Starting phenix.real_space_refine on Wed May 6 05:44:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vef_65006/05_2026/9vef_65006.map" } resolution = 3.75 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= 0.015 sd= 0.051 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 255 5.16 5 C 22977 2.51 5 N 5619 2.21 5 O 6006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34857 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 11465 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1339} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 154 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Restraints were copied for chains: C, E, D, F Time building chain proxies: 14.39, per 1000 atoms: 0.41 Number of scatterers: 34857 At special positions: 0 Unit cell: (195.175, 206.78, 152.975, 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 255 16.00 O 6006 8.00 N 5619 7.00 C 22977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1379 " - pdb=" SG CYS A1403 " distance=2.03 Simple disulfide: pdb=" SG CYS C1368 " - pdb=" SG CYS C1389 " distance=2.03 Simple disulfide: pdb=" SG CYS E1368 " - pdb=" SG CYS E1389 " distance=2.03 Simple disulfide: pdb=" SG CYS C1379 " - pdb=" SG CYS C1403 " distance=2.03 Simple disulfide: pdb=" SG CYS E1379 " - pdb=" SG CYS E1403 " 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 seconds 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8172 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 9 sheets defined 63.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 917 through 957 removed outlier: 3.536A pdb=" N PHE A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 978 through 1000 removed outlier: 4.244A pdb=" N SER A 984 " --> pdb=" O ARG A 980 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.870A pdb=" N GLN A1021 " --> pdb=" O ASN A1018 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1022 " --> pdb=" O GLU A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1022' Processing helix chain 'A' and resid 1040 through 1046 removed outlier: 3.695A pdb=" N TRP A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1061 through 1083 removed outlier: 4.072A pdb=" N PHE A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 3.999A pdb=" N ASP A1104 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 4.072A pdb=" N LYS A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1139 removed outlier: 3.716A pdb=" N CYS A1127 " --> pdb=" O GLY A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1156 removed outlier: 3.812A pdb=" N ARG A1156 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1164 removed outlier: 3.526A pdb=" N GLU A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1186 Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1205 through 1213 Processing helix chain 'A' and resid 1224 through 1244 removed outlier: 3.607A pdb=" N TYR A1228 " --> pdb=" O VAL A1224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP A1229 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1255 Processing helix chain 'A' and resid 1284 through 1295 Processing helix chain 'A' and resid 1297 through 1312 removed outlier: 4.730A pdb=" N THR A1303 " --> pdb=" O TRP A1299 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1335 removed outlier: 3.826A pdb=" N TYR A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP A1333 " --> pdb=" O LEU A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1369 removed outlier: 4.093A pdb=" N ILE A1342 " --> pdb=" O PRO A1338 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A1365 " --> pdb=" O ASN A1361 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1375 Processing helix chain 'A' and resid 1378 through 1386 removed outlier: 3.510A pdb=" N ILE A1382 " --> pdb=" O SER A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1430 removed outlier: 3.561A pdb=" N CYS A1418 " --> pdb=" O TRP A1414 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE A1419 " --> pdb=" O ASP A1415 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A1430 " --> pdb=" O ARG A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1498 removed outlier: 3.594A pdb=" N LEU A1435 " --> pdb=" O SER A1431 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU A1496 " --> pdb=" O LYS A1492 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1548 Processing helix chain 'A' and resid 1651 through 1693 removed outlier: 3.512A pdb=" N LEU A1655 " --> pdb=" O PHE A1651 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A1661 " --> pdb=" O LEU A1657 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A1662 " --> pdb=" O ALA A1658 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS A1674 " --> pdb=" O ILE A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1716 Processing helix chain 'A' and resid 1879 through 1886 Processing helix chain 'A' and resid 1891 through 1903 removed outlier: 3.701A pdb=" N GLU A1895 " --> pdb=" O ASP A1891 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A1898 " --> pdb=" O LEU A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1905 through 1921 Processing helix chain 'A' and resid 1921 through 1938 Processing helix chain 'A' and resid 1940 through 1943 Processing helix chain 'A' and resid 1944 through 1953 removed outlier: 3.652A pdb=" N LEU A1948 " --> pdb=" O LEU A1944 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1951 " --> pdb=" O ILE A1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1983 removed outlier: 3.611A pdb=" N TRP A1965 " --> pdb=" O SER A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2007 removed outlier: 4.355A pdb=" N ILE A2007 " --> pdb=" O PRO A2003 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2003 through 2007' Processing helix chain 'A' and resid 2016 through 2036 removed outlier: 4.073A pdb=" N GLN A2022 " --> pdb=" O TYR A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2180 Processing helix chain 'A' and resid 2190 through 2206 removed outlier: 4.662A pdb=" N ASP A2200 " --> pdb=" O ALA A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2231 through 2253 removed outlier: 3.886A pdb=" N VAL A2235 " --> pdb=" O GLY A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2274 Processing helix chain 'A' and resid 2277 through 2282 Processing helix chain 'A' and resid 2289 through 2312 removed outlier: 3.621A pdb=" N TRP A2295 " --> pdb=" O VAL A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2328 through 2341 removed outlier: 3.953A pdb=" N VAL A2341 " --> pdb=" O GLY A2337 " (cutoff:3.500A) Processing helix chain 'A' and resid 2344 through 2355 Processing helix chain 'A' and resid 2361 through 2388 Processing helix chain 'A' and resid 2397 through 2426 removed outlier: 3.596A pdb=" N LYS A2401 " --> pdb=" O LYS A2397 " (cutoff:3.500A) Proline residue: A2419 - end of helix Processing helix chain 'A' and resid 2479 through 2484 Processing helix chain 'A' and resid 2510 through 2522 Processing helix chain 'A' and resid 2560 through 2571 removed outlier: 4.082A pdb=" N ALA A2566 " --> pdb=" O ARG A2562 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A2571 " --> pdb=" O LYS A2567 " (cutoff:3.500A) Processing helix chain 'A' and resid 2575 through 2579 Processing helix chain 'A' and resid 2669 through 2689 Processing helix chain 'A' and resid 2690 through 2694 removed outlier: 3.718A pdb=" N SER A2693 " --> pdb=" O SER A2690 " (cutoff:3.500A) Processing helix chain 'A' and resid 2705 through 2721 removed outlier: 3.788A pdb=" N GLY A2721 " --> pdb=" O VAL A2717 " (cutoff:3.500A) Processing helix chain 'A' and resid 2724 through 2738 Processing helix chain 'A' and resid 2742 through 2746 removed outlier: 3.532A pdb=" N TRP A2746 " --> pdb=" O MET A2743 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.650A pdb=" N CYS B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 957 removed outlier: 3.536A pdb=" N PHE C 923 " --> pdb=" O LEU C 919 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP C 936 " --> pdb=" O VAL C 932 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE C 943 " --> pdb=" O GLU C 939 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 978 through 1000 removed outlier: 4.244A pdb=" N SER C 984 " --> pdb=" O ARG C 980 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP C 989 " --> pdb=" O VAL C 985 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1022 removed outlier: 3.871A pdb=" N GLN C1021 " --> pdb=" O ASN C1018 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C1022 " --> pdb=" O GLU C1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1018 through 1022' Processing helix chain 'C' and resid 1040 through 1046 removed outlier: 3.696A pdb=" N TRP C1044 " --> pdb=" O ASP C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1056 Processing helix chain 'C' and resid 1061 through 1083 removed outlier: 4.073A pdb=" N PHE C1069 " --> pdb=" O ALA C1065 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU C1078 " --> pdb=" O TYR C1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1104 removed outlier: 3.999A pdb=" N ASP C1104 " --> pdb=" O ARG C1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1118 removed outlier: 4.071A pdb=" N LYS C1112 " --> pdb=" O ILE C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1139 removed outlier: 3.715A pdb=" N CYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1156 removed outlier: 3.812A pdb=" N ARG C1156 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1164 removed outlier: 3.525A pdb=" N GLU C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1186 Processing helix chain 'C' and resid 1195 through 1199 Processing helix chain 'C' and resid 1205 through 1213 Processing helix chain 'C' and resid 1224 through 1244 removed outlier: 3.607A pdb=" N TYR C1228 " --> pdb=" O VAL C1224 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C1229 " --> pdb=" O PHE C1225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C1230 " --> pdb=" O LEU C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1255 Processing helix chain 'C' and resid 1284 through 1295 Processing helix chain 'C' and resid 1297 through 1312 removed outlier: 4.730A pdb=" N THR C1303 " --> pdb=" O TRP C1299 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C1312 " --> pdb=" O THR C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1335 removed outlier: 3.827A pdb=" N TYR C1320 " --> pdb=" O PHE C1316 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY C1332 " --> pdb=" O LEU C1328 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASP C1333 " --> pdb=" O LEU C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1369 removed outlier: 4.092A pdb=" N ILE C1342 " --> pdb=" O PRO C1338 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C1365 " --> pdb=" O ASN C1361 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C1366 " --> pdb=" O ILE C1362 " (cutoff:3.500A) Processing helix chain 'C' and resid 1370 through 1375 Processing helix chain 'C' and resid 1378 through 1386 removed outlier: 3.512A pdb=" N ILE C1382 " --> pdb=" O SER C1378 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1430 removed outlier: 3.561A pdb=" N CYS C1418 " --> pdb=" O TRP C1414 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE C1419 " --> pdb=" O ASP C1415 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET C1430 " --> pdb=" O ARG C1426 " (cutoff:3.500A) Processing helix chain 'C' and resid 1431 through 1498 removed outlier: 3.593A pdb=" N LEU C1435 " --> pdb=" O SER C1431 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU C1496 " --> pdb=" O LYS C1492 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG C1497 " --> pdb=" O LYS C1493 " (cutoff:3.500A) Processing helix chain 'C' and resid 1544 through 1548 Processing helix chain 'C' and resid 1651 through 1693 removed outlier: 3.512A pdb=" N LEU C1655 " --> pdb=" O PHE C1651 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C1661 " --> pdb=" O LEU C1657 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER C1662 " --> pdb=" O ALA C1658 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU C1673 " --> pdb=" O SER C1669 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS C1674 " --> pdb=" O ILE C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1699 through 1716 Processing helix chain 'C' and resid 1879 through 1886 Processing helix chain 'C' and resid 1891 through 1903 removed outlier: 3.702A pdb=" N GLU C1895 " --> pdb=" O ASP C1891 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C1898 " --> pdb=" O LEU C1894 " (cutoff:3.500A) Processing helix chain 'C' and resid 1905 through 1921 Processing helix chain 'C' and resid 1921 through 1938 Processing helix chain 'C' and resid 1940 through 1943 Processing helix chain 'C' and resid 1944 through 1953 removed outlier: 3.652A pdb=" N LEU C1948 " --> pdb=" O LEU C1944 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C1951 " --> pdb=" O ILE C1947 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1983 removed outlier: 3.613A pdb=" N TRP C1965 " --> pdb=" O SER C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 2016 through 2036 removed outlier: 4.074A pdb=" N GLN C2022 " --> pdb=" O TYR C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2180 Processing helix chain 'C' and resid 2190 through 2206 removed outlier: 4.662A pdb=" N ASP C2200 " --> pdb=" O ALA C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2231 through 2253 removed outlier: 3.886A pdb=" N VAL C2235 " --> pdb=" O GLY C2231 " (cutoff:3.500A) Processing helix chain 'C' and resid 2255 through 2274 Processing helix chain 'C' and resid 2277 through 2282 Processing helix chain 'C' and resid 2289 through 2312 removed outlier: 3.621A pdb=" N TRP C2295 " --> pdb=" O VAL C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2328 through 2341 removed outlier: 3.953A pdb=" N VAL C2341 " --> pdb=" O GLY C2337 " (cutoff:3.500A) Processing helix chain 'C' and resid 2344 through 2355 Processing helix chain 'C' and resid 2361 through 2388 Processing helix chain 'C' and resid 2397 through 2426 removed outlier: 3.595A pdb=" N LYS C2401 " --> pdb=" O LYS C2397 " (cutoff:3.500A) Proline residue: C2419 - end of helix Processing helix chain 'C' and resid 2479 through 2484 Processing helix chain 'C' and resid 2510 through 2522 Processing helix chain 'C' and resid 2560 through 2571 removed outlier: 4.082A pdb=" N ALA C2566 " --> pdb=" O ARG C2562 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C2571 " --> pdb=" O LYS C2567 " (cutoff:3.500A) Processing helix chain 'C' and resid 2575 through 2579 Processing helix chain 'C' and resid 2669 through 2689 Processing helix chain 'C' and resid 2690 through 2694 removed outlier: 3.717A pdb=" N SER C2693 " --> pdb=" O SER C2690 " (cutoff:3.500A) Processing helix chain 'C' and resid 2705 through 2721 removed outlier: 3.789A pdb=" N GLY C2721 " --> pdb=" O VAL C2717 " (cutoff:3.500A) Processing helix chain 'C' and resid 2724 through 2738 Processing helix chain 'C' and resid 2742 through 2746 removed outlier: 3.532A pdb=" N TRP C2746 " --> pdb=" O MET C2743 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.650A pdb=" N CYS D 240 " --> pdb=" O CYS D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 918 through 957 removed outlier: 3.536A pdb=" N PHE E 923 " --> pdb=" O LEU E 919 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP E 936 " --> pdb=" O VAL E 932 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE E 943 " --> pdb=" O GLU E 939 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS E 944 " --> pdb=" O LEU E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 964 through 973 Processing helix chain 'E' and resid 978 through 1000 removed outlier: 4.244A pdb=" N SER E 984 " --> pdb=" O ARG E 980 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP E 989 " --> pdb=" O VAL E 985 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 992 " --> pdb=" O VAL E 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 1018 through 1022 removed outlier: 3.870A pdb=" N GLN E1021 " --> pdb=" O ASN E1018 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR E1022 " --> pdb=" O GLU E1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1018 through 1022' Processing helix chain 'E' and resid 1040 through 1046 removed outlier: 3.696A pdb=" N TRP E1044 " --> pdb=" O ASP E1040 " (cutoff:3.500A) Processing helix chain 'E' and resid 1052 through 1056 Processing helix chain 'E' and resid 1061 through 1083 removed outlier: 4.073A pdb=" N PHE E1069 " --> pdb=" O ALA E1065 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU E1078 " --> pdb=" O TYR E1074 " (cutoff:3.500A) Processing helix chain 'E' and resid 1099 through 1104 removed outlier: 3.999A pdb=" N ASP E1104 " --> pdb=" O ARG E1100 " (cutoff:3.500A) Processing helix chain 'E' and resid 1106 through 1118 removed outlier: 4.071A pdb=" N LYS E1112 " --> pdb=" O ILE E1108 " (cutoff:3.500A) Processing helix chain 'E' and resid 1123 through 1139 removed outlier: 3.715A pdb=" N CYS E1127 " --> pdb=" O GLY E1123 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1156 removed outlier: 3.810A pdb=" N ARG E1156 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing helix chain 'E' and resid 1158 through 1164 removed outlier: 3.524A pdb=" N GLU E1164 " --> pdb=" O LYS E1160 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1186 Processing helix chain 'E' and resid 1195 through 1199 Processing helix chain 'E' and resid 1205 through 1213 Processing helix chain 'E' and resid 1224 through 1244 removed outlier: 3.608A pdb=" N TYR E1228 " --> pdb=" O VAL E1224 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP E1229 " --> pdb=" O PHE E1225 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE E1230 " --> pdb=" O LEU E1226 " (cutoff:3.500A) Processing helix chain 'E' and resid 1248 through 1255 Processing helix chain 'E' and resid 1284 through 1295 Processing helix chain 'E' and resid 1297 through 1312 removed outlier: 4.730A pdb=" N THR E1303 " --> pdb=" O TRP E1299 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG E1312 " --> pdb=" O THR E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1316 through 1335 removed outlier: 3.826A pdb=" N TYR E1320 " --> pdb=" O PHE E1316 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY E1332 " --> pdb=" O LEU E1328 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP E1333 " --> pdb=" O LEU E1329 " (cutoff:3.500A) Processing helix chain 'E' and resid 1338 through 1369 removed outlier: 4.092A pdb=" N ILE E1342 " --> pdb=" O PRO E1338 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE E1365 " --> pdb=" O ASN E1361 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY E1366 " --> pdb=" O ILE E1362 " (cutoff:3.500A) Processing helix chain 'E' and resid 1370 through 1375 Processing helix chain 'E' and resid 1378 through 1386 removed outlier: 3.511A pdb=" N ILE E1382 " --> pdb=" O SER E1378 " (cutoff:3.500A) Processing helix chain 'E' and resid 1411 through 1430 removed outlier: 3.561A pdb=" N CYS E1418 " --> pdb=" O TRP E1414 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE E1419 " --> pdb=" O ASP E1415 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E1430 " --> pdb=" O ARG E1426 " (cutoff:3.500A) Processing helix chain 'E' and resid 1431 through 1498 removed outlier: 3.593A pdb=" N LEU E1435 " --> pdb=" O SER E1431 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU E1496 " --> pdb=" O LYS E1492 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E1497 " --> pdb=" O LYS E1493 " (cutoff:3.500A) Processing helix chain 'E' and resid 1544 through 1548 Processing helix chain 'E' and resid 1651 through 1693 removed outlier: 3.511A pdb=" N LEU E1655 " --> pdb=" O PHE E1651 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP E1661 " --> pdb=" O LEU E1657 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER E1662 " --> pdb=" O ALA E1658 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLU E1673 " --> pdb=" O SER E1669 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS E1674 " --> pdb=" O ILE E1670 " (cutoff:3.500A) Processing helix chain 'E' and resid 1699 through 1716 Processing helix chain 'E' and resid 1879 through 1886 Processing helix chain 'E' and resid 1891 through 1903 removed outlier: 3.701A pdb=" N GLU E1895 " --> pdb=" O ASP E1891 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E1898 " --> pdb=" O LEU E1894 " (cutoff:3.500A) Processing helix chain 'E' and resid 1905 through 1921 Processing helix chain 'E' and resid 1921 through 1938 Processing helix chain 'E' and resid 1940 through 1943 Processing helix chain 'E' and resid 1944 through 1953 removed outlier: 3.652A pdb=" N LEU E1948 " --> pdb=" O LEU E1944 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E1951 " --> pdb=" O ILE E1947 " (cutoff:3.500A) Processing helix chain 'E' and resid 1961 through 1983 removed outlier: 3.612A pdb=" N TRP E1965 " --> pdb=" O SER E1961 " (cutoff:3.500A) Processing helix chain 'E' and resid 2003 through 2007 removed outlier: 4.355A pdb=" N ILE E2007 " --> pdb=" O PRO E2003 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2003 through 2007' Processing helix chain 'E' and resid 2016 through 2036 removed outlier: 4.074A pdb=" N GLN E2022 " --> pdb=" O TYR E2018 " (cutoff:3.500A) Processing helix chain 'E' and resid 2167 through 2180 Processing helix chain 'E' and resid 2190 through 2206 removed outlier: 4.662A pdb=" N ASP E2200 " --> pdb=" O ALA E2196 " (cutoff:3.500A) Processing helix chain 'E' and resid 2231 through 2253 removed outlier: 3.886A pdb=" N VAL E2235 " --> pdb=" O GLY E2231 " (cutoff:3.500A) Processing helix chain 'E' and resid 2255 through 2274 Processing helix chain 'E' and resid 2277 through 2282 Processing helix chain 'E' and resid 2289 through 2312 removed outlier: 3.622A pdb=" N TRP E2295 " --> pdb=" O VAL E2291 " (cutoff:3.500A) Processing helix chain 'E' and resid 2328 through 2341 removed outlier: 3.953A pdb=" N VAL E2341 " --> pdb=" O GLY E2337 " (cutoff:3.500A) Processing helix chain 'E' and resid 2344 through 2355 Processing helix chain 'E' and resid 2361 through 2388 Processing helix chain 'E' and resid 2397 through 2426 removed outlier: 3.595A pdb=" N LYS E2401 " --> pdb=" O LYS E2397 " (cutoff:3.500A) Proline residue: E2419 - end of helix Processing helix chain 'E' and resid 2479 through 2484 Processing helix chain 'E' and resid 2510 through 2522 Processing helix chain 'E' and resid 2560 through 2571 removed outlier: 4.082A pdb=" N ALA E2566 " --> pdb=" O ARG E2562 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E2571 " --> pdb=" O LYS E2567 " (cutoff:3.500A) Processing helix chain 'E' and resid 2575 through 2579 Processing helix chain 'E' and resid 2669 through 2689 Processing helix chain 'E' and resid 2690 through 2694 removed outlier: 3.716A pdb=" N SER E2693 " --> pdb=" O SER E2690 " (cutoff:3.500A) Processing helix chain 'E' and resid 2705 through 2721 removed outlier: 3.788A pdb=" N GLY E2721 " --> pdb=" O VAL E2717 " (cutoff:3.500A) Processing helix chain 'E' and resid 2724 through 2738 Processing helix chain 'E' and resid 2742 through 2746 removed outlier: 3.533A pdb=" N TRP E2746 " --> pdb=" O MET E2743 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.650A pdb=" N CYS F 240 " --> pdb=" O CYS F 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2450 through 2454 removed outlier: 6.088A pdb=" N LEU A2445 " --> pdb=" O PRO A2450 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET A2454 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A2441 " --> pdb=" O MET A2454 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A2438 " --> pdb=" O GLN A2537 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A2440 " --> pdb=" O SER A2535 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A2534 " --> pdb=" O ASP A2551 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A2551 " --> pdb=" O TRP A2534 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2461 through 2462 removed outlier: 3.659A pdb=" N LEU A2648 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2581 through 2587 removed outlier: 4.009A pdb=" N LYS A2585 " --> pdb=" O MET A2612 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET A2612 " --> pdb=" O LYS A2585 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A2615 " --> pdb=" O ASN A2634 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2450 through 2454 removed outlier: 6.088A pdb=" N LEU C2445 " --> pdb=" O PRO C2450 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C2454 " --> pdb=" O VAL C2441 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C2441 " --> pdb=" O MET C2454 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C2438 " --> pdb=" O GLN C2537 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C2440 " --> pdb=" O SER C2535 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C2534 " --> pdb=" O ASP C2551 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C2551 " --> pdb=" O TRP C2534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2461 through 2462 removed outlier: 3.658A pdb=" N LEU C2648 " --> pdb=" O LEU C2499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2581 through 2587 removed outlier: 4.011A pdb=" N LYS C2585 " --> pdb=" O MET C2612 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET C2612 " --> pdb=" O LYS C2585 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C2615 " --> pdb=" O ASN C2634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 2450 through 2454 removed outlier: 6.089A pdb=" N LEU E2445 " --> pdb=" O PRO E2450 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET E2454 " --> pdb=" O VAL E2441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E2441 " --> pdb=" O MET E2454 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP E2438 " --> pdb=" O GLN E2537 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER E2440 " --> pdb=" O SER E2535 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP E2534 " --> pdb=" O ASP E2551 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E2551 " --> pdb=" O TRP E2534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2461 through 2462 removed outlier: 3.659A pdb=" N LEU E2648 " --> pdb=" O LEU E2499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2581 through 2587 removed outlier: 4.011A pdb=" N LYS E2585 " --> pdb=" O MET E2612 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N MET E2612 " --> pdb=" O LYS E2585 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E2615 " --> pdb=" O ASN E2634 " (cutoff:3.500A) 1948 hydrogen bonds defined for protein. 5727 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: 6.64 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9635 1.33 - 1.46: 7893 1.46 - 1.58: 17866 1.58 - 1.70: 0 1.70 - 1.82: 396 Bond restraints: 35790 Sorted by residual: bond pdb=" CB TRP E2630 " pdb=" CG TRP E2630 " ideal model delta sigma weight residual 1.498 1.391 0.107 3.10e-02 1.04e+03 1.18e+01 bond pdb=" CB TRP C2630 " pdb=" CG TRP C2630 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.17e+01 bond pdb=" CB TRP A2630 " pdb=" CG TRP A2630 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.17e+01 bond pdb=" CA TYR C2489 " pdb=" CB TYR C2489 " ideal model delta sigma weight residual 1.527 1.455 0.072 2.48e-02 1.63e+03 8.54e+00 bond pdb=" CB PHE E2735 " pdb=" CG PHE E2735 " ideal model delta sigma weight residual 1.502 1.435 0.067 2.30e-02 1.89e+03 8.51e+00 ... (remaining 35785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 47115 2.39 - 4.78: 1169 4.78 - 7.18: 188 7.18 - 9.57: 35 9.57 - 11.96: 9 Bond angle restraints: 48516 Sorted by residual: angle pdb=" C MET E2454 " pdb=" N SER E2455 " pdb=" CA SER E2455 " ideal model delta sigma weight residual 121.71 114.82 6.89 1.39e+00 5.18e-01 2.45e+01 angle pdb=" C MET C2454 " pdb=" N SER C2455 " pdb=" CA SER C2455 " ideal model delta sigma weight residual 121.71 114.83 6.88 1.39e+00 5.18e-01 2.45e+01 angle pdb=" C MET A2454 " pdb=" N SER A2455 " pdb=" CA SER A2455 " ideal model delta sigma weight residual 121.71 114.83 6.88 1.39e+00 5.18e-01 2.45e+01 angle pdb=" C ASN C2703 " pdb=" N VAL C2704 " pdb=" CA VAL C2704 " ideal model delta sigma weight residual 121.97 113.68 8.29 1.80e+00 3.09e-01 2.12e+01 angle pdb=" C ASN A2703 " pdb=" N VAL A2704 " pdb=" CA VAL A2704 " ideal model delta sigma weight residual 121.97 113.75 8.22 1.80e+00 3.09e-01 2.08e+01 ... (remaining 48511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18784 17.89 - 35.78: 2015 35.78 - 53.67: 282 53.67 - 71.56: 27 71.56 - 89.45: 18 Dihedral angle restraints: 21126 sinusoidal: 8529 harmonic: 12597 Sorted by residual: dihedral pdb=" CA PHE A2653 " pdb=" C PHE A2653 " pdb=" N ASN A2654 " pdb=" CA ASN A2654 " ideal model delta harmonic sigma weight residual 180.00 142.71 37.29 0 5.00e+00 4.00e-02 5.56e+01 dihedral pdb=" CA PHE E2653 " pdb=" C PHE E2653 " pdb=" N ASN E2654 " pdb=" CA ASN E2654 " ideal model delta harmonic sigma weight residual 180.00 142.72 37.28 0 5.00e+00 4.00e-02 5.56e+01 dihedral pdb=" CA PHE C2653 " pdb=" C PHE C2653 " pdb=" N ASN C2654 " pdb=" CA ASN C2654 " ideal model delta harmonic sigma weight residual 180.00 142.75 37.25 0 5.00e+00 4.00e-02 5.55e+01 ... (remaining 21123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3635 0.045 - 0.091: 1418 0.091 - 0.136: 339 0.136 - 0.181: 29 0.181 - 0.226: 12 Chirality restraints: 5433 Sorted by residual: chirality pdb=" CB ILE E1098 " pdb=" CA ILE E1098 " pdb=" CG1 ILE E1098 " pdb=" CG2 ILE E1098 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A1098 " pdb=" CA ILE A1098 " pdb=" CG1 ILE A1098 " pdb=" CG2 ILE A1098 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C1098 " pdb=" CA ILE C1098 " pdb=" CG1 ILE C1098 " pdb=" CG2 ILE C1098 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5430 not shown) Planarity restraints: 5955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1965 " -0.028 2.00e-02 2.50e+03 2.77e-02 1.92e+01 pdb=" CG TRP A1965 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A1965 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP A1965 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1965 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1965 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1965 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1965 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1965 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1965 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1965 " 0.028 2.00e-02 2.50e+03 2.75e-02 1.89e+01 pdb=" CG TRP E1965 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP E1965 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP E1965 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E1965 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E1965 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E1965 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1965 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1965 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E1965 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1965 " 0.028 2.00e-02 2.50e+03 2.75e-02 1.89e+01 pdb=" CG TRP C1965 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C1965 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C1965 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C1965 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C1965 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C1965 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1965 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1965 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C1965 " 0.002 2.00e-02 2.50e+03 ... (remaining 5952 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 772 2.64 - 3.21: 37231 3.21 - 3.77: 55983 3.77 - 4.34: 73175 4.34 - 4.90: 113579 Nonbonded interactions: 280740 Sorted by model distance: nonbonded pdb=" OG SER A1449 " pdb=" NH1 ARG A1700 " model vdw 2.078 3.120 nonbonded pdb=" OG SER C1449 " pdb=" NH1 ARG C1700 " model vdw 2.078 3.120 nonbonded pdb=" OG SER E1449 " pdb=" NH1 ARG E1700 " model vdw 2.079 3.120 nonbonded pdb=" O CYS A1368 " pdb=" OH TYR A1394 " model vdw 2.091 3.040 nonbonded pdb=" O CYS E1368 " pdb=" OH TYR E1394 " model vdw 2.091 3.040 ... (remaining 280735 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 36.350 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.010 0.110 35796 Z= 0.448 Angle : 0.918 11.960 48528 Z= 0.504 Chirality : 0.049 0.226 5433 Planarity : 0.005 0.060 5955 Dihedral : 14.134 89.449 12936 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.81 % Favored : 86.12 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.52 (0.12), residues: 4194 helix: -0.57 (0.10), residues: 2592 sheet: -3.19 (0.36), residues: 168 loop : -3.50 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C2748 TYR 0.024 0.002 TYR E1706 PHE 0.030 0.002 PHE A2689 TRP 0.074 0.003 TRP A1965 HIS 0.014 0.002 HIS E1076 Details of bonding type rmsd covalent geometry : bond 0.00991 (35790) covalent geometry : angle 0.91774 (48516) SS BOND : bond 0.00134 ( 6) SS BOND : angle 1.87252 ( 12) hydrogen bonds : bond 0.14638 ( 1948) hydrogen bonds : angle 7.51324 ( 5727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.255 Fit side-chains REVERT: A 1231 MET cc_start: 0.8170 (mpp) cc_final: 0.7845 (mtm) REVERT: A 1656 PHE cc_start: 0.7480 (m-80) cc_final: 0.7065 (m-80) REVERT: A 1706 TYR cc_start: 0.8837 (m-80) cc_final: 0.8554 (m-80) REVERT: A 1924 MET cc_start: 0.7512 (mpp) cc_final: 0.7244 (mpt) REVERT: A 1935 MET cc_start: 0.7717 (mtp) cc_final: 0.7486 (mtp) REVERT: A 1967 MET cc_start: 0.8158 (tmm) cc_final: 0.7781 (tmm) REVERT: A 2236 MET cc_start: 0.7918 (tpt) cc_final: 0.7586 (tpp) REVERT: A 2454 MET cc_start: 0.8282 (tmm) cc_final: 0.7791 (tmm) REVERT: A 2568 MET cc_start: 0.7392 (tmm) cc_final: 0.7127 (tmm) REVERT: C 1130 MET cc_start: 0.8963 (tpp) cc_final: 0.8677 (tpp) REVERT: C 1474 MET cc_start: 0.8386 (tpp) cc_final: 0.7962 (tpp) REVERT: C 1656 PHE cc_start: 0.7470 (m-80) cc_final: 0.6989 (m-80) REVERT: C 1914 MET cc_start: 0.8708 (ttm) cc_final: 0.8446 (ttm) REVERT: C 1935 MET cc_start: 0.7744 (mtp) cc_final: 0.7513 (mtp) REVERT: C 1967 MET cc_start: 0.8260 (tmm) cc_final: 0.7775 (tmm) REVERT: C 2236 MET cc_start: 0.7981 (tpt) cc_final: 0.7517 (tpt) REVERT: C 2454 MET cc_start: 0.8311 (tmm) cc_final: 0.7456 (tmm) REVERT: C 2568 MET cc_start: 0.7402 (tmm) cc_final: 0.7137 (tmm) REVERT: E 1130 MET cc_start: 0.9050 (tpp) cc_final: 0.8741 (tpp) REVERT: E 1656 PHE cc_start: 0.7453 (m-80) cc_final: 0.7006 (m-80) REVERT: E 2236 MET cc_start: 0.8002 (tpt) cc_final: 0.7578 (tpt) REVERT: E 2351 MET cc_start: 0.7940 (mmp) cc_final: 0.7737 (mmp) REVERT: E 2454 MET cc_start: 0.8228 (tmm) cc_final: 0.7534 (tmm) REVERT: E 2568 MET cc_start: 0.7279 (tmm) cc_final: 0.7074 (tmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1795 time to fit residues: 60.7757 Evaluate side-chains 181 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1084 ASN A1137 GLN ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1713 ASN A2474 GLN C1084 ASN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1713 ASN C2474 GLN E1084 ASN E1137 GLN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1713 ASN E2474 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.092108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.064712 restraints weight = 206180.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.064003 restraints weight = 139526.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.064549 restraints weight = 115677.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.064753 restraints weight = 88942.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.064789 restraints weight = 85734.443| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35796 Z= 0.166 Angle : 0.667 11.115 48528 Z= 0.349 Chirality : 0.042 0.180 5433 Planarity : 0.005 0.058 5955 Dihedral : 5.742 32.308 4614 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.30 % Favored : 89.63 % Rotamer: Outliers : 0.75 % Allowed : 7.22 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.54 (0.13), residues: 4194 helix: 0.32 (0.10), residues: 2583 sheet: -3.10 (0.34), residues: 162 loop : -3.31 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1716 TYR 0.042 0.002 TYR E1706 PHE 0.019 0.001 PHE A 961 TRP 0.028 0.002 TRP C2209 HIS 0.010 0.001 HIS A1076 Details of bonding type rmsd covalent geometry : bond 0.00354 (35790) covalent geometry : angle 0.66695 (48516) SS BOND : bond 0.00206 ( 6) SS BOND : angle 1.25394 ( 12) hydrogen bonds : bond 0.05516 ( 1948) hydrogen bonds : angle 5.47406 ( 5727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.202 Fit side-chains REVERT: A 1683 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9168 (tt) REVERT: A 1706 TYR cc_start: 0.9147 (m-80) cc_final: 0.8769 (m-80) REVERT: A 1888 MET cc_start: 0.8503 (tpp) cc_final: 0.7884 (tpp) REVERT: A 1935 MET cc_start: 0.7549 (mtp) cc_final: 0.7308 (mtp) REVERT: A 1967 MET cc_start: 0.8189 (tmm) cc_final: 0.7637 (tmm) REVERT: A 2454 MET cc_start: 0.8427 (tmm) cc_final: 0.8153 (tmm) REVERT: A 2609 ASN cc_start: 0.8647 (m110) cc_final: 0.8437 (p0) REVERT: C 1130 MET cc_start: 0.8964 (tpp) cc_final: 0.8697 (tpp) REVERT: C 1139 MET cc_start: 0.7552 (mmm) cc_final: 0.7325 (mmm) REVERT: C 1144 MET cc_start: 0.8079 (mmm) cc_final: 0.7506 (tpp) REVERT: C 1231 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8135 (mpp) REVERT: C 1656 PHE cc_start: 0.7430 (m-80) cc_final: 0.7007 (m-80) REVERT: C 1683 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9183 (tt) REVERT: C 1888 MET cc_start: 0.8353 (tpp) cc_final: 0.7727 (tpp) REVERT: C 1935 MET cc_start: 0.7614 (mtp) cc_final: 0.7295 (mtp) REVERT: C 2236 MET cc_start: 0.7895 (tpt) cc_final: 0.7451 (tpt) REVERT: C 2454 MET cc_start: 0.8379 (tmm) cc_final: 0.7773 (tmm) REVERT: C 2609 ASN cc_start: 0.8775 (m110) cc_final: 0.8561 (p0) REVERT: E 1130 MET cc_start: 0.9121 (tpp) cc_final: 0.8866 (tpp) REVERT: E 1139 MET cc_start: 0.7630 (mmm) cc_final: 0.7367 (mmm) REVERT: E 1355 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7999 (t80) REVERT: E 1683 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9058 (tt) REVERT: E 1888 MET cc_start: 0.8269 (tpp) cc_final: 0.7567 (tpp) REVERT: E 1967 MET cc_start: 0.8439 (tmm) cc_final: 0.7785 (tmm) REVERT: E 2568 MET cc_start: 0.7228 (tmm) cc_final: 0.6713 (tmm) outliers start: 29 outliers final: 5 residues processed: 201 average time/residue: 0.1731 time to fit residues: 61.0008 Evaluate side-chains 190 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 2404 MET Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1359 MET Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 16 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 378 optimal weight: 0.7980 chunk 312 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 197 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 HIS ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1674 HIS ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.091974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.064707 restraints weight = 205980.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.065050 restraints weight = 142101.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.064585 restraints weight = 98285.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.064725 restraints weight = 99317.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.064780 restraints weight = 92640.397| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35796 Z= 0.173 Angle : 0.628 10.749 48528 Z= 0.327 Chirality : 0.041 0.175 5433 Planarity : 0.004 0.054 5955 Dihedral : 5.388 31.719 4614 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.54 % Favored : 89.32 % Rotamer: Outliers : 1.22 % Allowed : 10.22 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.12 (0.13), residues: 4194 helix: 0.65 (0.10), residues: 2595 sheet: -3.06 (0.33), residues: 156 loop : -3.16 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2478 TYR 0.036 0.001 TYR E1706 PHE 0.017 0.001 PHE A 961 TRP 0.014 0.001 TRP E2417 HIS 0.007 0.001 HIS E1076 Details of bonding type rmsd covalent geometry : bond 0.00383 (35790) covalent geometry : angle 0.62765 (48516) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.99679 ( 12) hydrogen bonds : bond 0.04933 ( 1948) hydrogen bonds : angle 5.02949 ( 5727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 1.253 Fit side-chains REVERT: A 1139 MET cc_start: 0.7787 (mmm) cc_final: 0.7580 (mmm) REVERT: A 1231 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: A 1359 MET cc_start: 0.7760 (mmm) cc_final: 0.7391 (tpt) REVERT: A 1683 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 1706 TYR cc_start: 0.9103 (m-80) cc_final: 0.8752 (m-80) REVERT: A 1888 MET cc_start: 0.8618 (tpp) cc_final: 0.8069 (tpp) REVERT: A 1935 MET cc_start: 0.7503 (mtp) cc_final: 0.7205 (mtp) REVERT: A 1967 MET cc_start: 0.8265 (tmm) cc_final: 0.7802 (tmm) REVERT: A 2454 MET cc_start: 0.8594 (tmm) cc_final: 0.7733 (tmm) REVERT: A 2464 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4854 (ttp) REVERT: A 2568 MET cc_start: 0.7438 (tmm) cc_final: 0.6958 (tmm) REVERT: A 2609 ASN cc_start: 0.8711 (m110) cc_final: 0.8496 (p0) REVERT: C 1130 MET cc_start: 0.9014 (tpp) cc_final: 0.8767 (tpp) REVERT: C 1139 MET cc_start: 0.7539 (mmm) cc_final: 0.7250 (mmm) REVERT: C 1144 MET cc_start: 0.8113 (mmm) cc_final: 0.7488 (tpp) REVERT: C 1231 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8166 (mtm) REVERT: C 1656 PHE cc_start: 0.7485 (m-80) cc_final: 0.7072 (m-80) REVERT: C 1683 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 1888 MET cc_start: 0.8708 (tpp) cc_final: 0.8138 (tpp) REVERT: C 1914 MET cc_start: 0.9116 (ttm) cc_final: 0.8877 (ttm) REVERT: C 1935 MET cc_start: 0.7560 (mtp) cc_final: 0.7279 (mtp) REVERT: C 2236 MET cc_start: 0.7959 (tpt) cc_final: 0.7460 (tpt) REVERT: C 2464 MET cc_start: 0.4698 (ttp) cc_final: 0.4355 (ttp) REVERT: C 2568 MET cc_start: 0.7643 (tmm) cc_final: 0.7181 (tmm) REVERT: C 2609 ASN cc_start: 0.8839 (m110) cc_final: 0.8600 (p0) REVERT: E 1130 MET cc_start: 0.9108 (tpp) cc_final: 0.8852 (tpp) REVERT: E 1139 MET cc_start: 0.7530 (mmm) cc_final: 0.7207 (mmm) REVERT: E 1231 MET cc_start: 0.8320 (mtp) cc_final: 0.7849 (mtm) REVERT: E 1355 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7971 (t80) REVERT: E 1683 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.8975 (tt) REVERT: E 1888 MET cc_start: 0.8257 (tpp) cc_final: 0.7552 (tpp) REVERT: E 1967 MET cc_start: 0.8392 (tmm) cc_final: 0.7828 (tmm) REVERT: E 2236 MET cc_start: 0.7941 (tpt) cc_final: 0.7594 (tpt) REVERT: E 2568 MET cc_start: 0.7284 (tmm) cc_final: 0.6570 (tmm) outliers start: 47 outliers final: 15 residues processed: 215 average time/residue: 0.1780 time to fit residues: 66.6358 Evaluate side-chains 200 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2464 MET Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1484 ILE Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1359 MET Chi-restraints excluded: chain E residue 1670 ILE Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2641 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 347 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 372 optimal weight: 3.9990 chunk 412 optimal weight: 5.9990 chunk 357 optimal weight: 0.9990 chunk 291 optimal weight: 30.0000 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1060 ASN A1137 GLN ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1060 ASN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1060 ASN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1674 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.091919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.064383 restraints weight = 204652.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.063809 restraints weight = 150117.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.063672 restraints weight = 104697.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.063989 restraints weight = 114290.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.063996 restraints weight = 98521.180| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35796 Z= 0.186 Angle : 0.617 10.488 48528 Z= 0.322 Chirality : 0.041 0.256 5433 Planarity : 0.004 0.053 5955 Dihedral : 5.247 30.682 4614 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.25 % Favored : 89.68 % Rotamer: Outliers : 1.50 % Allowed : 12.50 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.91 (0.13), residues: 4194 helix: 0.81 (0.10), residues: 2592 sheet: -3.14 (0.32), residues: 156 loop : -3.04 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2478 TYR 0.029 0.001 TYR E1706 PHE 0.017 0.001 PHE A 961 TRP 0.011 0.001 TRP E2417 HIS 0.005 0.001 HIS C2694 Details of bonding type rmsd covalent geometry : bond 0.00417 (35790) covalent geometry : angle 0.61714 (48516) SS BOND : bond 0.00236 ( 6) SS BOND : angle 0.88781 ( 12) hydrogen bonds : bond 0.04701 ( 1948) hydrogen bonds : angle 4.84476 ( 5727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1231 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8225 (mtm) REVERT: A 1355 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 1359 MET cc_start: 0.7678 (mmm) cc_final: 0.7294 (tpt) REVERT: A 1888 MET cc_start: 0.8439 (tpp) cc_final: 0.7427 (tpp) REVERT: A 1935 MET cc_start: 0.7466 (mtp) cc_final: 0.7196 (mtp) REVERT: A 1967 MET cc_start: 0.8310 (tmm) cc_final: 0.7531 (tmm) REVERT: A 2197 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7290 (t70) REVERT: A 2351 MET cc_start: 0.7805 (mmp) cc_final: 0.7573 (mmp) REVERT: A 2454 MET cc_start: 0.8644 (tmm) cc_final: 0.7519 (tmm) REVERT: A 2568 MET cc_start: 0.7459 (tmm) cc_final: 0.6853 (tmm) REVERT: C 1130 MET cc_start: 0.8955 (tpp) cc_final: 0.8732 (tpp) REVERT: C 1139 MET cc_start: 0.7478 (mmm) cc_final: 0.7194 (mmm) REVERT: C 1144 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7409 (tpp) REVERT: C 1231 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8223 (mtm) REVERT: C 1355 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 1474 MET cc_start: 0.8703 (tpp) cc_final: 0.8480 (tpp) REVERT: C 1656 PHE cc_start: 0.7559 (m-80) cc_final: 0.7154 (m-80) REVERT: C 1683 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9139 (tt) REVERT: C 1888 MET cc_start: 0.8591 (tpp) cc_final: 0.8016 (tpp) REVERT: C 1914 MET cc_start: 0.9161 (ttm) cc_final: 0.8944 (ttm) REVERT: C 1935 MET cc_start: 0.7577 (mtp) cc_final: 0.7274 (mtp) REVERT: C 2197 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7267 (t70) REVERT: C 2234 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7790 (tp) REVERT: C 2236 MET cc_start: 0.7863 (tpt) cc_final: 0.7502 (tpt) REVERT: C 2274 MET cc_start: 0.7352 (mtt) cc_final: 0.6934 (mtt) REVERT: C 2568 MET cc_start: 0.7730 (tmm) cc_final: 0.7161 (tmm) REVERT: C 2609 ASN cc_start: 0.8862 (m110) cc_final: 0.8627 (p0) REVERT: E 1130 MET cc_start: 0.9022 (tpp) cc_final: 0.8797 (tpp) REVERT: E 1139 MET cc_start: 0.7411 (mmm) cc_final: 0.7113 (mmm) REVERT: E 1263 MET cc_start: 0.7554 (tpt) cc_final: 0.7320 (tpt) REVERT: E 1355 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7965 (t80) REVERT: E 1683 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9070 (tt) REVERT: E 1888 MET cc_start: 0.8115 (tpp) cc_final: 0.6656 (tpp) REVERT: E 1967 MET cc_start: 0.8450 (tmm) cc_final: 0.7860 (tmm) REVERT: E 2454 MET cc_start: 0.8483 (tmm) cc_final: 0.8263 (tmm) REVERT: E 2464 MET cc_start: 0.6057 (ttp) cc_final: 0.5355 (ttp) REVERT: E 2612 MET cc_start: 0.6927 (tpp) cc_final: 0.6712 (tpp) outliers start: 58 outliers final: 25 residues processed: 227 average time/residue: 0.1842 time to fit residues: 73.0129 Evaluate side-chains 213 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1144 MET Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2404 MET Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1359 MET Chi-restraints excluded: chain E residue 1670 ILE Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2368 VAL Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2704 VAL Chi-restraints excluded: chain E residue 2714 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 254 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 394 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 359 optimal weight: 0.8980 chunk 374 optimal weight: 0.9980 chunk 228 optimal weight: 0.0980 chunk 216 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1383 GLN ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2180 HIS ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2537 GLN C1383 GLN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2180 HIS ** C2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2564 ASN E1383 GLN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1710 HIS ** E1934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2180 HIS ** E2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2466 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.081074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.063456 restraints weight = 212446.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064851 restraints weight = 117326.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.065571 restraints weight = 73023.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.065492 restraints weight = 81139.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.065461 restraints weight = 64569.273| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35796 Z= 0.115 Angle : 0.575 12.409 48528 Z= 0.295 Chirality : 0.039 0.182 5433 Planarity : 0.004 0.053 5955 Dihedral : 4.978 30.204 4614 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.30 % Favored : 90.68 % Rotamer: Outliers : 1.84 % Allowed : 13.95 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.50 (0.13), residues: 4194 helix: 1.20 (0.10), residues: 2571 sheet: -2.94 (0.34), residues: 156 loop : -2.95 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1138 TYR 0.029 0.001 TYR E1706 PHE 0.016 0.001 PHE A 961 TRP 0.018 0.001 TRP A2417 HIS 0.010 0.001 HIS E1710 Details of bonding type rmsd covalent geometry : bond 0.00241 (35790) covalent geometry : angle 0.57502 (48516) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.66552 ( 12) hydrogen bonds : bond 0.04095 ( 1948) hydrogen bonds : angle 4.44283 ( 5727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 177 time to evaluate : 1.270 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: A 1139 MET cc_start: 0.7953 (mmm) cc_final: 0.7705 (mmm) REVERT: A 1231 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: A 1355 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 1359 MET cc_start: 0.7740 (mmm) cc_final: 0.7245 (tpt) REVERT: A 1888 MET cc_start: 0.8448 (tpp) cc_final: 0.7776 (tpp) REVERT: A 1935 MET cc_start: 0.7433 (mtp) cc_final: 0.7166 (mtp) REVERT: A 1967 MET cc_start: 0.8203 (tmm) cc_final: 0.7670 (tmm) REVERT: A 2197 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7346 (t70) REVERT: A 2454 MET cc_start: 0.8550 (tmm) cc_final: 0.8045 (tmm) REVERT: A 2464 MET cc_start: 0.5943 (ttp) cc_final: 0.5681 (ttp) REVERT: A 2568 MET cc_start: 0.7066 (tmm) cc_final: 0.6132 (tmm) REVERT: C 1130 MET cc_start: 0.9037 (tpp) cc_final: 0.8766 (tpp) REVERT: C 1139 MET cc_start: 0.7666 (mmm) cc_final: 0.7309 (mmm) REVERT: C 1144 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7422 (tpp) REVERT: C 1231 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8169 (mtm) REVERT: C 1355 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 1683 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9219 (tt) REVERT: C 1888 MET cc_start: 0.8569 (tpp) cc_final: 0.7588 (tpp) REVERT: C 1935 MET cc_start: 0.7490 (mtp) cc_final: 0.7193 (mtp) REVERT: C 2197 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7220 (t70) REVERT: C 2234 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7860 (tp) REVERT: C 2236 MET cc_start: 0.7496 (tpt) cc_final: 0.6924 (tpt) REVERT: C 2464 MET cc_start: 0.5342 (ttt) cc_final: 0.3431 (mmm) REVERT: C 2568 MET cc_start: 0.7135 (tmm) cc_final: 0.6615 (tmm) REVERT: E 1130 MET cc_start: 0.9073 (tpp) cc_final: 0.8463 (mmm) REVERT: E 1139 MET cc_start: 0.7666 (mmm) cc_final: 0.7251 (mmm) REVERT: E 1144 MET cc_start: 0.8112 (tpp) cc_final: 0.7783 (mmm) REVERT: E 1355 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7736 (t80) REVERT: E 1683 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9183 (tt) REVERT: E 1888 MET cc_start: 0.8207 (tpp) cc_final: 0.7434 (tpp) REVERT: E 1935 MET cc_start: 0.7639 (mtp) cc_final: 0.7241 (ptp) REVERT: E 1967 MET cc_start: 0.8234 (tmm) cc_final: 0.7690 (tmm) REVERT: E 2197 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7106 (t70) REVERT: E 2236 MET cc_start: 0.7808 (tpt) cc_final: 0.7499 (mmm) REVERT: E 2568 MET cc_start: 0.7113 (ttp) cc_final: 0.6297 (tmm) outliers start: 71 outliers final: 33 residues processed: 231 average time/residue: 0.1663 time to fit residues: 67.6521 Evaluate side-chains 220 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2537 GLN Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1144 MET Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2244 MET Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2737 TYR Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2704 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 334 optimal weight: 1.9990 chunk 313 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 chunk 284 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1076 HIS ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2466 GLN A2564 ASN C1076 HIS ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1710 HIS E1076 HIS E1137 GLN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2466 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.092010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.064129 restraints weight = 204522.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.063867 restraints weight = 139825.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.063794 restraints weight = 101849.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.064121 restraints weight = 99098.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.064112 restraints weight = 91511.929| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35796 Z= 0.206 Angle : 0.629 11.677 48528 Z= 0.321 Chirality : 0.041 0.217 5433 Planarity : 0.004 0.052 5955 Dihedral : 4.976 29.239 4614 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.91 % Rotamer: Outliers : 1.89 % Allowed : 15.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.52 (0.13), residues: 4194 helix: 1.13 (0.10), residues: 2595 sheet: -2.95 (0.34), residues: 156 loop : -2.89 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E2718 TYR 0.027 0.001 TYR E1706 PHE 0.015 0.001 PHE A 961 TRP 0.018 0.001 TRP A2417 HIS 0.008 0.001 HIS C1710 Details of bonding type rmsd covalent geometry : bond 0.00467 (35790) covalent geometry : angle 0.62912 (48516) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.72936 ( 12) hydrogen bonds : bond 0.04376 ( 1948) hydrogen bonds : angle 4.56629 ( 5727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1139 MET cc_start: 0.7805 (mmm) cc_final: 0.7585 (mmm) REVERT: A 1231 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8344 (mtm) REVERT: A 1263 MET cc_start: 0.7508 (tpt) cc_final: 0.7294 (tpt) REVERT: A 1339 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 1355 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (t80) REVERT: A 1359 MET cc_start: 0.7584 (mmm) cc_final: 0.7185 (tpt) REVERT: A 1888 MET cc_start: 0.8297 (tpp) cc_final: 0.7640 (tpp) REVERT: A 1935 MET cc_start: 0.7451 (mtp) cc_final: 0.7164 (mtp) REVERT: A 1967 MET cc_start: 0.8384 (tmm) cc_final: 0.7825 (tmm) REVERT: A 2197 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7476 (t70) REVERT: A 2454 MET cc_start: 0.8688 (tmm) cc_final: 0.7713 (tmm) REVERT: A 2568 MET cc_start: 0.7675 (tmm) cc_final: 0.7021 (tmm) REVERT: C 1130 MET cc_start: 0.9024 (tpp) cc_final: 0.8788 (tpp) REVERT: C 1139 MET cc_start: 0.7577 (mmm) cc_final: 0.7280 (mmm) REVERT: C 1144 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7472 (tpp) REVERT: C 1231 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8272 (mtm) REVERT: C 1339 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7801 (tp) REVERT: C 1355 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7885 (t80) REVERT: C 1481 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8414 (tpp) REVERT: C 1683 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9173 (tt) REVERT: C 1888 MET cc_start: 0.8425 (tpp) cc_final: 0.8022 (tpp) REVERT: C 1935 MET cc_start: 0.7578 (mtp) cc_final: 0.7260 (mtp) REVERT: C 2197 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7297 (t70) REVERT: C 2234 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7799 (tp) REVERT: C 2568 MET cc_start: 0.7796 (tmm) cc_final: 0.7206 (tmm) REVERT: D 244 PHE cc_start: 0.7432 (m-80) cc_final: 0.7213 (m-80) REVERT: E 1130 MET cc_start: 0.9048 (tpp) cc_final: 0.8479 (mmm) REVERT: E 1139 MET cc_start: 0.7442 (mmm) cc_final: 0.7058 (mmm) REVERT: E 1144 MET cc_start: 0.8096 (tpp) cc_final: 0.7841 (mmm) REVERT: E 1263 MET cc_start: 0.7463 (tpt) cc_final: 0.7258 (tpt) REVERT: E 1355 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7878 (t80) REVERT: E 1683 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9098 (tt) REVERT: E 1888 MET cc_start: 0.7986 (tpp) cc_final: 0.7483 (tpp) REVERT: E 1935 MET cc_start: 0.7799 (mtp) cc_final: 0.7369 (ptp) REVERT: E 1967 MET cc_start: 0.8475 (tmm) cc_final: 0.7868 (tmm) REVERT: E 2195 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8170 (tp) REVERT: E 2197 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7119 (t70) REVERT: E 2236 MET cc_start: 0.8094 (tpt) cc_final: 0.7776 (mmm) REVERT: E 2612 MET cc_start: 0.7034 (tpp) cc_final: 0.6784 (tpp) outliers start: 73 outliers final: 44 residues processed: 236 average time/residue: 0.1669 time to fit residues: 69.8302 Evaluate side-chains 235 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1079 TYR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2347 LEU Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2615 THR Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1079 TYR Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1144 MET Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2714 ILE Chi-restraints excluded: chain E residue 1079 TYR Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2195 LEU Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2368 VAL Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2466 GLN Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2704 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 332 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 415 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 347 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 225 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1076 HIS ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2466 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.092258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.065201 restraints weight = 204763.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.064462 restraints weight = 158332.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.064851 restraints weight = 107203.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.065015 restraints weight = 97819.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065088 restraints weight = 91387.675| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35796 Z= 0.175 Angle : 0.617 13.021 48528 Z= 0.313 Chirality : 0.040 0.180 5433 Planarity : 0.004 0.052 5955 Dihedral : 4.960 29.147 4614 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.73 % Favored : 90.15 % Rotamer: Outliers : 2.10 % Allowed : 15.68 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.47 (0.13), residues: 4194 helix: 1.16 (0.10), residues: 2613 sheet: -2.90 (0.35), residues: 156 loop : -2.93 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E2718 TYR 0.050 0.001 TYR A1706 PHE 0.016 0.001 PHE A 961 TRP 0.016 0.001 TRP A2417 HIS 0.005 0.001 HIS A1710 Details of bonding type rmsd covalent geometry : bond 0.00396 (35790) covalent geometry : angle 0.61672 (48516) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.68994 ( 12) hydrogen bonds : bond 0.04265 ( 1948) hydrogen bonds : angle 4.48134 ( 5727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 176 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1139 MET cc_start: 0.7750 (mmm) cc_final: 0.7482 (mmm) REVERT: A 1144 MET cc_start: 0.7930 (mmm) cc_final: 0.7491 (tpp) REVERT: A 1231 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: A 1263 MET cc_start: 0.7393 (tpt) cc_final: 0.7110 (tpt) REVERT: A 1359 MET cc_start: 0.7610 (mmm) cc_final: 0.7243 (tpt) REVERT: A 1888 MET cc_start: 0.8401 (tpp) cc_final: 0.7827 (tpp) REVERT: A 1935 MET cc_start: 0.7406 (mtp) cc_final: 0.7144 (mtp) REVERT: A 1967 MET cc_start: 0.8341 (tmm) cc_final: 0.7796 (tmm) REVERT: A 2197 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7407 (t70) REVERT: A 2234 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 2454 MET cc_start: 0.8675 (tmm) cc_final: 0.7745 (tmm) REVERT: A 2568 MET cc_start: 0.7686 (tmm) cc_final: 0.6550 (tmm) REVERT: C 1130 MET cc_start: 0.9038 (tpp) cc_final: 0.8800 (tpp) REVERT: C 1139 MET cc_start: 0.7565 (mmm) cc_final: 0.7258 (mmm) REVERT: C 1144 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7481 (tpp) REVERT: C 1231 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8260 (mtm) REVERT: C 1339 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7920 (tp) REVERT: C 1355 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7872 (t80) REVERT: C 1683 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9178 (tt) REVERT: C 1888 MET cc_start: 0.8462 (tpp) cc_final: 0.7999 (tpp) REVERT: C 1935 MET cc_start: 0.7543 (mtp) cc_final: 0.7231 (mtp) REVERT: C 2197 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7287 (t70) REVERT: C 2234 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7800 (tp) REVERT: C 2568 MET cc_start: 0.7708 (tmm) cc_final: 0.7110 (tmm) REVERT: E 1130 MET cc_start: 0.9048 (tpp) cc_final: 0.8457 (mmm) REVERT: E 1139 MET cc_start: 0.7493 (mmm) cc_final: 0.7080 (mmm) REVERT: E 1144 MET cc_start: 0.8147 (tpp) cc_final: 0.7860 (mmm) REVERT: E 1263 MET cc_start: 0.7452 (tpt) cc_final: 0.7240 (tpt) REVERT: E 1355 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7866 (t80) REVERT: E 1683 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9149 (tt) REVERT: E 1888 MET cc_start: 0.8046 (tpp) cc_final: 0.7464 (tpp) REVERT: E 1935 MET cc_start: 0.7719 (mtp) cc_final: 0.7296 (ptp) REVERT: E 1967 MET cc_start: 0.8444 (tmm) cc_final: 0.7838 (tmm) REVERT: E 2195 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8188 (tp) REVERT: E 2197 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7035 (t70) REVERT: E 2236 MET cc_start: 0.8044 (tpt) cc_final: 0.7748 (mmm) REVERT: E 2568 MET cc_start: 0.7427 (ttt) cc_final: 0.6471 (tmm) outliers start: 81 outliers final: 52 residues processed: 245 average time/residue: 0.1673 time to fit residues: 72.4498 Evaluate side-chains 242 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1079 TYR Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2347 LEU Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2615 THR Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1079 TYR Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1144 MET Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2737 TYR Chi-restraints excluded: chain E residue 1079 TYR Chi-restraints excluded: chain E residue 1180 GLN Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1359 MET Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2195 LEU Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2368 VAL Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2466 GLN Chi-restraints excluded: chain E residue 2615 THR Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2703 ASN Chi-restraints excluded: chain E residue 2704 VAL Chi-restraints excluded: chain E residue 2714 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 250 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 390 optimal weight: 4.9990 chunk 385 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2466 GLN C1076 HIS C1180 GLN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2263 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 = 0.4055 r_free = 0.4055 target = 0.080524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.062884 restraints weight = 211561.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.064125 restraints weight = 116146.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.065558 restraints weight = 75178.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.065239 restraints weight = 75738.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.065192 restraints weight = 61350.514| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35796 Z= 0.127 Angle : 0.589 13.323 48528 Z= 0.297 Chirality : 0.039 0.181 5433 Planarity : 0.004 0.053 5955 Dihedral : 4.836 28.557 4614 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.15 % Allowed : 16.02 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.26 (0.13), residues: 4194 helix: 1.34 (0.10), residues: 2613 sheet: -2.69 (0.35), residues: 156 loop : -2.88 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E2718 TYR 0.043 0.001 TYR A1706 PHE 0.024 0.001 PHE C 927 TRP 0.015 0.001 TRP A2417 HIS 0.004 0.001 HIS E1542 Details of bonding type rmsd covalent geometry : bond 0.00281 (35790) covalent geometry : angle 0.58915 (48516) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.60433 ( 12) hydrogen bonds : bond 0.04004 ( 1948) hydrogen bonds : angle 4.34970 ( 5727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1139 MET cc_start: 0.7846 (mmm) cc_final: 0.7560 (mmm) REVERT: A 1144 MET cc_start: 0.7922 (mmm) cc_final: 0.7416 (tpp) REVERT: A 1231 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8192 (mtm) REVERT: A 1339 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8130 (tp) REVERT: A 1355 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7798 (t80) REVERT: A 1359 MET cc_start: 0.7675 (mmm) cc_final: 0.7179 (tpt) REVERT: A 1888 MET cc_start: 0.8455 (tpp) cc_final: 0.7672 (tpp) REVERT: A 1890 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7610 (p-80) REVERT: A 1935 MET cc_start: 0.7353 (mtp) cc_final: 0.7093 (mtp) REVERT: A 1967 MET cc_start: 0.8234 (tmm) cc_final: 0.7664 (tmm) REVERT: A 2036 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7602 (m90) REVERT: A 2197 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7387 (t70) REVERT: A 2454 MET cc_start: 0.8534 (tmm) cc_final: 0.7876 (tmm) REVERT: A 2568 MET cc_start: 0.7148 (tmm) cc_final: 0.6057 (tmm) REVERT: C 1130 MET cc_start: 0.9022 (tpp) cc_final: 0.8750 (tpp) REVERT: C 1139 MET cc_start: 0.7652 (mmm) cc_final: 0.7290 (mmm) REVERT: C 1180 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7752 (mm-40) REVERT: C 1231 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: C 1339 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8381 (tp) REVERT: C 1355 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 1683 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9225 (tt) REVERT: C 1888 MET cc_start: 0.8474 (tpp) cc_final: 0.8000 (tpp) REVERT: C 1935 MET cc_start: 0.7445 (mtp) cc_final: 0.7164 (mtp) REVERT: C 2197 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7240 (t70) REVERT: C 2234 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7874 (tp) REVERT: C 2404 MET cc_start: 0.8387 (tpp) cc_final: 0.8059 (tpp) REVERT: C 2568 MET cc_start: 0.7146 (tmm) cc_final: 0.6624 (tmm) REVERT: E 1130 MET cc_start: 0.9054 (tpp) cc_final: 0.8430 (mmm) REVERT: E 1139 MET cc_start: 0.7636 (mmm) cc_final: 0.7186 (mmm) REVERT: E 1144 MET cc_start: 0.8106 (tpp) cc_final: 0.7890 (tpp) REVERT: E 1355 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7609 (t80) REVERT: E 1683 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9176 (tt) REVERT: E 1705 MET cc_start: 0.8833 (tmm) cc_final: 0.8414 (ppp) REVERT: E 1888 MET cc_start: 0.8224 (tpp) cc_final: 0.7649 (tpp) REVERT: E 1935 MET cc_start: 0.7540 (mtp) cc_final: 0.7142 (ptp) REVERT: E 1967 MET cc_start: 0.8283 (tmm) cc_final: 0.7705 (tmm) REVERT: E 2195 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8123 (tp) REVERT: E 2197 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7026 (t70) REVERT: E 2236 MET cc_start: 0.7746 (tpt) cc_final: 0.7492 (mmm) REVERT: E 2568 MET cc_start: 0.6862 (ttt) cc_final: 0.6138 (tmm) outliers start: 83 outliers final: 46 residues processed: 241 average time/residue: 0.1664 time to fit residues: 70.6589 Evaluate side-chains 237 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 174 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1079 TYR Chi-restraints excluded: chain A residue 1231 MET Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1890 HIS Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2036 HIS Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2347 LEU Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2466 GLN Chi-restraints excluded: chain A residue 2615 THR Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1079 TYR Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1180 GLN Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2737 TYR Chi-restraints excluded: chain E residue 1079 TYR Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1355 PHE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2195 LEU Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2466 GLN Chi-restraints excluded: chain E residue 2615 THR Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2704 VAL Chi-restraints excluded: chain E residue 2714 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 53 optimal weight: 7.9990 chunk 356 optimal weight: 0.9980 chunk 362 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 170 optimal weight: 40.0000 chunk 296 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 GLN ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2466 GLN ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1425 GLN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1180 GLN E1425 GLN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2466 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.062480 restraints weight = 202044.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062418 restraints weight = 143449.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.062345 restraints weight = 105029.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.062555 restraints weight = 105107.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.062695 restraints weight = 94001.515| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 35796 Z= 0.288 Angle : 0.715 13.945 48528 Z= 0.364 Chirality : 0.043 0.282 5433 Planarity : 0.004 0.050 5955 Dihedral : 5.083 28.903 4614 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.54 % Favored : 89.32 % Rotamer: Outliers : 1.92 % Allowed : 16.54 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.55 (0.13), residues: 4194 helix: 1.10 (0.10), residues: 2616 sheet: -2.82 (0.33), residues: 180 loop : -2.97 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E2718 TYR 0.046 0.002 TYR A1706 PHE 0.019 0.002 PHE C 927 TRP 0.016 0.002 TRP A2417 HIS 0.009 0.001 HIS A1710 Details of bonding type rmsd covalent geometry : bond 0.00654 (35790) covalent geometry : angle 0.71508 (48516) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.80862 ( 12) hydrogen bonds : bond 0.04632 ( 1948) hydrogen bonds : angle 4.68943 ( 5727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 181 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1139 MET cc_start: 0.7670 (mmm) cc_final: 0.7407 (mmm) REVERT: A 1144 MET cc_start: 0.7836 (mmm) cc_final: 0.7402 (tpp) REVERT: A 1339 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7549 (tp) REVERT: A 1359 MET cc_start: 0.7590 (mmm) cc_final: 0.7253 (tpt) REVERT: A 1656 PHE cc_start: 0.7689 (m-80) cc_final: 0.7156 (m-80) REVERT: A 1888 MET cc_start: 0.8262 (tpp) cc_final: 0.7855 (tpp) REVERT: A 1935 MET cc_start: 0.7467 (mtp) cc_final: 0.7208 (mtp) REVERT: A 1967 MET cc_start: 0.8497 (tmm) cc_final: 0.7568 (tmm) REVERT: A 2036 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7753 (m90) REVERT: A 2197 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7527 (t70) REVERT: A 2454 MET cc_start: 0.8672 (tmm) cc_final: 0.7579 (tmm) REVERT: A 2568 MET cc_start: 0.7802 (tmm) cc_final: 0.7139 (tmm) REVERT: C 1130 MET cc_start: 0.8990 (tpp) cc_final: 0.8762 (tpp) REVERT: C 1139 MET cc_start: 0.7515 (mmm) cc_final: 0.7176 (mmm) REVERT: C 1144 MET cc_start: 0.8357 (tpp) cc_final: 0.8049 (tpp) REVERT: C 1355 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 1474 MET cc_start: 0.8706 (tpp) cc_final: 0.8434 (tpp) REVERT: C 1683 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9185 (tt) REVERT: C 1888 MET cc_start: 0.8322 (tpp) cc_final: 0.7916 (tpp) REVERT: C 1935 MET cc_start: 0.7566 (mtp) cc_final: 0.7276 (mtp) REVERT: C 2197 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7455 (t70) REVERT: C 2234 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7853 (tp) REVERT: C 2236 MET cc_start: 0.7894 (tpt) cc_final: 0.7418 (tpp) REVERT: C 2568 MET cc_start: 0.7864 (tmm) cc_final: 0.7277 (tmm) REVERT: D 246 SER cc_start: 0.5733 (t) cc_final: 0.5490 (p) REVERT: E 1130 MET cc_start: 0.8996 (tpp) cc_final: 0.8417 (mmm) REVERT: E 1139 MET cc_start: 0.7416 (mmm) cc_final: 0.7138 (mmm) REVERT: E 1683 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9103 (tt) REVERT: E 1705 MET cc_start: 0.8919 (tmm) cc_final: 0.8548 (ppp) REVERT: E 1888 MET cc_start: 0.7779 (tpp) cc_final: 0.7329 (tpp) REVERT: E 1935 MET cc_start: 0.7723 (mtp) cc_final: 0.7283 (ptp) REVERT: E 2195 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8247 (tp) REVERT: E 2197 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7210 (t70) REVERT: E 2236 MET cc_start: 0.8148 (tpt) cc_final: 0.7910 (tpt) REVERT: E 2568 MET cc_start: 0.7557 (ttt) cc_final: 0.7243 (ptm) REVERT: E 2612 MET cc_start: 0.7161 (tpp) cc_final: 0.6859 (tpp) outliers start: 74 outliers final: 49 residues processed: 243 average time/residue: 0.1666 time to fit residues: 71.4089 Evaluate side-chains 240 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1079 TYR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2036 HIS Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2261 ILE Chi-restraints excluded: chain A residue 2347 LEU Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2615 THR Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1079 TYR Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1924 MET Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2193 MET Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2464 MET Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2714 ILE Chi-restraints excluded: chain C residue 2737 TYR Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1484 ILE Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2195 LEU Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2345 THR Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2368 VAL Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2703 ASN Chi-restraints excluded: chain E residue 2704 VAL Chi-restraints excluded: chain E residue 2714 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 193 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 390 optimal weight: 0.1980 chunk 180 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 154 optimal weight: 0.0050 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1710 HIS ** A2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.093062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067643 restraints weight = 205805.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.065809 restraints weight = 154625.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.065859 restraints weight = 119778.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.065919 restraints weight = 125536.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065994 restraints weight = 109212.812| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35796 Z= 0.125 Angle : 0.609 14.216 48528 Z= 0.306 Chirality : 0.040 0.196 5433 Planarity : 0.004 0.051 5955 Dihedral : 4.875 27.967 4614 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 1.60 % Allowed : 16.82 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.13), residues: 4194 helix: 1.37 (0.10), residues: 2619 sheet: -2.39 (0.37), residues: 156 loop : -2.93 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2478 TYR 0.045 0.001 TYR A1706 PHE 0.021 0.001 PHE C 927 TRP 0.015 0.001 TRP E2353 HIS 0.007 0.001 HIS A1710 Details of bonding type rmsd covalent geometry : bond 0.00273 (35790) covalent geometry : angle 0.60899 (48516) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.60156 ( 12) hydrogen bonds : bond 0.04009 ( 1948) hydrogen bonds : angle 4.33853 ( 5727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8388 Ramachandran restraints generated. 4194 Oldfield, 0 Emsley, 4194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1130 MET cc_start: 0.8952 (tpp) cc_final: 0.8460 (mmm) REVERT: A 1139 MET cc_start: 0.7635 (mmm) cc_final: 0.7352 (mmm) REVERT: A 1231 MET cc_start: 0.8518 (mtm) cc_final: 0.7797 (mtm) REVERT: A 1339 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7699 (tp) REVERT: A 1359 MET cc_start: 0.7509 (mmm) cc_final: 0.7144 (tpt) REVERT: A 1888 MET cc_start: 0.8405 (tpp) cc_final: 0.7935 (tpp) REVERT: A 1890 HIS cc_start: 0.8669 (p-80) cc_final: 0.8252 (p90) REVERT: A 1935 MET cc_start: 0.7273 (mtp) cc_final: 0.7038 (mtp) REVERT: A 1967 MET cc_start: 0.8283 (tmm) cc_final: 0.7737 (tmm) REVERT: A 2197 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7187 (t70) REVERT: A 2454 MET cc_start: 0.8618 (tmm) cc_final: 0.7621 (tmm) REVERT: A 2568 MET cc_start: 0.7442 (tmm) cc_final: 0.6937 (tmm) REVERT: C 1139 MET cc_start: 0.7611 (mmm) cc_final: 0.7241 (mmm) REVERT: C 1144 MET cc_start: 0.8364 (tpp) cc_final: 0.7910 (tpp) REVERT: C 1231 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: C 1355 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7851 (t80) REVERT: C 1481 MET cc_start: 0.8693 (tpp) cc_final: 0.8475 (tpp) REVERT: C 1683 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9158 (tt) REVERT: C 1888 MET cc_start: 0.8343 (tpp) cc_final: 0.7884 (tpp) REVERT: C 1935 MET cc_start: 0.7339 (mtp) cc_final: 0.7087 (mtp) REVERT: C 2197 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7015 (t70) REVERT: C 2234 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7789 (tp) REVERT: C 2236 MET cc_start: 0.7656 (tpt) cc_final: 0.7256 (tpt) REVERT: C 2454 MET cc_start: 0.8358 (tmm) cc_final: 0.7766 (tmm) REVERT: C 2568 MET cc_start: 0.7515 (tmm) cc_final: 0.6896 (tmm) REVERT: E 1130 MET cc_start: 0.8995 (tpp) cc_final: 0.8387 (mmm) REVERT: E 1139 MET cc_start: 0.7461 (mmm) cc_final: 0.7033 (mmm) REVERT: E 1683 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9117 (tt) REVERT: E 1705 MET cc_start: 0.8962 (tmm) cc_final: 0.8577 (ppp) REVERT: E 1888 MET cc_start: 0.8042 (tpp) cc_final: 0.7581 (tpp) REVERT: E 1935 MET cc_start: 0.7553 (mtp) cc_final: 0.7187 (ptp) REVERT: E 2195 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (tp) REVERT: E 2197 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6853 (t70) REVERT: E 2236 MET cc_start: 0.7926 (tpt) cc_final: 0.7675 (tpt) REVERT: E 2454 MET cc_start: 0.8372 (tmm) cc_final: 0.7546 (tmm) REVERT: E 2612 MET cc_start: 0.6716 (tpp) cc_final: 0.6434 (tpp) outliers start: 62 outliers final: 44 residues processed: 233 average time/residue: 0.1684 time to fit residues: 69.8166 Evaluate side-chains 229 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1079 TYR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1884 LEU Chi-restraints excluded: chain A residue 1981 PHE Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2234 LEU Chi-restraints excluded: chain A residue 2244 MET Chi-restraints excluded: chain A residue 2347 LEU Chi-restraints excluded: chain A residue 2368 VAL Chi-restraints excluded: chain A residue 2416 VAL Chi-restraints excluded: chain A residue 2615 THR Chi-restraints excluded: chain A residue 2641 TYR Chi-restraints excluded: chain A residue 2688 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2704 VAL Chi-restraints excluded: chain C residue 1079 TYR Chi-restraints excluded: chain C residue 1094 ILE Chi-restraints excluded: chain C residue 1231 MET Chi-restraints excluded: chain C residue 1286 LEU Chi-restraints excluded: chain C residue 1355 PHE Chi-restraints excluded: chain C residue 1418 CYS Chi-restraints excluded: chain C residue 1683 ILE Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2234 LEU Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2368 VAL Chi-restraints excluded: chain C residue 2453 THR Chi-restraints excluded: chain C residue 2615 THR Chi-restraints excluded: chain C residue 2641 TYR Chi-restraints excluded: chain C residue 2688 PHE Chi-restraints excluded: chain C residue 2704 VAL Chi-restraints excluded: chain C residue 2737 TYR Chi-restraints excluded: chain E residue 1079 TYR Chi-restraints excluded: chain E residue 1286 LEU Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1683 ILE Chi-restraints excluded: chain E residue 1884 LEU Chi-restraints excluded: chain E residue 1981 PHE Chi-restraints excluded: chain E residue 2195 LEU Chi-restraints excluded: chain E residue 2197 ASP Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2347 LEU Chi-restraints excluded: chain E residue 2368 VAL Chi-restraints excluded: chain E residue 2453 THR Chi-restraints excluded: chain E residue 2615 THR Chi-restraints excluded: chain E residue 2641 TYR Chi-restraints excluded: chain E residue 2688 PHE Chi-restraints excluded: chain E residue 2703 ASN Chi-restraints excluded: chain E residue 2704 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 168 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 330 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 GLN ** C1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2036 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2466 GLN ** E1436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.091279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.063330 restraints weight = 202607.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.062835 restraints weight = 144842.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062521 restraints weight = 105072.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.062925 restraints weight = 103590.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.062886 restraints weight = 94750.404| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 35796 Z= 0.301 Angle : 0.733 14.459 48528 Z= 0.371 Chirality : 0.043 0.287 5433 Planarity : 0.004 0.048 5955 Dihedral : 5.095 30.150 4614 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.56 % Favored : 89.29 % Rotamer: Outliers : 1.73 % Allowed : 16.87 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.51 (0.13), residues: 4194 helix: 1.12 (0.10), residues: 2619 sheet: -2.39 (0.38), residues: 162 loop : -3.01 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C2718 TYR 0.045 0.002 TYR A1706 PHE 0.018 0.002 PHE C2689 TRP 0.015 0.002 TRP A2417 HIS 0.006 0.001 HIS E2271 Details of bonding type rmsd covalent geometry : bond 0.00685 (35790) covalent geometry : angle 0.73270 (48516) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.82390 ( 12) hydrogen bonds : bond 0.04641 ( 1948) hydrogen bonds : angle 4.71602 ( 5727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6380.59 seconds wall clock time: 111 minutes 2.66 seconds (6662.66 seconds total)