 52560.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.154378 restraints weight = 51871.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154631 restraints weight = 36887.819| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30084 Z= 0.137 Angle : 0.606 7.370 40815 Z= 0.308 Chirality : 0.040 0.183 4683 Planarity : 0.005 0.085 5091 Dihedral : 4.717 28.076 4026 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.13 % Allowed : 8.84 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.14), residues: 3636 helix: 1.60 (0.11), residues: 2391 sheet: -1.82 (0.30), residues: 261 loop : -1.54 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2361 TYR 0.019 0.001 TYR C1803 PHE 0.020 0.001 PHE C1794 TRP 0.011 0.001 TRP C2140 HIS 0.005 0.001 HIS C2116 Details of bonding type rmsd covalent geometry : bond 0.00308 (30084) covalent geometry : angle 0.60602 (40815) hydrogen bonds : bond 0.03890 ( 1860) hydrogen bonds : angle 4.11841 ( 5589) *********************** 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 427 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 393 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 2321 TRP cc_start: 0.8660 (p90) cc_final: 0.8382 (p90) REVERT: C 2270 MET cc_start: 0.3780 (tpt) cc_final: 0.3306 (tpt) REVERT: C 2315 ILE cc_start: 0.8515 (tp) cc_final: 0.8293 (tp) REVERT: C 2321 TRP cc_start: 0.8557 (p90) cc_final: 0.8087 (p90) REVERT: C 2517 ARG cc_start: 0.7018 (mpt180) cc_final: 0.6565 (tmm160) REVERT: B 2061 MET cc_start: 0.7129 (tpt) cc_final: 0.6874 (tpt) REVERT: B 2133 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: B 2270 MET cc_start: 0.3807 (tpt) cc_final: 0.3575 (tpt) REVERT: B 2321 TRP cc_start: 0.8493 (p90) cc_final: 0.8039 (p90) REVERT: B 2337 ASN cc_start: 0.7747 (p0) cc_final: 0.7389 (p0) REVERT: B 2372 PHE cc_start: 0.8011 (t80) cc_final: 0.7693 (t80) REVERT: B 2517 ARG cc_start: 0.7000 (mpt180) cc_final: 0.6643 (tmm160) outliers start: 34 outliers final: 18 residues processed: 407 average time/residue: 0.1799 time to fit residues: 119.8454 Evaluate side-chains 357 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 338 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 2293 LEU 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 2252 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 2464 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 131 optimal weight: 10.0000 chunk 126 optimal weight: 120.0000 chunk 208 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2322 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1304 HIS ** 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 = 0.4309 r_free = 0.4309 target = 0.170823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.154031 restraints weight = 55438.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.150716 restraints weight = 129574.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.148599 restraints weight = 75398.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.148593 restraints weight = 80102.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.148752 restraints weight = 49604.106| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1659 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= 0.169 Angle : 0.607 11.137 40815 Z= 0.306 Chirality : 0.040 0.177 4683 Planarity : 0.005 0.070 5091 Dihedral : 4.560 28.770 4026 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.26 % Allowed : 13.09 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3636 helix: 1.71 (0.11), residues: 2400 sheet: -1.61 (0.31), residues: 258 loop : -1.60 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1664 TYR 0.017 0.001 TYR A1803 PHE 0.028 0.002 PHE B2426 TRP 0.010 0.001 TRP B2142 HIS 0.006 0.001 HIS C2116 Details of bonding type rmsd covalent geometry : bond 0.00405 (30084) covalent geometry : angle 0.60704 (40815) hydrogen bonds : bond 0.03820 ( 1860) hydrogen bonds : angle 3.97039 ( 5589) *********************** 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 443 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 375 time to evaluate : 1.292 Fit side-chains REVERT: A 1100 LEU cc_start: 0.8078 (tt) cc_final: 0.7472 (tp) REVERT: A 1226 MET cc_start: 0.8057 (tpp) cc_final: 0.7678 (mmm) REVERT: C 1226 MET cc_start: 0.7691 (tpp) cc_final: 0.7485 (mmm) REVERT: C 2270 MET cc_start: 0.4197 (tpt) cc_final: 0.3921 (tpt) REVERT: C 2315 ILE cc_start: 0.8454 (tp) cc_final: 0.8239 (tp) REVERT: C 2321 TRP cc_start: 0.8533 (p90) cc_final: 0.8069 (p90) REVERT: C 2517 ARG cc_start: 0.7005 (mpt180) cc_final: 0.6492 (tmm160) REVERT: B 1226 MET cc_start: 0.7960 (tpp) cc_final: 0.7700 (mmm) REVERT: B 2034 ASP cc_start: 0.8385 (t0) cc_final: 0.8065 (t0) REVERT: B 2061 MET cc_start: 0.6933 (tpt) cc_final: 0.6727 (tpt) REVERT: B 2133 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: B 2270 MET cc_start: 0.3905 (tpt) cc_final: 0.3595 (tpt) REVERT: B 2321 TRP cc_start: 0.8558 (p90) cc_final: 0.8241 (p90) REVERT: B 2372 PHE cc_start: 0.8038 (t80) cc_final: 0.7803 (t80) REVERT: B 2517 ARG cc_start: 0.6996 (mpt180) cc_final: 0.6792 (tmm160) outliers start: 68 outliers final: 38 residues processed: 421 average time/residue: 0.1768 time to fit residues: 122.8991 Evaluate side-chains 386 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 347 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL 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 2065 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 2227 THR 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 2432 ILE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain C residue 1157 VAL 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 2078 VAL Chi-restraints excluded: chain C residue 2138 MET Chi-restraints excluded: chain C residue 2202 ILE 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 2471 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1157 VAL 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 2078 VAL 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 2471 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 229 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 316 optimal weight: 0.7980 chunk 344 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 233 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 A2322 ASN C1013 HIS ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 HIS ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2356 GLN ** 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 = 0.4335 r_free = 0.4335 target = 0.172664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154187 restraints weight = 54659.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.154445 restraints weight = 119867.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.152299 restraints weight = 57389.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.152168 restraints weight = 71037.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152161 restraints weight = 50860.320| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30084 Z= 0.143 Angle : 0.580 10.898 40815 Z= 0.290 Chirality : 0.039 0.176 4683 Planarity : 0.004 0.057 5091 Dihedral : 4.388 28.052 4026 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.76 % Allowed : 15.89 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3636 helix: 1.77 (0.11), residues: 2418 sheet: -1.51 (0.31), residues: 261 loop : -1.68 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2407 TYR 0.015 0.001 TYR B1803 PHE 0.027 0.001 PHE A2426 TRP 0.009 0.001 TRP B2142 HIS 0.005 0.001 HIS C2116 Details of bonding type rmsd covalent geometry : bond 0.00339 (30084) covalent geometry : angle 0.57986 (40815) hydrogen bonds : bond 0.03519 ( 1860) hydrogen bonds : angle 3.82762 ( 5589) *********************** 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 452 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 369 time to evaluate : 0.720 Fit side-chains REVERT: A 1226 MET cc_start: 0.8034 (tpp) cc_final: 0.7777 (mmm) REVERT: C 1010 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7426 (m) REVERT: C 2270 MET cc_start: 0.4171 (tpt) cc_final: 0.3864 (tpt) REVERT: C 2321 TRP cc_start: 0.8554 (p90) cc_final: 0.8074 (p90) REVERT: C 2492 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9156 (tt) REVERT: C 2517 ARG cc_start: 0.6986 (mpt180) cc_final: 0.6624 (tmm160) REVERT: B 1100 LEU cc_start: 0.8276 (tt) cc_final: 0.7675 (tp) REVERT: B 1349 MET cc_start: 0.8404 (mmm) cc_final: 0.7987 (mmp) REVERT: B 2034 ASP cc_start: 0.8332 (t0) cc_final: 0.7972 (t0) REVERT: B 2133 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: B 2153 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: B 2270 MET cc_start: 0.3751 (tpt) cc_final: 0.3516 (tpt) REVERT: B 2321 TRP cc_start: 0.8576 (p90) cc_final: 0.8196 (p90) REVERT: B 2517 ARG cc_start: 0.6975 (mpt180) cc_final: 0.6669 (tmm160) outliers start: 83 outliers final: 46 residues processed: 433 average time/residue: 0.1470 time to fit residues: 105.9669 Evaluate side-chains 401 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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 C residue 1010 VAL Chi-restraints excluded: chain C residue 1045 LEU 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 1304 HIS Chi-restraints excluded: chain C residue 1655 HIS 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 2138 MET Chi-restraints excluded: chain C residue 2202 ILE Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2492 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 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 1961 PHE Chi-restraints excluded: chain B residue 2020 PHE 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 2228 VAL Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2252 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 336 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 318 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 228 optimal weight: 0.3980 chunk 251 optimal weight: 70.0000 chunk 175 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** A2254 GLN A2306 GLN C1013 HIS ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1304 HIS B2356 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.173435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.152903 restraints weight = 54887.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155009 restraints weight = 121472.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155154 restraints weight = 55346.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155366 restraints weight = 42735.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155572 restraints weight = 35447.453| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2114 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= 0.123 Angle : 0.572 12.394 40815 Z= 0.284 Chirality : 0.039 0.257 4683 Planarity : 0.004 0.055 5091 Dihedral : 4.273 27.529 4026 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.86 % Allowed : 17.08 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.14), residues: 3636 helix: 1.89 (0.11), residues: 2421 sheet: -1.40 (0.32), residues: 261 loop : -1.68 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2407 TYR 0.014 0.001 TYR B1803 PHE 0.026 0.001 PHE A2426 TRP 0.009 0.001 TRP B2321 HIS 0.017 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00282 (30084) covalent geometry : angle 0.57178 (40815) hydrogen bonds : bond 0.03371 ( 1860) hydrogen bonds : angle 3.73367 ( 5589) *********************** 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 458 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 372 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 1226 MET cc_start: 0.8086 (tpp) cc_final: 0.7795 (mmm) REVERT: A 2492 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9121 (tt) REVERT: C 1010 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7313 (m) REVERT: C 2270 MET cc_start: 0.4042 (tpt) cc_final: 0.3773 (tpt) REVERT: C 2321 TRP cc_start: 0.8511 (p90) cc_final: 0.7995 (p90) REVERT: C 2492 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9132 (tt) REVERT: C 2517 ARG cc_start: 0.6969 (mpt180) cc_final: 0.6573 (tmm160) REVERT: B 1349 MET cc_start: 0.8402 (mmm) cc_final: 0.8025 (mmp) REVERT: B 2034 ASP cc_start: 0.8282 (t0) cc_final: 0.7927 (t0) REVERT: B 2133 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: B 2517 ARG cc_start: 0.7004 (mpt180) cc_final: 0.6727 (tmm160) outliers start: 86 outliers final: 58 residues processed: 441 average time/residue: 0.1492 time to fit residues: 109.7382 Evaluate side-chains 412 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 350 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 1102 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 VAL 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 2293 LEU 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 1010 VAL Chi-restraints excluded: chain C residue 1021 LEU 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 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 2228 VAL Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL 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 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 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 2426 PHE Chi-restraints excluded: chain B residue 2428 GLU 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 187 optimal weight: 0.0060 chunk 160 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 299 optimal weight: 0.0770 chunk 358 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9758 ------------------------------------------------------------------------------- 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** A2254 GLN C1013 HIS ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2285 GLN C2353 GLN C2356 GLN ** 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 = 0.4328 r_free = 0.4328 target = 0.172257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.152083 restraints weight = 55080.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.153921 restraints weight = 122969.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.153554 restraints weight = 54371.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.153357 restraints weight = 56642.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154012 restraints weight = 37413.872| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30084 Z= 0.131 Angle : 0.584 12.825 40815 Z= 0.289 Chirality : 0.039 0.212 4683 Planarity : 0.004 0.045 5091 Dihedral : 4.247 27.321 4026 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.59 % Allowed : 17.41 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.14), residues: 3636 helix: 1.92 (0.11), residues: 2421 sheet: -1.33 (0.32), residues: 261 loop : -1.69 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2104 TYR 0.012 0.001 TYR B1803 PHE 0.033 0.001 PHE A2426 TRP 0.009 0.001 TRP B2142 HIS 0.018 0.001 HIS B1304 Details of bonding type rmsd covalent geometry : bond 0.00307 (30084) covalent geometry : angle 0.58448 (40815) hydrogen bonds : bond 0.03337 ( 1860) hydrogen bonds : angle 3.69760 ( 5589) *********************** 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 464 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 356 time to evaluate : 0.797 Fit side-chains REVERT: A 1100 LEU cc_start: 0.7776 (tt) cc_final: 0.7228 (tp) REVERT: A 1226 MET cc_start: 0.8057 (tpp) cc_final: 0.7837 (mmm) REVERT: A 1342 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 2251 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: A 2492 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9126 (tt) REVERT: C 1010 VAL cc_start: 0.7362 (OUTLIER) cc_final: 0.7133 (m) REVERT: C 1342 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8226 (tp) REVERT: C 2270 MET cc_start: 0.4085 (tpt) cc_final: 0.3758 (tpt) REVERT: C 2321 TRP cc_start: 0.8445 (p90) cc_final: 0.7917 (p90) REVERT: C 2492 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9135 (tt) REVERT: C 2517 ARG cc_start: 0.7031 (mpt180) cc_final: 0.6577 (tmm160) REVERT: B 1100 LEU cc_start: 0.8005 (tt) cc_final: 0.7418 (tp) REVERT: B 1342 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 2034 ASP cc_start: 0.8306 (t0) cc_final: 0.7942 (t0) REVERT: B 2133 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: B 2517 ARG cc_start: 0.7161 (mpt180) cc_final: 0.6737 (tmm160) outliers start: 108 outliers final: 68 residues processed: 445 average time/residue: 0.1583 time to fit residues: 118.2211 Evaluate side-chains 423 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 347 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 2202 ILE Chi-restraints excluded: chain A residue 2227 THR Chi-restraints excluded: chain A residue 2251 PHE 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 2471 VAL Chi-restraints excluded: chain A residue 2492 ILE Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1021 LEU 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 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 1985 ILE 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 2245 GLN 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 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE 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 1102 LEU Chi-restraints excluded: chain B residue 1157 VAL 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 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 2251 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 23 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 chunk 66 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 358 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 353 optimal weight: 0.0670 chunk 289 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 overall best weight: 0.8724 ------------------------------------------------------------------------------- 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** C1013 HIS ** 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 = 0.4335 r_free = 0.4335 target = 0.172858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152517 restraints weight = 55108.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154468 restraints weight = 124846.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154789 restraints weight = 54587.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.154891 restraints weight = 44683.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.155105 restraints weight = 36073.688| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30084 Z= 0.124 Angle : 0.574 12.633 40815 Z= 0.283 Chirality : 0.039 0.207 4683 Planarity : 0.004 0.048 5091 Dihedral : 4.196 27.731 4026 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.26 % Allowed : 18.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.14), residues: 3636 helix: 1.98 (0.11), residues: 2418 sheet: -1.25 (0.32), residues: 261 loop : -1.62 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2104 TYR 0.012 0.001 TYR B1803 PHE 0.049 0.001 PHE B1665 TRP 0.010 0.001 TRP C2321 HIS 0.003 0.001 HIS C2116 Details of bonding type rmsd covalent geometry : bond 0.00286 (30084) covalent geometry : angle 0.57407 (40815) hydrogen bonds : bond 0.03253 ( 1860) hydrogen bonds : angle 3.65381 ( 5589) *********************** 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 463 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 365 time to evaluate : 0.894 Fit side-chains REVERT: A 1100 LEU cc_start: 0.7750 (tt) cc_final: 0.7220 (tp) REVERT: A 1342 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 1782 TYR cc_start: 0.7377 (p90) cc_final: 0.7001 (p90) REVERT: A 1794 PHE cc_start: 0.7854 (m-80) cc_final: 0.7496 (m-80) REVERT: A 2492 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9107 (tt) REVERT: C 1342 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 2270 MET cc_start: 0.4006 (tpt) cc_final: 0.3751 (tpt) REVERT: C 2492 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9039 (tt) REVERT: C 2517 ARG cc_start: 0.6886 (mpt180) cc_final: 0.6459 (tmm160) REVERT: B 1072 MET cc_start: 0.3381 (ptt) cc_final: 0.2715 (ttm) REVERT: B 1342 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8253 (tp) REVERT: B 2034 ASP cc_start: 0.8289 (t0) cc_final: 0.7910 (t0) REVERT: B 2133 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: B 2517 ARG cc_start: 0.7073 (mpt180) cc_final: 0.6539 (tmm160) outliers start: 98 outliers final: 74 residues processed: 443 average time/residue: 0.1699 time to fit residues: 125.6082 Evaluate side-chains 432 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 352 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 1045 LEU Chi-restraints excluded: chain A residue 1168 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 2252 THR Chi-restraints excluded: chain A residue 2293 LEU Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2421 THR 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 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 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 1985 ILE 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 2245 GLN 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 2399 LEU Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE 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 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1323 TYR 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 2296 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 99 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 331 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 120.0000 chunk 202 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 311 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** A2356 GLN C1013 HIS B1013 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.173078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.152565 restraints weight = 55262.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154767 restraints weight = 123870.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.154911 restraints weight = 53518.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.155082 restraints weight = 44196.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.155294 restraints weight = 35894.739| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2491 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= 0.123 Angle : 0.586 12.873 40815 Z= 0.287 Chirality : 0.039 0.288 4683 Planarity : 0.004 0.051 5091 Dihedral : 4.149 28.144 4026 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.46 % Allowed : 18.64 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.14), residues: 3636 helix: 2.03 (0.11), residues: 2418 sheet: -1.25 (0.32), residues: 261 loop : -1.67 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2104 TYR 0.011 0.001 TYR B1803 PHE 0.032 0.001 PHE B1665 TRP 0.009 0.001 TRP A2321 HIS 0.003 0.001 HIS B1526 Details of bonding type rmsd covalent geometry : bond 0.00283 (30084) covalent geometry : angle 0.58555 (40815) hydrogen bonds : bond 0.03220 ( 1860) hydrogen bonds : angle 3.61851 ( 5589) *********************** 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 472 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 368 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1072 MET cc_start: 0.3609 (ptt) cc_final: 0.3196 (ttp) REVERT: A 1100 LEU cc_start: 0.7733 (tt) cc_final: 0.7222 (tp) REVERT: A 1342 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8242 (tp) REVERT: A 1782 TYR cc_start: 0.7382 (p90) cc_final: 0.6898 (p90) REVERT: A 1794 PHE cc_start: 0.7851 (m-80) cc_final: 0.7454 (m-80) REVERT: A 2251 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: A 2266 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5503 (m-80) REVERT: A 2492 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9088 (tt) REVERT: C 1016 TRP cc_start: 0.6832 (t-100) cc_final: 0.6310 (t-100) REVERT: C 1342 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 2492 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9059 (tt) REVERT: C 2517 ARG cc_start: 0.6858 (mpt180) cc_final: 0.6501 (tmm160) REVERT: B 1072 MET cc_start: 0.3596 (ptt) cc_final: 0.3366 (ttp) REVERT: B 1100 LEU cc_start: 0.7968 (tt) cc_final: 0.7377 (tp) REVERT: B 1342 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 2034 ASP cc_start: 0.8294 (t0) cc_final: 0.7903 (t0) REVERT: B 2133 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: B 2517 ARG cc_start: 0.7004 (mpt180) cc_final: 0.6528 (tmm160) outliers start: 104 outliers final: 77 residues processed: 450 average time/residue: 0.1746 time to fit residues: 131.0023 Evaluate side-chains 438 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 1045 LEU Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain A residue 1168 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 2266 TYR Chi-restraints excluded: chain A residue 2332 THR 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 981 PHE Chi-restraints excluded: chain C residue 1021 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 1648 LEU Chi-restraints excluded: chain C residue 1655 HIS Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE 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 2245 GLN 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 2399 LEU Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE 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 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1323 TYR 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 1709 VAL 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 2251 PHE Chi-restraints excluded: chain B residue 2296 ILE 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 2471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 286 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 359 optimal weight: 2.9990 chunk 268 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 342 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 326 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** A2356 GLN C1013 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 = 0.4308 r_free = 0.4308 target = 0.170539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.149940 restraints weight = 55178.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.147328 restraints weight = 81903.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.144980 restraints weight = 86581.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.145211 restraints weight = 79747.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.144859 restraints weight = 68101.366| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30084 Z= 0.188 Angle : 0.645 12.976 40815 Z= 0.316 Chirality : 0.041 0.288 4683 Planarity : 0.004 0.046 5091 Dihedral : 4.312 29.522 4026 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.36 % Allowed : 19.21 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 3636 helix: 1.89 (0.11), residues: 2421 sheet: -1.35 (0.32), residues: 261 loop : -1.71 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2104 TYR 0.013 0.001 TYR C2533 PHE 0.031 0.002 PHE C2426 TRP 0.010 0.001 TRP A2321 HIS 0.004 0.001 HIS A2116 Details of bonding type rmsd covalent geometry : bond 0.00454 (30084) covalent geometry : angle 0.64453 (40815) hydrogen bonds : bond 0.03591 ( 1860) hydrogen bonds : angle 3.73657 ( 5589) *********************** 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 460 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 359 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.7902 (tt) cc_final: 0.7369 (tp) REVERT: A 1342 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8285 (tp) REVERT: A 1546 LEU cc_start: 0.7984 (mt) cc_final: 0.7696 (mt) REVERT: A 1740 MET cc_start: 0.7622 (tpt) cc_final: 0.7283 (tmm) REVERT: A 1782 TYR cc_start: 0.7377 (p90) cc_final: 0.6999 (p90) REVERT: A 2251 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.6385 (m-80) REVERT: A 2266 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: C 1016 TRP cc_start: 0.6895 (t-100) cc_final: 0.6405 (t-100) REVERT: C 1072 MET cc_start: 0.3119 (ptt) cc_final: 0.2761 (ttp) REVERT: C 1342 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8260 (tp) REVERT: C 2266 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: C 2270 MET cc_start: 0.4127 (tpt) cc_final: 0.3742 (tpt) REVERT: C 2492 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9223 (tt) REVERT: C 2517 ARG cc_start: 0.6956 (mpt180) cc_final: 0.6721 (tmm160) REVERT: B 1100 LEU cc_start: 0.8116 (tt) cc_final: 0.7534 (tp) REVERT: B 1226 MET cc_start: 0.8219 (mmm) cc_final: 0.8018 (mmm) REVERT: B 1342 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 2034 ASP cc_start: 0.8392 (t0) cc_final: 0.8020 (t0) REVERT: B 2133 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: B 2517 ARG cc_start: 0.6891 (mpt180) cc_final: 0.6602 (tmm160) outliers start: 101 outliers final: 77 residues processed: 441 average time/residue: 0.1717 time to fit residues: 127.1723 Evaluate side-chains 439 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 354 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 2266 TYR Chi-restraints excluded: chain A residue 2332 THR 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 2513 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1051 CYS 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 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 1709 VAL Chi-restraints excluded: chain C residue 1961 PHE Chi-restraints excluded: chain C residue 1985 ILE 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 2245 GLN 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 2428 GLU Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2492 ILE 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 1157 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1281 ILE Chi-restraints excluded: chain B residue 1323 TYR 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 2251 PHE Chi-restraints excluded: chain B residue 2296 ILE 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 251 optimal weight: 70.0000 chunk 369 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 109 optimal weight: 0.0030 chunk 197 optimal weight: 0.5980 chunk 203 optimal weight: 0.5980 chunk 242 optimal weight: 0.0970 chunk 166 optimal weight: 0.9980 chunk 335 optimal weight: 0.5980 chunk 364 optimal weight: 0.0010 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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** A2116 HIS ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2245 GLN C2245 GLN C2356 GLN ** B1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.176137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.154881 restraints weight = 54494.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.156456 restraints weight = 121267.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157274 restraints weight = 69866.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.157616 restraints weight = 44846.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.158084 restraints weight = 38913.347| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30084 Z= 0.105 Angle : 0.593 13.947 40815 Z= 0.287 Chirality : 0.039 0.276 4683 Planarity : 0.004 0.046 5091 Dihedral : 4.078 26.628 4026 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.13 % Allowed : 20.31 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.14), residues: 3636 helix: 2.10 (0.11), residues: 2412 sheet: -1.16 (0.33), residues: 255 loop : -1.70 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1664 TYR 0.011 0.001 TYR B1977 PHE 0.026 0.001 PHE B1665 TRP 0.010 0.001 TRP A2321 HIS 0.003 0.001 HIS B1526 Details of bonding type rmsd covalent geometry : bond 0.00226 (30084) covalent geometry : angle 0.59259 (40815) hydrogen bonds : bond 0.03058 ( 1860) hydrogen bonds : angle 3.56963 ( 5589) ********************** 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 444 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1100 LEU cc_start: 0.7667 (tt) cc_final: 0.7026 (tt) REVERT: A 1342 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 1794 PHE cc_start: 0.7739 (m-80) cc_final: 0.7386 (m-80) REVERT: A 2251 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.6298 (m-80) REVERT: A 2285 GLN cc_start: 0.7642 (mm110) cc_final: 0.7242 (mm110) REVERT: E 238 MET cc_start: 0.7147 (tpp) cc_final: 0.6689 (ttt) REVERT: C 1072 MET cc_start: 0.3304 (ptt) cc_final: 0.3029 (ttp) REVERT: C 1342 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8173 (tp) REVERT: C 1648 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7195 (mt) REVERT: C 2270 MET cc_start: 0.4138 (tpt) cc_final: 0.3766 (tpt) REVERT: C 2517 ARG cc_start: 0.6853 (mpt180) cc_final: 0.6485 (tmm160) REVERT: B 1100 LEU cc_start: 0.7904 (tt) cc_final: 0.7318 (tp) REVERT: B 1215 LEU cc_start: 0.7788 (tt) cc_final: 0.7272 (mp) REVERT: B 1226 MET cc_start: 0.8151 (mmm) cc_final: 0.7900 (mmm) REVERT: B 1342 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 1349 MET cc_start: 0.8635 (mmm) cc_final: 0.8011 (mmp) REVERT: B 2034 ASP cc_start: 0.8287 (t0) cc_final: 0.7892 (t0) REVERT: B 2133 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: B 2196 ILE cc_start: 0.8698 (mt) cc_final: 0.8443 (mt) REVERT: B 2279 GLU cc_start: 0.8168 (pp20) cc_final: 0.7558 (pp20) REVERT: B 2285 GLN cc_start: 0.7806 (mm110) cc_final: 0.7365 (mm110) outliers start: 64 outliers final: 52 residues processed: 432 average time/residue: 0.1567 time to fit residues: 112.8403 Evaluate side-chains 416 residues out of total 3339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 358 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 2216 VAL Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2252 THR 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 2513 VAL Chi-restraints excluded: chain C residue 1021 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 2039 LEU 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 2296 ILE Chi-restraints excluded: chain C residue 2421 THR Chi-restraints excluded: chain C residue 2428 GLU 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 1961 PHE 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 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 2296 ILE Chi-restraints excluded: chain B residue 2421 THR Chi-restraints excluded: chain B residue 2426 PHE Chi-restraints excluded: chain B residue 2432 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 301 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 368 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 chunk 258 optimal weight: 50.0000 chunk 362 optimal weight: 0.9990 chunk 117 optimal weight: 0.0170 chunk 45 optimal weight: 0.0040 chunk 32 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- 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** A2245 GLN A2254 GLN A2261 GLN C2254 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.175682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.155229 restraints weight = 54868.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157221 restraints weight = 121082.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157677 restraints weight = 55787.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.157783 restraints weight = 42938.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157985 restraints weight = 37311.943| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30084 Z= 0.111 Angle : 0.605 13.130 40815 Z= 0.293 Chirality : 0.039 0.287 4683 Planarity : 0.004 0.045 5091 Dihedral : 4.024 28.374 4026 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.19 % Allowed : 20.90 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.15), residues: 3636 helix: 2.19 (0.11), residues: 2406 sheet: -1.28 (0.32), residues: 276 loop : -1.61 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1664 TYR 0.013 0.001 TYR B2256 PHE 0.055 0.001 PHE C1665 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS B2116 Details of bonding type rmsd covalent geometry : bond 0.00250 (30084) covalent geometry : angle 0.60505 (40815) hydrogen bonds : bond 0.03025 ( 1860) hydrogen bonds : angle 3.51348 ( 5589) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4414.81 seconds wall clock time: 77 minutes 16.48 seconds (4636.48 seconds total)