Starting phenix.real_space_refine on Sat Jun 6 18:16:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ye_76184/06_2026/11ye_76184.map" } resolution = 3.7 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= -0.010 sd= 0.997 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 153 5.16 5 C 18729 2.51 5 N 5145 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29295 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 9765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 9765 Classifications: {'peptide': 1335} Incomplete info: {'backbone_only': 271, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 1280} Chain breaks: 10 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1878 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 367 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 20, 'ARG:plan': 22, 'GLN:plan1': 15, 'GLU:plan': 13, 'HIS:plan': 5, 'TYR:plan': 13, 'TRP:plan': 9, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 658 Restraints were copied for chains: D, E Time building chain proxies: 12.88, per 1000 atoms: 0.44 Number of scatterers: 29295 At special positions: 0 Unit cell: (200.22, 208.68, 156.04, 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 153 16.00 O 5268 8.00 N 5145 7.00 C 18729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C1243 " - pdb=" SG CYS C1271 " distance=2.03 Simple disulfide: pdb=" SG CYS D1243 " - pdb=" SG CYS D1271 " distance=2.03 Simple disulfide: pdb=" SG CYS E1243 " - pdb=" SG CYS E1271 " distance=2.03 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: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 9 sheets defined 70.8% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'C' and resid 784 through 825 removed outlier: 4.400A pdb=" N LEU C 804 " --> pdb=" O PHE C 800 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU C 807 " --> pdb=" O ARG C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 840 removed outlier: 3.674A pdb=" N ASN C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 865 Processing helix chain 'C' and resid 899 through 904 Processing helix chain 'C' and resid 922 through 951 removed outlier: 3.663A pdb=" N ASN C 926 " --> pdb=" O GLY C 922 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 927 " --> pdb=" O TYR C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 984 removed outlier: 3.696A pdb=" N LYS C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 998 removed outlier: 4.176A pdb=" N ILE C 993 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET C 997 " --> pdb=" O ILE C 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 998 " --> pdb=" O CYS C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1004 Processing helix chain 'C' and resid 1005 through 1017 removed outlier: 4.164A pdb=" N ILE C1011 " --> pdb=" O ASN C1007 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS C1015 " --> pdb=" O ILE C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 Processing helix chain 'C' and resid 1025 through 1052 removed outlier: 4.225A pdb=" N ILE C1029 " --> pdb=" O ARG C1025 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing helix chain 'C' and resid 1073 through 1081 Processing helix chain 'C' and resid 1091 through 1113 removed outlier: 3.658A pdb=" N ILE C1095 " --> pdb=" O SER C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1145 removed outlier: 4.376A pdb=" N ILE C1144 " --> pdb=" O PRO C1141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS C1145 " --> pdb=" O ASN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1145' Processing helix chain 'C' and resid 1148 through 1177 removed outlier: 5.181A pdb=" N PHE C1162 " --> pdb=" O PHE C1158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP C1163 " --> pdb=" O ARG C1159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE C1177 " --> pdb=" O GLY C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1202 removed outlier: 3.809A pdb=" N LEU C1182 " --> pdb=" O SER C1178 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C1183 " --> pdb=" O ILE C1179 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN C1200 " --> pdb=" O THR C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1231 removed outlier: 4.452A pdb=" N VAL C1208 " --> pdb=" O ARG C1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 1232 through 1234 No H-bonds generated for 'chain 'C' and resid 1232 through 1234' Processing helix chain 'C' and resid 1242 through 1249 removed outlier: 3.558A pdb=" N ILE C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1262 through 1268 Processing helix chain 'C' and resid 1279 through 1292 Processing helix chain 'C' and resid 1295 through 1300 Processing helix chain 'C' and resid 1302 through 1365 removed outlier: 3.507A pdb=" N ASP C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1408 Processing helix chain 'C' and resid 1412 through 1416 removed outlier: 4.003A pdb=" N GLU C1416 " --> pdb=" O PHE C1413 " (cutoff:3.500A) Processing helix chain 'C' and resid 1417 through 1421 Processing helix chain 'C' and resid 1496 through 1524 Processing helix chain 'C' and resid 1524 through 1548 removed outlier: 3.840A pdb=" N LEU C1540 " --> pdb=" O ALA C1536 " (cutoff:3.500A) Processing helix chain 'C' and resid 1552 through 1559 removed outlier: 4.436A pdb=" N LEU C1556 " --> pdb=" O ARG C1552 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1670 removed outlier: 4.001A pdb=" N GLY C1670 " --> pdb=" O GLU C1666 " (cutoff:3.500A) Processing helix chain 'C' and resid 1671 through 1686 removed outlier: 3.732A pdb=" N LEU C1675 " --> pdb=" O ARG C1671 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN C1681 " --> pdb=" O ARG C1677 " (cutoff:3.500A) Processing helix chain 'C' and resid 1686 through 1700 removed outlier: 3.577A pdb=" N TYR C1692 " --> pdb=" O GLU C1688 " (cutoff:3.500A) Processing helix chain 'C' and resid 1705 through 1717 Proline residue: C1711 - end of helix Processing helix chain 'C' and resid 1725 through 1748 removed outlier: 3.815A pdb=" N PHE C1729 " --> pdb=" O PRO C1725 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1756 removed outlier: 3.517A pdb=" N SER C1756 " --> pdb=" O PRO C1753 " (cutoff:3.500A) Processing helix chain 'C' and resid 1757 through 1762 Processing helix chain 'C' and resid 1769 through 1775 Processing helix chain 'C' and resid 1785 through 1804 removed outlier: 3.520A pdb=" N GLY C1804 " --> pdb=" O LEU C1800 " (cutoff:3.500A) Processing helix chain 'C' and resid 1947 through 1968 Proline residue: C1957 - end of helix Processing helix chain 'C' and resid 1976 through 1997 Processing helix chain 'C' and resid 2016 through 2040 removed outlier: 4.167A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C2029 " --> pdb=" O LEU C2025 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C2033 " --> pdb=" O GLY C2029 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2063 removed outlier: 3.596A pdb=" N ALA C2048 " --> pdb=" O LEU C2044 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2069 Processing helix chain 'C' and resid 2076 through 2099 removed outlier: 4.095A pdb=" N GLN C2080 " --> pdb=" O ASN C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2116 through 2128 removed outlier: 4.415A pdb=" N PHE C2120 " --> pdb=" O HIS C2116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C2128 " --> pdb=" O GLY C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2130 through 2144 removed outlier: 4.136A pdb=" N ASP C2144 " --> pdb=" O TRP C2140 " (cutoff:3.500A) Processing helix chain 'C' and resid 2150 through 2175 Processing helix chain 'C' and resid 2184 through 2215 Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2244 through 2246 No H-bonds generated for 'chain 'C' and resid 2244 through 2246' Processing helix chain 'C' and resid 2251 through 2263 Processing helix chain 'C' and resid 2266 through 2275 removed outlier: 3.743A pdb=" N PHE C2272 " --> pdb=" O LEU C2268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C2275 " --> pdb=" O GLN C2271 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2326 through 2330 removed outlier: 3.720A pdb=" N LYS C2329 " --> pdb=" O ASP C2326 " (cutoff:3.500A) Processing helix chain 'C' and resid 2348 through 2359 Processing helix chain 'C' and resid 2478 through 2499 removed outlier: 4.302A pdb=" N LEU C2482 " --> pdb=" O GLY C2478 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE C2497 " --> pdb=" O PHE C2493 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C2498 " --> pdb=" O VAL C2494 " (cutoff:3.500A) Processing helix chain 'C' and resid 2501 through 2503 No H-bonds generated for 'chain 'C' and resid 2501 through 2503' Processing helix chain 'C' and resid 2504 through 2509 Processing helix chain 'C' and resid 2513 through 2529 removed outlier: 3.699A pdb=" N LEU C2519 " --> pdb=" O ARG C2515 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C2522 " --> pdb=" O LYS C2518 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C2524 " --> pdb=" O CYS C2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR C2529 " --> pdb=" O LEU C2525 " (cutoff:3.500A) Processing helix chain 'C' and resid 2531 through 2546 removed outlier: 3.656A pdb=" N GLU C2535 " --> pdb=" O GLU C2531 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C2537 " --> pdb=" O GLU C2533 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C2540 " --> pdb=" O GLU C2536 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C2545 " --> pdb=" O LYS C2541 " (cutoff:3.500A) Processing helix chain 'C' and resid 2548 through 2556 Processing helix chain 'D' and resid 785 through 825 removed outlier: 4.401A pdb=" N LEU D 804 " --> pdb=" O PHE D 800 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU D 807 " --> pdb=" O ARG D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 840 removed outlier: 3.674A pdb=" N ASN D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 865 Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 922 through 951 removed outlier: 3.663A pdb=" N ASN D 926 " --> pdb=" O GLY D 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS D 927 " --> pdb=" O TYR D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 984 removed outlier: 3.696A pdb=" N LYS D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 998 removed outlier: 4.176A pdb=" N ILE D 993 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 998 " --> pdb=" O CYS D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 999 through 1004 Processing helix chain 'D' and resid 1005 through 1017 removed outlier: 4.163A pdb=" N ILE D1011 " --> pdb=" O ASN D1007 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS D1015 " --> pdb=" O ILE D1011 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1024 Processing helix chain 'D' and resid 1025 through 1052 removed outlier: 4.225A pdb=" N ILE D1029 " --> pdb=" O ARG D1025 " (cutoff:3.500A) Proline residue: D1034 - end of helix Processing helix chain 'D' and resid 1073 through 1081 Processing helix chain 'D' and resid 1091 through 1113 removed outlier: 3.658A pdb=" N ILE D1095 " --> pdb=" O SER D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1145 removed outlier: 4.376A pdb=" N ILE D1144 " --> pdb=" O PRO D1141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS D1145 " --> pdb=" O ASN D1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1141 through 1145' Processing helix chain 'D' and resid 1148 through 1177 removed outlier: 5.181A pdb=" N PHE D1162 " --> pdb=" O PHE D1158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP D1163 " --> pdb=" O ARG D1159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D1177 " --> pdb=" O GLY D1173 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1202 removed outlier: 3.808A pdb=" N LEU D1182 " --> pdb=" O SER D1178 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D1183 " --> pdb=" O ILE D1179 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR D1196 " --> pdb=" O LEU D1192 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR D1197 " --> pdb=" O LEU D1193 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN D1200 " --> pdb=" O THR D1196 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1231 removed outlier: 4.453A pdb=" N VAL D1208 " --> pdb=" O ARG D1204 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1234 No H-bonds generated for 'chain 'D' and resid 1232 through 1234' Processing helix chain 'D' and resid 1242 through 1249 removed outlier: 3.558A pdb=" N ILE D1246 " --> pdb=" O PHE D1242 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1268 Processing helix chain 'D' and resid 1279 through 1292 Processing helix chain 'D' and resid 1295 through 1300 Processing helix chain 'D' and resid 1302 through 1365 removed outlier: 3.506A pdb=" N ASP D1308 " --> pdb=" O HIS D1304 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER D1317 " --> pdb=" O ALA D1313 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG D1318 " --> pdb=" O LEU D1314 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1408 Processing helix chain 'D' and resid 1412 through 1416 removed outlier: 4.003A pdb=" N GLU D1416 " --> pdb=" O PHE D1413 " (cutoff:3.500A) Processing helix chain 'D' and resid 1417 through 1421 Processing helix chain 'D' and resid 1496 through 1524 Processing helix chain 'D' and resid 1524 through 1548 removed outlier: 3.841A pdb=" N LEU D1540 " --> pdb=" O ALA D1536 " (cutoff:3.500A) Processing helix chain 'D' and resid 1552 through 1559 removed outlier: 4.437A pdb=" N LEU D1556 " --> pdb=" O ARG D1552 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1670 removed outlier: 4.000A pdb=" N GLY D1670 " --> pdb=" O GLU D1666 " (cutoff:3.500A) Processing helix chain 'D' and resid 1671 through 1686 removed outlier: 3.732A pdb=" N LEU D1675 " --> pdb=" O ARG D1671 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN D1681 " --> pdb=" O ARG D1677 " (cutoff:3.500A) Processing helix chain 'D' and resid 1686 through 1700 removed outlier: 3.576A pdb=" N TYR D1692 " --> pdb=" O GLU D1688 " (cutoff:3.500A) Processing helix chain 'D' and resid 1705 through 1717 Proline residue: D1711 - end of helix Processing helix chain 'D' and resid 1725 through 1748 removed outlier: 3.815A pdb=" N PHE D1729 " --> pdb=" O PRO D1725 " (cutoff:3.500A) Processing helix chain 'D' and resid 1752 through 1756 removed outlier: 3.517A pdb=" N SER D1756 " --> pdb=" O PRO D1753 " (cutoff:3.500A) Processing helix chain 'D' and resid 1757 through 1762 Processing helix chain 'D' and resid 1769 through 1775 Processing helix chain 'D' and resid 1785 through 1804 removed outlier: 3.520A pdb=" N GLY D1804 " --> pdb=" O LEU D1800 " (cutoff:3.500A) Processing helix chain 'D' and resid 1947 through 1968 Proline residue: D1957 - end of helix Processing helix chain 'D' and resid 1976 through 1997 Processing helix chain 'D' and resid 2016 through 2040 removed outlier: 4.167A pdb=" N PHE D2022 " --> pdb=" O GLN D2018 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D2029 " --> pdb=" O LEU D2025 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D2033 " --> pdb=" O GLY D2029 " (cutoff:3.500A) Processing helix chain 'D' and resid 2042 through 2063 removed outlier: 3.597A pdb=" N ALA D2048 " --> pdb=" O LEU D2044 " (cutoff:3.500A) Processing helix chain 'D' and resid 2064 through 2069 Processing helix chain 'D' and resid 2076 through 2099 removed outlier: 4.094A pdb=" N GLN D2080 " --> pdb=" O ASN D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2116 through 2128 removed outlier: 4.415A pdb=" N PHE D2120 " --> pdb=" O HIS D2116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D2128 " --> pdb=" O GLY D2124 " (cutoff:3.500A) Processing helix chain 'D' and resid 2130 through 2144 removed outlier: 4.136A pdb=" N ASP D2144 " --> pdb=" O TRP D2140 " (cutoff:3.500A) Processing helix chain 'D' and resid 2150 through 2175 Processing helix chain 'D' and resid 2184 through 2215 Proline residue: D2206 - end of helix Processing helix chain 'D' and resid 2244 through 2246 No H-bonds generated for 'chain 'D' and resid 2244 through 2246' Processing helix chain 'D' and resid 2251 through 2263 Processing helix chain 'D' and resid 2266 through 2275 removed outlier: 3.743A pdb=" N PHE D2272 " --> pdb=" O LEU D2268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D2275 " --> pdb=" O GLN D2271 " (cutoff:3.500A) Processing helix chain 'D' and resid 2297 through 2311 Processing helix chain 'D' and resid 2326 through 2330 removed outlier: 3.720A pdb=" N LYS D2329 " --> pdb=" O ASP D2326 " (cutoff:3.500A) Processing helix chain 'D' and resid 2348 through 2359 Processing helix chain 'D' and resid 2478 through 2499 removed outlier: 4.303A pdb=" N LEU D2482 " --> pdb=" O GLY D2478 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE D2497 " --> pdb=" O PHE D2493 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D2498 " --> pdb=" O VAL D2494 " (cutoff:3.500A) Processing helix chain 'D' and resid 2501 through 2503 No H-bonds generated for 'chain 'D' and resid 2501 through 2503' Processing helix chain 'D' and resid 2504 through 2509 Processing helix chain 'D' and resid 2513 through 2529 removed outlier: 3.699A pdb=" N LEU D2519 " --> pdb=" O ARG D2515 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP D2522 " --> pdb=" O LYS D2518 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D2524 " --> pdb=" O CYS D2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR D2529 " --> pdb=" O LEU D2525 " (cutoff:3.500A) Processing helix chain 'D' and resid 2531 through 2546 removed outlier: 3.656A pdb=" N GLU D2535 " --> pdb=" O GLU D2531 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU D2537 " --> pdb=" O GLU D2533 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA D2540 " --> pdb=" O GLU D2536 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D2545 " --> pdb=" O LYS D2541 " (cutoff:3.500A) Processing helix chain 'D' and resid 2548 through 2556 Processing helix chain 'E' and resid 785 through 825 removed outlier: 4.400A pdb=" N LEU E 804 " --> pdb=" O PHE E 800 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU E 807 " --> pdb=" O ARG E 803 " (cutoff:3.500A) Processing helix chain 'E' and resid 825 through 840 removed outlier: 3.674A pdb=" N ASN E 829 " --> pdb=" O VAL E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 865 Processing helix chain 'E' and resid 899 through 904 Processing helix chain 'E' and resid 922 through 951 removed outlier: 3.663A pdb=" N ASN E 926 " --> pdb=" O GLY E 922 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS E 927 " --> pdb=" O TYR E 923 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 984 removed outlier: 3.696A pdb=" N LYS E 979 " --> pdb=" O LEU E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 989 through 998 removed outlier: 4.176A pdb=" N ILE E 993 " --> pdb=" O PHE E 989 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU E 996 " --> pdb=" O GLU E 992 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET E 997 " --> pdb=" O ILE E 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 998 " --> pdb=" O CYS E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1004 Processing helix chain 'E' and resid 1005 through 1017 removed outlier: 4.164A pdb=" N ILE E1011 " --> pdb=" O ASN E1007 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS E1015 " --> pdb=" O ILE E1011 " (cutoff:3.500A) Processing helix chain 'E' and resid 1019 through 1024 Processing helix chain 'E' and resid 1025 through 1052 removed outlier: 4.225A pdb=" N ILE E1029 " --> pdb=" O ARG E1025 " (cutoff:3.500A) Proline residue: E1034 - end of helix Processing helix chain 'E' and resid 1073 through 1081 Processing helix chain 'E' and resid 1091 through 1113 removed outlier: 3.658A pdb=" N ILE E1095 " --> pdb=" O SER E1091 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1145 removed outlier: 4.377A pdb=" N ILE E1144 " --> pdb=" O PRO E1141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS E1145 " --> pdb=" O ASN E1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1141 through 1145' Processing helix chain 'E' and resid 1148 through 1177 removed outlier: 5.181A pdb=" N PHE E1162 " --> pdb=" O PHE E1158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TRP E1163 " --> pdb=" O ARG E1159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE E1177 " --> pdb=" O GLY E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1202 removed outlier: 3.809A pdb=" N LEU E1182 " --> pdb=" O SER E1178 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY E1183 " --> pdb=" O ILE E1179 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR E1197 " --> pdb=" O LEU E1193 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLN E1200 " --> pdb=" O THR E1196 " (cutoff:3.500A) Processing helix chain 'E' and resid 1204 through 1231 removed outlier: 4.452A pdb=" N VAL E1208 " --> pdb=" O ARG E1204 " (cutoff:3.500A) Processing helix chain 'E' and resid 1232 through 1234 No H-bonds generated for 'chain 'E' and resid 1232 through 1234' Processing helix chain 'E' and resid 1242 through 1249 removed outlier: 3.558A pdb=" N ILE E1246 " --> pdb=" O PHE E1242 " (cutoff:3.500A) Processing helix chain 'E' and resid 1262 through 1268 Processing helix chain 'E' and resid 1279 through 1292 Processing helix chain 'E' and resid 1295 through 1300 Processing helix chain 'E' and resid 1302 through 1365 removed outlier: 3.507A pdb=" N ASP E1308 " --> pdb=" O HIS E1304 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER E1317 " --> pdb=" O ALA E1313 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG E1318 " --> pdb=" O LEU E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1408 Processing helix chain 'E' and resid 1412 through 1416 removed outlier: 4.002A pdb=" N GLU E1416 " --> pdb=" O PHE E1413 " (cutoff:3.500A) Processing helix chain 'E' and resid 1417 through 1421 Processing helix chain 'E' and resid 1496 through 1524 Processing helix chain 'E' and resid 1524 through 1548 removed outlier: 3.841A pdb=" N LEU E1540 " --> pdb=" O ALA E1536 " (cutoff:3.500A) Processing helix chain 'E' and resid 1552 through 1559 removed outlier: 4.436A pdb=" N LEU E1556 " --> pdb=" O ARG E1552 " (cutoff:3.500A) Processing helix chain 'E' and resid 1656 through 1670 removed outlier: 4.000A pdb=" N GLY E1670 " --> pdb=" O GLU E1666 " (cutoff:3.500A) Processing helix chain 'E' and resid 1671 through 1686 removed outlier: 3.733A pdb=" N LEU E1675 " --> pdb=" O ARG E1671 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN E1681 " --> pdb=" O ARG E1677 " (cutoff:3.500A) Processing helix chain 'E' and resid 1686 through 1700 removed outlier: 3.577A pdb=" N TYR E1692 " --> pdb=" O GLU E1688 " (cutoff:3.500A) Processing helix chain 'E' and resid 1705 through 1717 Proline residue: E1711 - end of helix Processing helix chain 'E' and resid 1725 through 1748 removed outlier: 3.815A pdb=" N PHE E1729 " --> pdb=" O PRO E1725 " (cutoff:3.500A) Processing helix chain 'E' and resid 1752 through 1756 removed outlier: 3.517A pdb=" N SER E1756 " --> pdb=" O PRO E1753 " (cutoff:3.500A) Processing helix chain 'E' and resid 1757 through 1762 Processing helix chain 'E' and resid 1769 through 1775 Processing helix chain 'E' and resid 1785 through 1804 removed outlier: 3.520A pdb=" N GLY E1804 " --> pdb=" O LEU E1800 " (cutoff:3.500A) Processing helix chain 'E' and resid 1947 through 1968 Proline residue: E1957 - end of helix Processing helix chain 'E' and resid 1976 through 1997 Processing helix chain 'E' and resid 2016 through 2040 removed outlier: 4.167A pdb=" N PHE E2022 " --> pdb=" O GLN E2018 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E2029 " --> pdb=" O LEU E2025 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E2033 " --> pdb=" O GLY E2029 " (cutoff:3.500A) Processing helix chain 'E' and resid 2042 through 2063 removed outlier: 3.596A pdb=" N ALA E2048 " --> pdb=" O LEU E2044 " (cutoff:3.500A) Processing helix chain 'E' and resid 2064 through 2069 Processing helix chain 'E' and resid 2076 through 2099 removed outlier: 4.094A pdb=" N GLN E2080 " --> pdb=" O ASN E2076 " (cutoff:3.500A) Processing helix chain 'E' and resid 2116 through 2128 removed outlier: 4.415A pdb=" N PHE E2120 " --> pdb=" O HIS E2116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL E2128 " --> pdb=" O GLY E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2130 through 2144 removed outlier: 4.136A pdb=" N ASP E2144 " --> pdb=" O TRP E2140 " (cutoff:3.500A) Processing helix chain 'E' and resid 2150 through 2175 Processing helix chain 'E' and resid 2184 through 2215 Proline residue: E2206 - end of helix Processing helix chain 'E' and resid 2244 through 2246 No H-bonds generated for 'chain 'E' and resid 2244 through 2246' Processing helix chain 'E' and resid 2251 through 2263 Processing helix chain 'E' and resid 2266 through 2275 removed outlier: 3.743A pdb=" N PHE E2272 " --> pdb=" O LEU E2268 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN E2275 " --> pdb=" O GLN E2271 " (cutoff:3.500A) Processing helix chain 'E' and resid 2297 through 2311 Processing helix chain 'E' and resid 2326 through 2330 removed outlier: 3.720A pdb=" N LYS E2329 " --> pdb=" O ASP E2326 " (cutoff:3.500A) Processing helix chain 'E' and resid 2348 through 2359 Processing helix chain 'E' and resid 2478 through 2499 removed outlier: 4.303A pdb=" N LEU E2482 " --> pdb=" O GLY E2478 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE E2497 " --> pdb=" O PHE E2493 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E2498 " --> pdb=" O VAL E2494 " (cutoff:3.500A) Processing helix chain 'E' and resid 2501 through 2503 No H-bonds generated for 'chain 'E' and resid 2501 through 2503' Processing helix chain 'E' and resid 2504 through 2509 Processing helix chain 'E' and resid 2513 through 2529 removed outlier: 3.699A pdb=" N LEU E2519 " --> pdb=" O ARG E2515 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E2522 " --> pdb=" O LYS E2518 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E2524 " --> pdb=" O CYS E2520 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR E2529 " --> pdb=" O LEU E2525 " (cutoff:3.500A) Processing helix chain 'E' and resid 2531 through 2546 removed outlier: 3.656A pdb=" N GLU E2535 " --> pdb=" O GLU E2531 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E2537 " --> pdb=" O GLU E2533 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E2540 " --> pdb=" O GLU E2536 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E2545 " --> pdb=" O LYS E2541 " (cutoff:3.500A) Processing helix chain 'E' and resid 2548 through 2556 Processing sheet with id=AA1, first strand: chain 'C' and resid 2240 through 2243 Processing sheet with id=AA2, first strand: chain 'C' and resid 2248 through 2250 Processing sheet with id=AA3, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 3.859A pdb=" N VAL C2401 " --> pdb=" O ILE C2368 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS C2370 " --> pdb=" O LEU C2399 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C2399 " --> pdb=" O HIS C2370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 2240 through 2243 Processing sheet with id=AA5, first strand: chain 'D' and resid 2248 through 2250 Processing sheet with id=AA6, first strand: chain 'D' and resid 2366 through 2372 removed outlier: 3.858A pdb=" N VAL D2401 " --> pdb=" O ILE D2368 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS D2370 " --> pdb=" O LEU D2399 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU D2399 " --> pdb=" O HIS D2370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2240 through 2243 Processing sheet with id=AA8, first strand: chain 'E' and resid 2248 through 2250 Processing sheet with id=AA9, first strand: chain 'E' and resid 2366 through 2372 removed outlier: 3.859A pdb=" N VAL E2401 " --> pdb=" O ILE E2368 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS E2370 " --> pdb=" O LEU E2399 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU E2399 " --> pdb=" O HIS E2370 " (cutoff:3.500A) 2050 hydrogen bonds defined for protein. 6051 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: 6.35 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9702 1.34 - 1.46: 7044 1.46 - 1.58: 12957 1.58 - 1.69: 0 1.69 - 1.81: 243 Bond restraints: 29946 Sorted by residual: bond pdb=" N ILE D2296 " pdb=" CA ILE D2296 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.17e-02 7.31e+03 9.95e+00 bond pdb=" N ILE C2296 " pdb=" CA ILE C2296 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.61e+00 bond pdb=" N ILE E2296 " pdb=" CA ILE E2296 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.39e+00 bond pdb=" N ASP D1260 " pdb=" CA ASP D1260 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.27e+00 bond pdb=" N ASP C1260 " pdb=" CA ASP C1260 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.24e+00 ... (remaining 29941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 39614 1.91 - 3.82: 519 3.82 - 5.73: 70 5.73 - 7.64: 15 7.64 - 9.55: 6 Bond angle restraints: 40224 Sorted by residual: angle pdb=" C PRO D2298 " pdb=" CA PRO D2298 " pdb=" CB PRO D2298 " ideal model delta sigma weight residual 110.92 115.60 -4.68 1.22e+00 6.72e-01 1.47e+01 angle pdb=" C PRO C2298 " pdb=" CA PRO C2298 " pdb=" CB PRO C2298 " ideal model delta sigma weight residual 110.92 115.57 -4.65 1.22e+00 6.72e-01 1.45e+01 angle pdb=" C PRO E2298 " pdb=" CA PRO E2298 " pdb=" CB PRO E2298 " ideal model delta sigma weight residual 110.92 115.56 -4.64 1.22e+00 6.72e-01 1.45e+01 angle pdb=" C PRO D1261 " pdb=" N LYS D1262 " pdb=" CA LYS D1262 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C PRO E1261 " pdb=" N LYS E1262 " pdb=" CA LYS E1262 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 ... (remaining 40219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 15532 17.08 - 34.16: 836 34.16 - 51.24: 198 51.24 - 68.33: 18 68.33 - 85.41: 12 Dihedral angle restraints: 16596 sinusoidal: 6429 harmonic: 10167 Sorted by residual: dihedral pdb=" CA PRO E1725 " pdb=" C PRO E1725 " pdb=" N SER E1726 " pdb=" CA SER E1726 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PRO C1725 " pdb=" C PRO C1725 " pdb=" N SER C1726 " pdb=" CA SER C1726 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA PRO D1725 " pdb=" C PRO D1725 " pdb=" N SER D1726 " pdb=" CA SER D1726 " ideal model delta harmonic sigma weight residual 180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 16593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2814 0.036 - 0.072: 930 0.072 - 0.108: 248 0.108 - 0.144: 49 0.144 - 0.179: 9 Chirality restraints: 4050 Sorted by residual: chirality pdb=" CG LEU E1776 " pdb=" CB LEU E1776 " pdb=" CD1 LEU E1776 " pdb=" CD2 LEU E1776 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CG LEU C1776 " pdb=" CB LEU C1776 " pdb=" CD1 LEU C1776 " pdb=" CD2 LEU C1776 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CG LEU D1776 " pdb=" CB LEU D1776 " pdb=" CD1 LEU D1776 " pdb=" CD2 LEU D1776 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 4047 not shown) Planarity restraints: 5310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D1257 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C GLY D1257 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY D1257 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR D1258 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E1257 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C GLY E1257 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY E1257 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR E1258 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C1257 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C GLY C1257 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C1257 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR C1258 " -0.013 2.00e-02 2.50e+03 ... (remaining 5307 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4228 2.76 - 3.29: 28927 3.29 - 3.83: 46358 3.83 - 4.36: 48564 4.36 - 4.90: 84014 Nonbonded interactions: 212091 Sorted by model distance: nonbonded pdb=" OD1 ASP C2139 " pdb=" CG2 THR C2143 " model vdw 2.219 3.460 nonbonded pdb=" OD1 ASP E2139 " pdb=" CG2 THR E2143 " model vdw 2.219 3.460 nonbonded pdb=" OD1 ASP D2139 " pdb=" CG2 THR D2143 " model vdw 2.220 3.460 nonbonded pdb=" O TRP E1282 " pdb=" CG2 ILE E1285 " model vdw 2.249 3.460 nonbonded pdb=" O PRO D2129 " pdb=" NH2 ARG E2495 " model vdw 2.249 3.120 ... (remaining 212086 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: 0.08 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 5.710 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: 0.050 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29949 Z= 0.159 Angle : 0.564 9.554 40230 Z= 0.325 Chirality : 0.039 0.179 4050 Planarity : 0.004 0.052 5310 Dihedral : 10.930 85.407 10527 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.38 % Favored : 91.17 % Rotamer: Outliers : 0.85 % Allowed : 9.47 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3939 helix: 1.36 (0.11), residues: 2541 sheet: -0.01 (0.35), residues: 255 loop : -2.72 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2495 TYR 0.017 0.001 TYR E1259 PHE 0.010 0.001 PHE D2109 TRP 0.011 0.001 TRP E1210 HIS 0.005 0.001 HIS E2340 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (29946) covalent geometry : angle 0.56432 / 0.32 (40224) SS BOND : bond 0.00103 / 0.05 ( 3) SS BOND : angle 0.43956 / 0.26 ( 6) hydrogen bonds : bond 0.12872 / 9.26 ( 2050) hydrogen bonds : angle 6.32711 / 4.65 ( 6051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 567 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1176 ARG cc_start: 0.7554 (ttt-90) cc_final: 0.6800 (ttt180) REVERT: C 1293 GLN cc_start: 0.7928 (mp10) cc_final: 0.7152 (pt0) REVERT: C 1504 PHE cc_start: 0.8351 (t80) cc_final: 0.8019 (m-80) REVERT: C 1689 LEU cc_start: 0.8958 (mp) cc_final: 0.8742 (tt) REVERT: C 2031 MET cc_start: 0.7692 (mtp) cc_final: 0.6887 (mtp) REVERT: C 2080 GLN cc_start: 0.7973 (tt0) cc_final: 0.7755 (tt0) REVERT: C 2202 ILE cc_start: 0.9145 (mp) cc_final: 0.8923 (mm) REVERT: C 2306 GLN cc_start: 0.8638 (tt0) cc_final: 0.8363 (tm-30) REVERT: C 2550 GLU cc_start: 0.7885 (mp0) cc_final: 0.7629 (mp0) REVERT: D 1261 PRO cc_start: 0.7529 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: D 1502 MET cc_start: 0.8246 (ttt) cc_final: 0.7932 (ppp) REVERT: D 1656 ILE cc_start: 0.7915 (tt) cc_final: 0.7529 (mm) REVERT: D 2031 MET cc_start: 0.7558 (mtp) cc_final: 0.6826 (mtp) REVERT: D 2202 ILE cc_start: 0.9216 (mp) cc_final: 0.8940 (mm) REVERT: D 2306 GLN cc_start: 0.8320 (tt0) cc_final: 0.7604 (tp-100) REVERT: E 1216 TYR cc_start: 0.3949 (m-80) cc_final: 0.3196 (t80) REVERT: E 1293 GLN cc_start: 0.7827 (mp10) cc_final: 0.7356 (pt0) REVERT: E 1300 HIS cc_start: 0.3375 (OUTLIER) cc_final: 0.2915 (p-80) REVERT: E 1349 MET cc_start: 0.7836 (tmt) cc_final: 0.7336 (tmm) REVERT: E 1504 PHE cc_start: 0.8403 (t80) cc_final: 0.8148 (m-80) REVERT: E 1506 TRP cc_start: 0.7108 (m-10) cc_final: 0.6810 (m-10) REVERT: E 1519 TRP cc_start: 0.8726 (t60) cc_final: 0.8477 (t-100) REVERT: E 1971 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7688 (ptt90) REVERT: E 2031 MET cc_start: 0.7559 (mtp) cc_final: 0.6778 (mtp) REVERT: E 2065 LEU cc_start: 0.9474 (tp) cc_final: 0.9205 (tt) REVERT: E 2080 GLN cc_start: 0.7928 (tt0) cc_final: 0.7591 (tt0) REVERT: E 2264 ASP cc_start: 0.8737 (t70) cc_final: 0.8504 (t0) REVERT: E 2306 GLN cc_start: 0.8734 (tt0) cc_final: 0.8492 (tm-30) outliers start: 24 outliers final: 12 residues processed: 586 average time/residue: 0.1924 time to fit residues: 177.8937 Evaluate side-chains 346 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 332 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1699 HIS Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2020 PHE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1699 HIS Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 2020 PHE Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1699 HIS Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2020 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1247 GLN ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1344 GLN C1755 ASN C1789 GLN C2076 ASN C2503 HIS D1344 GLN D1755 ASN D1789 GLN ** D2080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2370 HIS D2503 HIS E1145 HIS E1225 ASN E1247 GLN E1344 GLN E1755 ASN E1789 GLN E2076 ASN ** E2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.099954 restraints weight = 82790.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.100508 restraints weight = 46765.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101133 restraints weight = 42044.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101274 restraints weight = 33837.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102243 restraints weight = 30713.872| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29949 Z= 0.158 Angle : 0.613 10.669 40230 Z= 0.316 Chirality : 0.042 0.253 4050 Planarity : 0.004 0.053 5310 Dihedral : 4.955 55.426 4330 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.95 % Favored : 91.67 % Rotamer: Outliers : 3.09 % Allowed : 14.75 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3939 helix: 1.84 (0.10), residues: 2595 sheet: 0.09 (0.36), residues: 255 loop : -2.75 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D2325 TYR 0.009 0.001 TYR E2256 PHE 0.030 0.002 PHE D2251 TRP 0.013 0.001 TRP C1244 HIS 0.006 0.001 HIS E2503 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (29946) covalent geometry : angle 0.61289 / 0.32 (40224) SS BOND : bond 0.00238 / 0.12 ( 3) SS BOND : angle 0.17915 / 0.09 ( 6) hydrogen bonds : bond 0.04561 / 3.31 ( 2050) hydrogen bonds : angle 4.67207 / 3.47 ( 6051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 341 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1168 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9246 (p) REVERT: C 1264 MET cc_start: 0.5468 (mpp) cc_final: 0.5167 (mpp) REVERT: C 1689 LEU cc_start: 0.8912 (mp) cc_final: 0.8590 (tt) REVERT: C 1757 TYR cc_start: 0.7978 (t80) cc_final: 0.7580 (t80) REVERT: C 1766 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8928 (mmmm) REVERT: C 1971 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7891 (ptt90) REVERT: C 2202 ILE cc_start: 0.9243 (mp) cc_final: 0.9039 (mm) REVERT: C 2296 ILE cc_start: 0.5420 (OUTLIER) cc_final: 0.5220 (mt) REVERT: C 2550 GLU cc_start: 0.7643 (mp0) cc_final: 0.7305 (mp0) REVERT: D 1495 MET cc_start: 0.5436 (ptp) cc_final: 0.4355 (mtp) REVERT: D 1531 SER cc_start: 0.8806 (t) cc_final: 0.8589 (p) REVERT: D 1757 TYR cc_start: 0.7986 (t80) cc_final: 0.7742 (t80) REVERT: D 1971 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8113 (pmt100) REVERT: D 2073 PHE cc_start: 0.7361 (t80) cc_final: 0.7095 (m-80) REVERT: D 2080 GLN cc_start: 0.7819 (tt0) cc_final: 0.7561 (tt0) REVERT: D 2202 ILE cc_start: 0.9262 (mp) cc_final: 0.9012 (mm) REVERT: D 2306 GLN cc_start: 0.8205 (tt0) cc_final: 0.7721 (tp-100) REVERT: E 1216 TYR cc_start: 0.4251 (m-80) cc_final: 0.3437 (t80) REVERT: E 1264 MET cc_start: 0.5305 (mpp) cc_final: 0.4841 (mpp) REVERT: E 1300 HIS cc_start: 0.3662 (OUTLIER) cc_final: 0.3400 (p-80) REVERT: E 1349 MET cc_start: 0.7803 (tmt) cc_final: 0.7248 (tmm) REVERT: E 1757 TYR cc_start: 0.8136 (t80) cc_final: 0.7701 (t80) REVERT: E 1971 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7873 (ptt90) REVERT: E 2025 LEU cc_start: 0.9272 (tp) cc_final: 0.9016 (mt) REVERT: E 2552 MET cc_start: 0.8089 (tpp) cc_final: 0.7770 (ttp) outliers start: 87 outliers final: 43 residues processed: 408 average time/residue: 0.1891 time to fit residues: 124.6165 Evaluate side-chains 351 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2081 LEU Chi-restraints excluded: chain C residue 2143 THR Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1242 PHE Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1296 ILE Chi-restraints excluded: chain D residue 1322 LEU Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2081 LEU Chi-restraints excluded: chain D residue 2143 THR Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2370 HIS Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2026 VAL Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 388 optimal weight: 0.4980 chunk 230 optimal weight: 8.9990 chunk 357 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 141 optimal weight: 50.0000 chunk 165 optimal weight: 10.0000 chunk 382 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1225 ASN ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1344 GLN C2080 GLN ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2347 ASN D1225 ASN D2080 GLN D2370 HIS E1344 GLN E1789 GLN E2245 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.120388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098293 restraints weight = 85269.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.097969 restraints weight = 51730.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098360 restraints weight = 54114.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099050 restraints weight = 38532.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099445 restraints weight = 33667.426| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29949 Z= 0.166 Angle : 0.606 9.762 40230 Z= 0.313 Chirality : 0.042 0.188 4050 Planarity : 0.004 0.055 5310 Dihedral : 4.843 54.629 4316 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.58 % Favored : 91.06 % Rotamer: Outliers : 4.01 % Allowed : 16.06 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.14), residues: 3939 helix: 2.06 (0.10), residues: 2565 sheet: 0.19 (0.37), residues: 249 loop : -2.71 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1521 TYR 0.012 0.001 TYR C2256 PHE 0.021 0.002 PHE C2544 TRP 0.017 0.001 TRP C1506 HIS 0.016 0.001 HIS D2370 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (29946) covalent geometry : angle 0.60577 / 0.31 (40224) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.15118 / 0.08 ( 6) hydrogen bonds : bond 0.04274 / 3.10 ( 2050) hydrogen bonds : angle 4.47645 / 3.33 ( 6051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 324 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1293 GLN cc_start: 0.8087 (mp10) cc_final: 0.7733 (mt0) REVERT: C 1757 TYR cc_start: 0.8070 (t80) cc_final: 0.7552 (t80) REVERT: C 1971 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7846 (ptt90) REVERT: C 2285 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7989 (mm-40) REVERT: C 2550 GLU cc_start: 0.7837 (mp0) cc_final: 0.6391 (mp0) REVERT: D 1495 MET cc_start: 0.5464 (ptp) cc_final: 0.4904 (mtm) REVERT: D 1508 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 1531 SER cc_start: 0.8839 (t) cc_final: 0.8607 (p) REVERT: D 1757 TYR cc_start: 0.8168 (t80) cc_final: 0.7836 (t80) REVERT: D 1971 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7985 (pmt100) REVERT: D 2202 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9052 (mm) REVERT: D 2306 GLN cc_start: 0.8310 (tt0) cc_final: 0.7844 (tp-100) REVERT: D 2550 GLU cc_start: 0.7756 (mp0) cc_final: 0.7352 (mp0) REVERT: E 1216 TYR cc_start: 0.4266 (m-80) cc_final: 0.3467 (t80) REVERT: E 1264 MET cc_start: 0.5209 (mpp) cc_final: 0.4970 (mpp) REVERT: E 1349 MET cc_start: 0.7862 (tmt) cc_final: 0.7222 (tmm) REVERT: E 1502 MET cc_start: 0.6989 (ppp) cc_final: 0.6504 (ppp) REVERT: E 1757 TYR cc_start: 0.8239 (t80) cc_final: 0.7734 (t80) REVERT: E 1774 LEU cc_start: 0.8152 (tp) cc_final: 0.7947 (tt) REVERT: E 1791 MET cc_start: 0.7988 (mmm) cc_final: 0.7785 (tpt) REVERT: E 1971 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8053 (ptt90) REVERT: E 2550 GLU cc_start: 0.7285 (mp0) cc_final: 0.6552 (mp0) outliers start: 113 outliers final: 57 residues processed: 406 average time/residue: 0.1767 time to fit residues: 118.5360 Evaluate side-chains 356 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1698 ASN Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2143 THR Chi-restraints excluded: chain C residue 2147 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2285 GLN Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2370 HIS Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1296 ILE Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1707 SER Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2202 ILE Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2394 GLU Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2026 VAL Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2394 GLU Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 394 optimal weight: 0.6980 chunk 369 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 chunk 15 optimal weight: 40.0000 chunk 116 optimal weight: 0.8980 chunk 206 optimal weight: 10.0000 chunk 171 optimal weight: 0.0980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2261 GLN C2306 GLN D1247 GLN E1344 GLN E2080 GLN ** E2261 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 = 0.3988 r_free = 0.3988 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099124 restraints weight = 85080.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099089 restraints weight = 51200.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099468 restraints weight = 53131.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100086 restraints weight = 38108.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100826 restraints weight = 33588.996| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29949 Z= 0.127 Angle : 0.579 9.443 40230 Z= 0.296 Chirality : 0.040 0.170 4050 Planarity : 0.004 0.054 5310 Dihedral : 4.714 59.946 4314 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.50 % Favored : 91.11 % Rotamer: Outliers : 3.72 % Allowed : 17.80 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.14), residues: 3939 helix: 2.21 (0.10), residues: 2562 sheet: 0.03 (0.36), residues: 249 loop : -2.65 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1294 TYR 0.018 0.001 TYR C2175 PHE 0.030 0.001 PHE C2251 TRP 0.020 0.001 TRP C1506 HIS 0.004 0.001 HIS C1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (29946) covalent geometry : angle 0.57949 / 0.30 (40224) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 0.33752 / 0.20 ( 6) hydrogen bonds : bond 0.03820 / 2.78 ( 2050) hydrogen bonds : angle 4.24917 / 3.17 ( 6051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 324 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1168 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9156 (p) REVERT: C 1293 GLN cc_start: 0.8033 (mp10) cc_final: 0.7746 (mt0) REVERT: C 1322 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 1502 MET cc_start: 0.7228 (ppp) cc_final: 0.6909 (ppp) REVERT: C 1508 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8328 (mt) REVERT: C 1971 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7935 (pmt100) REVERT: C 2285 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: C 2296 ILE cc_start: 0.5819 (OUTLIER) cc_final: 0.5463 (mt) REVERT: C 2550 GLU cc_start: 0.7627 (mp0) cc_final: 0.7310 (mp0) REVERT: D 1495 MET cc_start: 0.5546 (OUTLIER) cc_final: 0.4950 (mtm) REVERT: D 1508 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 1531 SER cc_start: 0.8945 (t) cc_final: 0.8717 (p) REVERT: D 1801 LEU cc_start: 0.9107 (tt) cc_final: 0.8770 (tp) REVERT: D 1971 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7789 (pmt100) REVERT: D 2023 MET cc_start: 0.8687 (ttp) cc_final: 0.8475 (ttm) REVERT: D 2072 MET cc_start: 0.6303 (ppp) cc_final: 0.5856 (ttt) REVERT: D 2117 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8437 (tp) REVERT: D 2202 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9020 (mm) REVERT: D 2306 GLN cc_start: 0.8315 (tt0) cc_final: 0.7885 (tp-100) REVERT: D 2550 GLU cc_start: 0.7642 (mp0) cc_final: 0.7424 (mp0) REVERT: E 1216 TYR cc_start: 0.4208 (m-80) cc_final: 0.3398 (t80) REVERT: E 1265 MET cc_start: 0.7086 (mmm) cc_final: 0.6749 (mpp) REVERT: E 1349 MET cc_start: 0.7907 (tmt) cc_final: 0.7262 (tmm) REVERT: E 1655 HIS cc_start: 0.6399 (t70) cc_final: 0.5952 (t70) REVERT: E 1757 TYR cc_start: 0.8269 (t80) cc_final: 0.7717 (t80) REVERT: E 1774 LEU cc_start: 0.8061 (tp) cc_final: 0.7830 (tt) REVERT: E 1971 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7893 (ptt90) outliers start: 105 outliers final: 56 residues processed: 403 average time/residue: 0.1741 time to fit residues: 116.9575 Evaluate side-chains 367 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1322 LEU Chi-restraints excluded: chain C residue 1508 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1698 ASN Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2285 GLN Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1247 GLN Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2039 LEU Chi-restraints excluded: chain D residue 2117 LEU Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2202 ILE Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2471 LEU Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1164 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2026 VAL Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2039 LEU Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2471 LEU Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 240 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 300 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 351 optimal weight: 0.6980 chunk 345 optimal weight: 1.9990 chunk 273 optimal weight: 50.0000 chunk 105 optimal weight: 0.9980 chunk 335 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1247 GLN E1344 GLN E2261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099393 restraints weight = 88305.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.099359 restraints weight = 55372.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099704 restraints weight = 56740.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100418 restraints weight = 40126.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100856 restraints weight = 34900.190| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29949 Z= 0.122 Angle : 0.578 9.457 40230 Z= 0.293 Chirality : 0.040 0.175 4050 Planarity : 0.004 0.053 5310 Dihedral : 4.579 56.321 4312 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.40 % Favored : 91.27 % Rotamer: Outliers : 4.15 % Allowed : 18.09 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 3939 helix: 2.23 (0.10), residues: 2571 sheet: 0.03 (0.36), residues: 255 loop : -2.62 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1294 TYR 0.011 0.001 TYR E2235 PHE 0.032 0.001 PHE D2073 TRP 0.014 0.001 TRP D1244 HIS 0.010 0.001 HIS E1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (29946) covalent geometry : angle 0.57799 / 0.29 (40224) SS BOND : bond 0.00260 / 0.13 ( 3) SS BOND : angle 0.57555 / 0.33 ( 6) hydrogen bonds : bond 0.03720 / 2.72 ( 2050) hydrogen bonds : angle 4.16804 / 3.11 ( 6051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 310 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1502 MET cc_start: 0.7518 (ppp) cc_final: 0.7166 (ppp) REVERT: C 1971 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7868 (pmt100) REVERT: C 2285 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: C 2550 GLU cc_start: 0.7695 (mp0) cc_final: 0.7428 (mp0) REVERT: D 1495 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5041 (mtm) REVERT: D 1502 MET cc_start: 0.6183 (ppp) cc_final: 0.5788 (ppp) REVERT: D 1508 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8370 (mt) REVERT: D 1531 SER cc_start: 0.8957 (t) cc_final: 0.8744 (p) REVERT: D 1971 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7773 (pmt100) REVERT: D 2072 MET cc_start: 0.5641 (ppp) cc_final: 0.5188 (ttt) REVERT: D 2073 PHE cc_start: 0.6847 (m-80) cc_final: 0.6383 (m-80) REVERT: D 2117 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8341 (tp) REVERT: D 2202 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.9029 (mm) REVERT: D 2306 GLN cc_start: 0.8324 (tt0) cc_final: 0.7906 (tp-100) REVERT: D 2550 GLU cc_start: 0.7543 (mp0) cc_final: 0.7203 (mp0) REVERT: E 1216 TYR cc_start: 0.4095 (m-80) cc_final: 0.3289 (t80) REVERT: E 1262 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6963 (tmtt) REVERT: E 1265 MET cc_start: 0.7090 (mmm) cc_final: 0.6768 (mpp) REVERT: E 1349 MET cc_start: 0.7929 (tmt) cc_final: 0.7322 (tmm) REVERT: E 1508 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8156 (mt) REVERT: E 1530 MET cc_start: 0.8421 (tpp) cc_final: 0.8162 (tpp) REVERT: E 1757 TYR cc_start: 0.8278 (t80) cc_final: 0.7726 (t80) REVERT: E 1774 LEU cc_start: 0.8058 (tp) cc_final: 0.7824 (tt) REVERT: E 1971 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7916 (ptt90) REVERT: E 2550 GLU cc_start: 0.7254 (mp0) cc_final: 0.6660 (mp0) outliers start: 117 outliers final: 64 residues processed: 394 average time/residue: 0.1737 time to fit residues: 114.2907 Evaluate side-chains 368 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 294 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1184 TYR Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1221 ILE Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2285 GLN Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2370 HIS Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1191 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2117 LEU Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2202 ILE Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2471 LEU Chi-restraints excluded: chain D residue 2506 MET Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1262 LYS Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1508 LEU Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2026 VAL Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2471 LEU Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 271 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 225 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 349 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1344 GLN C2261 GLN ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1344 GLN ** E2261 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.120670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098462 restraints weight = 87953.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.098418 restraints weight = 55519.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098760 restraints weight = 56774.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099382 restraints weight = 40377.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099897 restraints weight = 35599.506| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29949 Z= 0.133 Angle : 0.583 10.010 40230 Z= 0.296 Chirality : 0.040 0.190 4050 Planarity : 0.004 0.053 5310 Dihedral : 4.554 56.156 4312 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.61 % Favored : 91.04 % Rotamer: Outliers : 3.62 % Allowed : 18.76 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3939 helix: 2.30 (0.10), residues: 2553 sheet: -0.04 (0.36), residues: 255 loop : -2.50 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1294 TYR 0.012 0.001 TYR D2477 PHE 0.053 0.001 PHE D2251 TRP 0.015 0.001 TRP D1244 HIS 0.005 0.001 HIS E1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (29946) covalent geometry : angle 0.58253 / 0.30 (40224) SS BOND : bond 0.00213 / 0.11 ( 3) SS BOND : angle 0.41004 / 0.25 ( 6) hydrogen bonds : bond 0.03713 / 2.70 ( 2050) hydrogen bonds : angle 4.16575 / 3.11 ( 6051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 305 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1502 MET cc_start: 0.7569 (ppp) cc_final: 0.7310 (ppp) REVERT: C 1971 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7958 (pmt100) REVERT: C 2285 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7837 (mm-40) REVERT: D 1495 MET cc_start: 0.5617 (ptp) cc_final: 0.5006 (mtm) REVERT: D 1508 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8397 (mt) REVERT: D 1531 SER cc_start: 0.8966 (t) cc_final: 0.8754 (p) REVERT: D 1971 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7810 (pmt100) REVERT: D 2073 PHE cc_start: 0.7025 (m-80) cc_final: 0.6490 (m-10) REVERT: D 2306 GLN cc_start: 0.8449 (tt0) cc_final: 0.8018 (tp-100) REVERT: D 2550 GLU cc_start: 0.7566 (mp0) cc_final: 0.7337 (mp0) REVERT: E 1216 TYR cc_start: 0.4121 (m-80) cc_final: 0.3320 (t80) REVERT: E 1262 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6976 (tmtt) REVERT: E 1265 MET cc_start: 0.7052 (mmm) cc_final: 0.6807 (mpp) REVERT: E 1349 MET cc_start: 0.7897 (tmt) cc_final: 0.7283 (tmm) REVERT: E 1502 MET cc_start: 0.6936 (ppp) cc_final: 0.6378 (ppp) REVERT: E 1530 MET cc_start: 0.8454 (tpp) cc_final: 0.8159 (tpp) REVERT: E 1757 TYR cc_start: 0.8328 (t80) cc_final: 0.7798 (t80) REVERT: E 1971 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7944 (pmt100) REVERT: E 2296 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5126 (mt) outliers start: 102 outliers final: 73 residues processed: 376 average time/residue: 0.1739 time to fit residues: 108.7694 Evaluate side-chains 367 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2285 GLN Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2370 HIS Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2445 ILE Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1776 LEU Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 1993 PHE Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2240 THR Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2471 LEU Chi-restraints excluded: chain D residue 2506 MET Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1262 LYS Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1315 GLN Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2026 VAL Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2296 ILE Chi-restraints excluded: chain E residue 2297 SER Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2394 GLU Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2471 LEU Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 382 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 4 optimal weight: 40.0000 chunk 365 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1344 GLN C2261 GLN ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1344 GLN E2261 GLN E2306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.120877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098735 restraints weight = 87672.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.098727 restraints weight = 54602.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.099153 restraints weight = 55073.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099680 restraints weight = 39849.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.100272 restraints weight = 35505.477| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29949 Z= 0.124 Angle : 0.588 10.566 40230 Z= 0.296 Chirality : 0.040 0.159 4050 Planarity : 0.004 0.054 5310 Dihedral : 4.515 56.940 4312 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.43 % Favored : 91.24 % Rotamer: Outliers : 3.76 % Allowed : 19.26 % Favored : 76.99 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.14), residues: 3939 helix: 2.34 (0.10), residues: 2535 sheet: -0.07 (0.36), residues: 255 loop : -2.37 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1294 TYR 0.012 0.001 TYR C2477 PHE 0.026 0.001 PHE C2251 TRP 0.016 0.001 TRP D1244 HIS 0.007 0.001 HIS C1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (29946) covalent geometry : angle 0.58808 / 0.30 (40224) SS BOND : bond 0.00192 / 0.10 ( 3) SS BOND : angle 0.44932 / 0.27 ( 6) hydrogen bonds : bond 0.03618 / 2.63 ( 2050) hydrogen bonds : angle 4.12001 / 3.08 ( 6051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 296 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1502 MET cc_start: 0.7677 (ppp) cc_final: 0.7418 (ppp) REVERT: C 1971 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7985 (pmt100) REVERT: C 2285 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: C 2550 GLU cc_start: 0.7518 (mp0) cc_final: 0.7312 (mp0) REVERT: D 1495 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.4951 (mtm) REVERT: D 1502 MET cc_start: 0.6234 (ppp) cc_final: 0.5953 (ppp) REVERT: D 1508 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8385 (mt) REVERT: D 1531 SER cc_start: 0.8964 (t) cc_final: 0.8753 (p) REVERT: D 1971 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7819 (pmt100) REVERT: D 2285 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7656 (mm-40) REVERT: D 2306 GLN cc_start: 0.8433 (tt0) cc_final: 0.8011 (tp-100) REVERT: E 1168 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9097 (p) REVERT: E 1265 MET cc_start: 0.7156 (mmm) cc_final: 0.6882 (mpp) REVERT: E 1349 MET cc_start: 0.7893 (tmt) cc_final: 0.7294 (tmm) REVERT: E 1508 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8123 (mt) REVERT: E 1757 TYR cc_start: 0.8347 (t80) cc_final: 0.7802 (t80) REVERT: E 1971 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7955 (pmt100) REVERT: E 2296 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5320 (mt) REVERT: E 2550 GLU cc_start: 0.7484 (mp0) cc_final: 0.7256 (mp0) outliers start: 106 outliers final: 67 residues processed: 374 average time/residue: 0.1705 time to fit residues: 106.2453 Evaluate side-chains 361 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 284 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2238 LEU Chi-restraints excluded: chain C residue 2261 GLN Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2285 GLN Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2370 HIS Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1221 ILE Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 1993 PHE Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2207 LEU Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2240 THR Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2285 GLN Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2471 LEU Chi-restraints excluded: chain D residue 2477 TYR Chi-restraints excluded: chain D residue 2506 MET Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1508 LEU Chi-restraints excluded: chain E residue 1534 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2296 ILE Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1344 GLN ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1344 GLN E2245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.119713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.097452 restraints weight = 88042.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097499 restraints weight = 55446.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.097873 restraints weight = 55506.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.098343 restraints weight = 40695.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.099207 restraints weight = 36368.403| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29949 Z= 0.146 Angle : 0.613 11.239 40230 Z= 0.308 Chirality : 0.041 0.228 4050 Planarity : 0.004 0.060 5310 Dihedral : 4.568 56.617 4312 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.50 % Favored : 91.17 % Rotamer: Outliers : 3.44 % Allowed : 19.75 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3939 helix: 2.39 (0.11), residues: 2517 sheet: -0.08 (0.35), residues: 255 loop : -2.34 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1294 TYR 0.016 0.001 TYR D1160 PHE 0.053 0.001 PHE D2251 TRP 0.016 0.001 TRP D1244 HIS 0.007 0.001 HIS C1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (29946) covalent geometry : angle 0.61275 / 0.31 (40224) SS BOND : bond 0.00199 / 0.10 ( 3) SS BOND : angle 0.44099 / 0.27 ( 6) hydrogen bonds : bond 0.03796 / 2.75 ( 2050) hydrogen bonds : angle 4.15661 / 3.10 ( 6051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 297 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1210 TRP cc_start: 0.7786 (m-90) cc_final: 0.7526 (m100) REVERT: C 1502 MET cc_start: 0.7666 (ppp) cc_final: 0.7357 (ppp) REVERT: C 1971 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8004 (pmt100) REVERT: C 2148 SER cc_start: 0.6986 (m) cc_final: 0.6712 (p) REVERT: C 2550 GLU cc_start: 0.7712 (mp0) cc_final: 0.7302 (mp0) REVERT: D 1495 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.4953 (mtm) REVERT: D 1502 MET cc_start: 0.6253 (ppp) cc_final: 0.5948 (ppp) REVERT: D 1508 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8382 (mt) REVERT: D 1531 SER cc_start: 0.8973 (t) cc_final: 0.8763 (p) REVERT: D 1656 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7635 (mp) REVERT: D 1971 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7909 (pmt100) REVERT: D 2285 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7689 (mm-40) REVERT: D 2306 GLN cc_start: 0.8466 (tt0) cc_final: 0.8127 (tm-30) REVERT: D 2488 LEU cc_start: 0.8987 (tt) cc_final: 0.8460 (mt) REVERT: D 2550 GLU cc_start: 0.7411 (mp0) cc_final: 0.7013 (mp0) REVERT: E 1168 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9091 (p) REVERT: E 1265 MET cc_start: 0.6836 (mmm) cc_final: 0.6620 (mpp) REVERT: E 1349 MET cc_start: 0.7883 (tmt) cc_final: 0.7285 (tmm) REVERT: E 1502 MET cc_start: 0.6869 (ppp) cc_final: 0.6337 (ppp) REVERT: E 1508 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8151 (mt) REVERT: E 1774 LEU cc_start: 0.8230 (tp) cc_final: 0.8029 (tt) REVERT: E 1971 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8035 (pmt100) REVERT: E 2536 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7983 (tp30) outliers start: 97 outliers final: 78 residues processed: 364 average time/residue: 0.1715 time to fit residues: 103.6843 Evaluate side-chains 372 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 285 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1296 ILE Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 1971 ARG Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2238 LEU Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2370 HIS Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1184 TYR Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1221 ILE Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1280 ILE Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1656 ILE Chi-restraints excluded: chain D residue 1689 LEU Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1776 LEU Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 1993 PHE Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2061 MET Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2207 LEU Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2240 THR Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2285 GLN Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2336 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2477 TYR Chi-restraints excluded: chain D residue 2506 MET Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1508 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1689 LEU Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2296 ILE Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2394 GLU Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 390 optimal weight: 0.0370 chunk 269 optimal weight: 50.0000 chunk 327 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 347 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 278 optimal weight: 40.0000 chunk 368 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1304 HIS D2118 ASN E1344 GLN E2245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.118760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092522 restraints weight = 87940.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093144 restraints weight = 60114.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094310 restraints weight = 44672.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094411 restraints weight = 40494.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094502 restraints weight = 36569.410| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29949 Z= 0.159 Angle : 0.636 11.635 40230 Z= 0.321 Chirality : 0.042 0.230 4050 Planarity : 0.004 0.064 5310 Dihedral : 4.657 56.812 4312 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.91 % Favored : 90.73 % Rotamer: Outliers : 3.30 % Allowed : 19.86 % Favored : 76.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.14), residues: 3939 helix: 2.34 (0.11), residues: 2520 sheet: -0.10 (0.35), residues: 255 loop : -2.38 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1294 TYR 0.029 0.001 TYR E2256 PHE 0.031 0.001 PHE C2251 TRP 0.018 0.001 TRP D1244 HIS 0.006 0.001 HIS D1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (29946) covalent geometry : angle 0.63611 / 0.32 (40224) SS BOND : bond 0.00207 / 0.10 ( 3) SS BOND : angle 0.44003 / 0.28 ( 6) hydrogen bonds : bond 0.03984 / 2.89 ( 2050) hydrogen bonds : angle 4.21954 / 3.15 ( 6051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 290 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1210 TRP cc_start: 0.7942 (m-90) cc_final: 0.7643 (m100) REVERT: C 1502 MET cc_start: 0.7730 (ppp) cc_final: 0.7454 (ppp) REVERT: C 2189 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7822 (t80) REVERT: C 2550 GLU cc_start: 0.7952 (mp0) cc_final: 0.7126 (mp0) REVERT: D 1495 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.4963 (mtm) REVERT: D 1502 MET cc_start: 0.6404 (ppp) cc_final: 0.6139 (ppp) REVERT: D 1508 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8437 (mt) REVERT: D 1531 SER cc_start: 0.8998 (t) cc_final: 0.8771 (p) REVERT: D 1656 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7629 (mp) REVERT: D 1971 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8090 (pmt100) REVERT: D 2285 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7725 (mm-40) REVERT: D 2306 GLN cc_start: 0.8483 (tt0) cc_final: 0.8201 (tm-30) REVERT: D 2477 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4489 (t80) REVERT: D 2550 GLU cc_start: 0.7930 (mp0) cc_final: 0.7707 (mp0) REVERT: E 1168 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9115 (p) REVERT: E 1265 MET cc_start: 0.6835 (mmm) cc_final: 0.6569 (mpp) REVERT: E 1349 MET cc_start: 0.7952 (tmt) cc_final: 0.7305 (tmm) REVERT: E 1502 MET cc_start: 0.6882 (ppp) cc_final: 0.6422 (ppp) REVERT: E 1508 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8220 (mt) REVERT: E 1652 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.5197 (mpp-170) REVERT: E 1971 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8078 (pmt100) REVERT: E 2536 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8073 (tp30) REVERT: E 2550 GLU cc_start: 0.7637 (mp0) cc_final: 0.7216 (mp0) outliers start: 93 outliers final: 70 residues processed: 354 average time/residue: 0.1661 time to fit residues: 97.8494 Evaluate side-chains 360 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 279 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1258 TYR Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 2026 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2039 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2189 TYR Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2296 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1280 ILE Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1656 ILE Chi-restraints excluded: chain D residue 1689 LEU Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2061 MET Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2207 LEU Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2240 THR Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2285 GLN Chi-restraints excluded: chain D residue 2332 THR Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2477 TYR Chi-restraints excluded: chain D residue 2506 MET Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1508 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1652 ARG Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1683 VAL Chi-restraints excluded: chain E residue 1689 LEU Chi-restraints excluded: chain E residue 1749 PHE Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2296 ILE Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2394 GLU Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 25 optimal weight: 20.0000 chunk 293 optimal weight: 0.0970 chunk 208 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 277 optimal weight: 0.1980 chunk 237 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 3 optimal weight: 50.0000 chunk 310 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 GLN E1344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.119530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.097166 restraints weight = 86497.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097161 restraints weight = 52213.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097420 restraints weight = 56745.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.098177 restraints weight = 39617.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.098771 restraints weight = 34375.763| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29949 Z= 0.124 Angle : 0.621 12.528 40230 Z= 0.309 Chirality : 0.041 0.216 4050 Planarity : 0.004 0.065 5310 Dihedral : 4.550 59.742 4308 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.33 % Favored : 91.34 % Rotamer: Outliers : 2.62 % Allowed : 20.46 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.14), residues: 3939 helix: 2.36 (0.11), residues: 2529 sheet: -0.12 (0.35), residues: 255 loop : -2.31 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1294 TYR 0.014 0.001 TYR E2256 PHE 0.050 0.001 PHE D2251 TRP 0.024 0.001 TRP C1244 HIS 0.005 0.001 HIS E1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (29946) covalent geometry : angle 0.62143 / 0.31 (40224) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 0.48052 / 0.30 ( 6) hydrogen bonds : bond 0.03648 / 2.65 ( 2050) hydrogen bonds : angle 4.09946 / 3.06 ( 6051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7878 Ramachandran restraints generated. 3939 Oldfield, 0 Emsley, 3939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1502 MET cc_start: 0.7689 (ppp) cc_final: 0.7387 (ppp) REVERT: D 1495 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.4973 (mtm) REVERT: D 1502 MET cc_start: 0.6400 (ppp) cc_final: 0.6095 (ppp) REVERT: D 1508 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8350 (mt) REVERT: D 1531 SER cc_start: 0.8969 (t) cc_final: 0.8759 (p) REVERT: D 1656 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7765 (mp) REVERT: D 1971 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8009 (pmt100) REVERT: D 2285 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7710 (mm-40) REVERT: D 2306 GLN cc_start: 0.8484 (tt0) cc_final: 0.8199 (tm-30) REVERT: D 2477 TYR cc_start: 0.5052 (OUTLIER) cc_final: 0.4002 (t80) REVERT: E 1168 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.9069 (p) REVERT: E 1265 MET cc_start: 0.6849 (mmm) cc_final: 0.6624 (mpp) REVERT: E 1349 MET cc_start: 0.7914 (tmt) cc_final: 0.7293 (tmm) REVERT: E 1502 MET cc_start: 0.6867 (ppp) cc_final: 0.6346 (ppp) REVERT: E 1508 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8375 (pp) REVERT: E 1971 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7934 (pmt100) outliers start: 74 outliers final: 57 residues processed: 351 average time/residue: 0.1719 time to fit residues: 100.1237 Evaluate side-chains 344 residues out of total 3588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain C residue 1300 HIS Chi-restraints excluded: chain C residue 1506 TRP Chi-restraints excluded: chain C residue 1534 LEU Chi-restraints excluded: chain C residue 1665 PHE Chi-restraints excluded: chain C residue 1683 VAL Chi-restraints excluded: chain C residue 1712 VAL Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2217 VAL Chi-restraints excluded: chain C residue 2268 LEU Chi-restraints excluded: chain C residue 2410 VAL Chi-restraints excluded: chain C residue 2477 TYR Chi-restraints excluded: chain C residue 2532 LEU Chi-restraints excluded: chain C residue 2543 ILE Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1258 TYR Chi-restraints excluded: chain D residue 1495 MET Chi-restraints excluded: chain D residue 1506 TRP Chi-restraints excluded: chain D residue 1508 LEU Chi-restraints excluded: chain D residue 1656 ILE Chi-restraints excluded: chain D residue 1712 VAL Chi-restraints excluded: chain D residue 1971 ARG Chi-restraints excluded: chain D residue 1979 LEU Chi-restraints excluded: chain D residue 1993 PHE Chi-restraints excluded: chain D residue 2026 VAL Chi-restraints excluded: chain D residue 2031 MET Chi-restraints excluded: chain D residue 2061 MET Chi-restraints excluded: chain D residue 2174 LYS Chi-restraints excluded: chain D residue 2207 LEU Chi-restraints excluded: chain D residue 2208 LEU Chi-restraints excluded: chain D residue 2217 VAL Chi-restraints excluded: chain D residue 2240 THR Chi-restraints excluded: chain D residue 2261 GLN Chi-restraints excluded: chain D residue 2268 LEU Chi-restraints excluded: chain D residue 2285 GLN Chi-restraints excluded: chain D residue 2410 VAL Chi-restraints excluded: chain D residue 2477 TYR Chi-restraints excluded: chain D residue 2532 LEU Chi-restraints excluded: chain D residue 2543 ILE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain E residue 1186 LEU Chi-restraints excluded: chain E residue 1207 LEU Chi-restraints excluded: chain E residue 1250 SER Chi-restraints excluded: chain E residue 1258 TYR Chi-restraints excluded: chain E residue 1300 HIS Chi-restraints excluded: chain E residue 1508 LEU Chi-restraints excluded: chain E residue 1540 LEU Chi-restraints excluded: chain E residue 1665 PHE Chi-restraints excluded: chain E residue 1689 LEU Chi-restraints excluded: chain E residue 1749 PHE Chi-restraints excluded: chain E residue 1776 LEU Chi-restraints excluded: chain E residue 1971 ARG Chi-restraints excluded: chain E residue 2031 MET Chi-restraints excluded: chain E residue 2054 VAL Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2217 VAL Chi-restraints excluded: chain E residue 2332 THR Chi-restraints excluded: chain E residue 2370 HIS Chi-restraints excluded: chain E residue 2410 VAL Chi-restraints excluded: chain E residue 2506 MET Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2543 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 355 optimal weight: 3.9990 chunk 268 optimal weight: 40.0000 chunk 359 optimal weight: 0.6980 chunk 314 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1344 GLN ** C2261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN ** D1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2261 GLN E1344 GLN E2096 GLN ** E2261 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 = 0.3917 r_free = 0.3917 target = 0.116683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088181 restraints weight = 88429.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091494 restraints weight = 48866.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091694 restraints weight = 31445.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092259 restraints weight = 28826.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092445 restraints weight = 27770.143| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29949 Z= 0.225 Angle : 0.712 12.235 40230 Z= 0.361 Chirality : 0.044 0.327 4050 Planarity : 0.004 0.070 5310 Dihedral : 4.740 41.808 4306 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.24 % Favored : 90.40 % Rotamer: Outliers : 2.84 % Allowed : 20.53 % Favored : 76.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.14), residues: 3939 helix: 2.21 (0.11), residues: 2535 sheet: -0.14 (0.35), residues: 255 loop : -2.39 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1294 TYR 0.050 0.002 TYR D2256 PHE 0.031 0.002 PHE C2251 TRP 0.019 0.001 TRP C1244 HIS 0.009 0.001 HIS D1699 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (29946) covalent geometry : angle 0.71241 / 0.36 (40224) SS BOND : bond 0.00210 / 0.11 ( 3) SS BOND : angle 0.45916 / 0.28 ( 6) hydrogen bonds : bond 0.04397 / 3.19 ( 2050) hydrogen bonds : angle 4.39463 / 3.27 ( 6051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5270.33 seconds wall clock time: 91 minutes 42.42 seconds (5502.42 seconds total)