Starting phenix.real_space_refine on Wed May 6 05:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vee_65005/05_2026/9vee_65005.map" } resolution = 3.36 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= 0.019 sd= 0.066 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 243 5.16 5 C 23004 2.51 5 N 5631 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s 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: 34893 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: "F" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Restraints were copied for chains: B, C, D, E Time building chain proxies: 14.53, per 1000 atoms: 0.42 Number of scatterers: 34893 At special positions: 0 Unit cell: (196.23, 209.945, 155.085, 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 243 16.00 O 6015 8.00 N 5631 7.00 C 23004 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 B1368 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS C1368 " - pdb=" SG CYS C1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1379 " - pdb=" SG CYS B1403 " distance=2.03 Simple disulfide: pdb=" SG CYS C1379 " - pdb=" SG CYS C1403 " 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 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: 174 helices and 9 sheets defined 65.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 917 through 957 removed outlier: 3.614A pdb=" N LEU A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 978 through 1002 removed outlier: 3.661A pdb=" N LEU A1002 " --> pdb=" O MET A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.689A pdb=" N THR A1022 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1032 removed outlier: 3.886A pdb=" N LYS A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1046 removed outlier: 3.837A pdb=" N TRP A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1056 removed outlier: 3.878A pdb=" N VAL A1055 " --> pdb=" O PRO A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1085 removed outlier: 3.984A pdb=" N PHE A1069 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1104 removed outlier: 4.501A pdb=" N ASP A1104 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 Processing helix chain 'A' and resid 1123 through 1139 Processing helix chain 'A' and resid 1140 through 1155 Processing helix chain 'A' and resid 1158 through 1185 removed outlier: 3.712A pdb=" N GLU A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A1165 " --> pdb=" O ALA A1161 " (cutoff:3.500A) Proline residue: A1167 - end of helix 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: 4.141A pdb=" N TYR A1228 " --> pdb=" O VAL A1224 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A1229 " --> pdb=" O PHE A1225 " (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: 4.630A pdb=" N THR A1303 " --> pdb=" O TRP A1299 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1335 removed outlier: 4.012A pdb=" N TYR A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY A1332 " --> pdb=" O LEU A1328 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASP A1333 " --> pdb=" O LEU A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1369 removed outlier: 4.067A pdb=" N ILE A1342 " --> pdb=" O PRO A1338 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE A1365 " --> pdb=" O ASN A1361 " (cutoff:3.500A) removed outlier: 4.487A 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 Processing helix chain 'A' and resid 1411 through 1430 removed outlier: 4.064A pdb=" N PHE A1419 " --> pdb=" O ASP A1415 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A1430 " --> pdb=" O ARG A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1497 removed outlier: 4.368A pdb=" N GLU A1496 " --> pdb=" O LYS A1492 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1548 removed outlier: 3.754A pdb=" N ARG A1547 " --> pdb=" O SER A1544 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A1548 " --> pdb=" O MET A1545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1544 through 1548' Processing helix chain 'A' and resid 1651 through 1694 removed outlier: 3.672A pdb=" N SER A1662 " --> pdb=" O ALA A1658 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU A1673 " --> pdb=" O SER A1669 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N HIS A1674 " --> pdb=" O ILE A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1717 Processing helix chain 'A' and resid 1873 through 1878 Processing helix chain 'A' and resid 1879 through 1886 Processing helix chain 'A' and resid 1891 through 1903 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 1942 No H-bonds generated for 'chain 'A' and resid 1940 through 1942' Processing helix chain 'A' and resid 1943 through 1953 removed outlier: 3.675A pdb=" N ILE A1947 " --> pdb=" O LEU A1943 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1982 Processing helix chain 'A' and resid 2016 through 2036 Processing helix chain 'A' and resid 2167 through 2180 Processing helix chain 'A' and resid 2190 through 2206 removed outlier: 4.151A pdb=" N ASP A2200 " --> pdb=" O ALA A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2207 through 2211 Processing helix chain 'A' and resid 2231 through 2253 removed outlier: 3.632A pdb=" N VAL A2235 " --> pdb=" O GLY A2231 " (cutoff:3.500A) Processing helix chain 'A' and resid 2255 through 2277 Processing helix chain 'A' and resid 2277 through 2283 Processing helix chain 'A' and resid 2285 through 2288 Processing helix chain 'A' and resid 2289 through 2312 Processing helix chain 'A' and resid 2328 through 2341 removed outlier: 3.561A 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 2425 Proline residue: A2419 - end of helix Processing helix chain 'A' and resid 2490 through 2494 removed outlier: 4.065A pdb=" N ILE A2494 " --> pdb=" O LYS A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2510 through 2522 Processing helix chain 'A' and resid 2560 through 2571 Processing helix chain 'A' and resid 2574 through 2578 Processing helix chain 'A' and resid 2607 through 2611 removed outlier: 3.706A pdb=" N PHE A2611 " --> pdb=" O GLU A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2669 through 2691 removed outlier: 4.250A pdb=" N GLY A2691 " --> pdb=" O GLU A2687 " (cutoff:3.500A) Processing helix chain 'A' and resid 2705 through 2721 removed outlier: 3.579A pdb=" N GLY A2721 " --> pdb=" O VAL A2717 " (cutoff:3.500A) Processing helix chain 'A' and resid 2723 through 2738 removed outlier: 4.150A pdb=" N GLU A2727 " --> pdb=" O LEU A2723 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A2728 " --> pdb=" O GLU A2724 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 189 removed outlier: 4.108A pdb=" N ARG F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 957 removed outlier: 5.300A pdb=" N ILE B 943 " --> pdb=" O GLU B 939 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 978 through 1002 removed outlier: 3.662A pdb=" N LEU B1002 " --> pdb=" O MET B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1022 removed outlier: 3.688A pdb=" N THR B1022 " --> pdb=" O GLU B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1032 removed outlier: 3.886A pdb=" N LYS B1031 " --> pdb=" O ASN B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1046 removed outlier: 3.836A pdb=" N TRP B1044 " --> pdb=" O ASP B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1056 removed outlier: 3.879A pdb=" N VAL B1055 " --> pdb=" O PRO B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1085 removed outlier: 3.986A pdb=" N PHE B1069 " --> pdb=" O ALA B1065 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B1078 " --> pdb=" O TYR B1074 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B1084 " --> pdb=" O TYR B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1104 removed outlier: 4.501A pdb=" N ASP B1104 " --> pdb=" O ARG B1100 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1118 Processing helix chain 'B' and resid 1123 through 1139 Processing helix chain 'B' and resid 1140 through 1155 Processing helix chain 'B' and resid 1158 through 1185 removed outlier: 3.713A pdb=" N GLU B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B1165 " --> pdb=" O ALA B1161 " (cutoff:3.500A) Proline residue: B1167 - end of helix Processing helix chain 'B' and resid 1195 through 1199 Processing helix chain 'B' and resid 1205 through 1213 Processing helix chain 'B' and resid 1224 through 1244 removed outlier: 4.140A pdb=" N TYR B1228 " --> pdb=" O VAL B1224 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B1229 " --> pdb=" O PHE B1225 " (cutoff:3.500A) Processing helix chain 'B' and resid 1248 through 1255 Processing helix chain 'B' and resid 1284 through 1295 Processing helix chain 'B' and resid 1297 through 1312 removed outlier: 4.630A pdb=" N THR B1303 " --> pdb=" O TRP B1299 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG B1312 " --> pdb=" O THR B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1335 removed outlier: 4.010A pdb=" N TYR B1320 " --> pdb=" O PHE B1316 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY B1332 " --> pdb=" O LEU B1328 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP B1333 " --> pdb=" O LEU B1329 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1369 removed outlier: 4.066A pdb=" N ILE B1342 " --> pdb=" O PRO B1338 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE B1365 " --> pdb=" O ASN B1361 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B1366 " --> pdb=" O ILE B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1375 Processing helix chain 'B' and resid 1378 through 1386 Processing helix chain 'B' and resid 1411 through 1430 removed outlier: 4.063A pdb=" N PHE B1419 " --> pdb=" O ASP B1415 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET B1430 " --> pdb=" O ARG B1426 " (cutoff:3.500A) Processing helix chain 'B' and resid 1431 through 1497 removed outlier: 4.367A pdb=" N GLU B1496 " --> pdb=" O LYS B1492 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B1497 " --> pdb=" O LYS B1493 " (cutoff:3.500A) Processing helix chain 'B' and resid 1544 through 1548 removed outlier: 3.753A pdb=" N ARG B1547 " --> pdb=" O SER B1544 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B1548 " --> pdb=" O MET B1545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1544 through 1548' Processing helix chain 'B' and resid 1651 through 1694 removed outlier: 3.672A pdb=" N SER B1662 " --> pdb=" O ALA B1658 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU B1673 " --> pdb=" O SER B1669 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B1674 " --> pdb=" O ILE B1670 " (cutoff:3.500A) Processing helix chain 'B' and resid 1699 through 1717 Processing helix chain 'B' and resid 1873 through 1878 Processing helix chain 'B' and resid 1879 through 1886 Processing helix chain 'B' and resid 1891 through 1903 Processing helix chain 'B' and resid 1905 through 1921 Processing helix chain 'B' and resid 1921 through 1938 Processing helix chain 'B' and resid 1940 through 1942 No H-bonds generated for 'chain 'B' and resid 1940 through 1942' Processing helix chain 'B' and resid 1943 through 1953 removed outlier: 3.675A pdb=" N ILE B1947 " --> pdb=" O LEU B1943 " (cutoff:3.500A) Processing helix chain 'B' and resid 1961 through 1982 Processing helix chain 'B' and resid 2016 through 2036 Processing helix chain 'B' and resid 2167 through 2180 Processing helix chain 'B' and resid 2190 through 2206 removed outlier: 4.150A pdb=" N ASP B2200 " --> pdb=" O ALA B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2207 through 2211 Processing helix chain 'B' and resid 2231 through 2253 removed outlier: 3.630A pdb=" N VAL B2235 " --> pdb=" O GLY B2231 " (cutoff:3.500A) Processing helix chain 'B' and resid 2255 through 2277 Processing helix chain 'B' and resid 2277 through 2283 Processing helix chain 'B' and resid 2285 through 2288 Processing helix chain 'B' and resid 2289 through 2312 Processing helix chain 'B' and resid 2328 through 2341 removed outlier: 3.562A pdb=" N VAL B2341 " --> pdb=" O GLY B2337 " (cutoff:3.500A) Processing helix chain 'B' and resid 2344 through 2355 Processing helix chain 'B' and resid 2361 through 2388 Processing helix chain 'B' and resid 2397 through 2425 Proline residue: B2419 - end of helix Processing helix chain 'B' and resid 2490 through 2494 removed outlier: 4.066A pdb=" N ILE B2494 " --> pdb=" O LYS B2491 " (cutoff:3.500A) Processing helix chain 'B' and resid 2510 through 2522 Processing helix chain 'B' and resid 2560 through 2571 Processing helix chain 'B' and resid 2574 through 2578 Processing helix chain 'B' and resid 2607 through 2611 removed outlier: 3.706A pdb=" N PHE B2611 " --> pdb=" O GLU B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2669 through 2691 removed outlier: 4.250A pdb=" N GLY B2691 " --> pdb=" O GLU B2687 " (cutoff:3.500A) Processing helix chain 'B' and resid 2705 through 2721 removed outlier: 3.581A pdb=" N GLY B2721 " --> pdb=" O VAL B2717 " (cutoff:3.500A) Processing helix chain 'B' and resid 2723 through 2738 removed outlier: 4.149A pdb=" N GLU B2727 " --> pdb=" O LEU B2723 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B2728 " --> pdb=" O GLU B2724 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 189 removed outlier: 4.108A pdb=" N ARG D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 957 removed outlier: 5.299A pdb=" N ILE C 943 " --> pdb=" O GLU C 939 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 978 through 1002 removed outlier: 3.662A pdb=" N LEU C1002 " --> pdb=" O MET C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1022 removed outlier: 3.689A pdb=" N THR C1022 " --> pdb=" O GLU C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1032 removed outlier: 3.885A pdb=" N LYS C1031 " --> pdb=" O ASN C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1046 removed outlier: 3.838A pdb=" N TRP C1044 " --> pdb=" O ASP C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1056 removed outlier: 3.878A pdb=" N VAL C1055 " --> pdb=" O PRO C1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1085 removed outlier: 3.985A pdb=" N PHE C1069 " --> pdb=" O ALA C1065 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1078 " --> pdb=" O TYR C1074 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN C1084 " --> pdb=" O TYR C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1104 removed outlier: 4.501A pdb=" N ASP C1104 " --> pdb=" O ARG C1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1118 Processing helix chain 'C' and resid 1123 through 1139 Processing helix chain 'C' and resid 1140 through 1155 Processing helix chain 'C' and resid 1158 through 1185 removed outlier: 3.713A pdb=" N GLU C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C1165 " --> pdb=" O ALA C1161 " (cutoff:3.500A) Proline residue: C1167 - end of helix 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: 4.141A pdb=" N TYR C1228 " --> pdb=" O VAL C1224 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C1229 " --> pdb=" O PHE C1225 " (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: 4.630A pdb=" N THR C1303 " --> pdb=" O TRP C1299 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG C1312 " --> pdb=" O THR C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1335 removed outlier: 4.010A pdb=" N TYR C1320 " --> pdb=" O PHE C1316 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY C1332 " --> pdb=" O LEU C1328 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP C1333 " --> pdb=" O LEU C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1369 removed outlier: 4.066A pdb=" N ILE C1342 " --> pdb=" O PRO C1338 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE C1365 " --> pdb=" O ASN C1361 " (cutoff:3.500A) removed outlier: 4.487A 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 Processing helix chain 'C' and resid 1411 through 1430 removed outlier: 4.063A pdb=" N PHE C1419 " --> pdb=" O ASP C1415 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET C1430 " --> pdb=" O ARG C1426 " (cutoff:3.500A) Processing helix chain 'C' and resid 1431 through 1497 removed outlier: 4.366A pdb=" N GLU C1496 " --> pdb=" O LYS C1492 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C1497 " --> pdb=" O LYS C1493 " (cutoff:3.500A) Processing helix chain 'C' and resid 1544 through 1548 removed outlier: 3.753A pdb=" N ARG C1547 " --> pdb=" O SER C1544 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C1548 " --> pdb=" O MET C1545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1544 through 1548' Processing helix chain 'C' and resid 1651 through 1694 removed outlier: 3.673A pdb=" N SER C1662 " --> pdb=" O ALA C1658 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU C1673 " --> pdb=" O SER C1669 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS C1674 " --> pdb=" O ILE C1670 " (cutoff:3.500A) Processing helix chain 'C' and resid 1699 through 1717 Processing helix chain 'C' and resid 1873 through 1878 Processing helix chain 'C' and resid 1879 through 1886 Processing helix chain 'C' and resid 1891 through 1903 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 1942 No H-bonds generated for 'chain 'C' and resid 1940 through 1942' Processing helix chain 'C' and resid 1943 through 1953 removed outlier: 3.674A pdb=" N ILE C1947 " --> pdb=" O LEU C1943 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1982 Processing helix chain 'C' and resid 2016 through 2036 Processing helix chain 'C' and resid 2167 through 2180 Processing helix chain 'C' and resid 2190 through 2206 removed outlier: 4.150A pdb=" N ASP C2200 " --> pdb=" O ALA C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2207 through 2211 Processing helix chain 'C' and resid 2231 through 2253 removed outlier: 3.631A pdb=" N VAL C2235 " --> pdb=" O GLY C2231 " (cutoff:3.500A) Processing helix chain 'C' and resid 2255 through 2277 Processing helix chain 'C' and resid 2277 through 2283 Processing helix chain 'C' and resid 2285 through 2288 Processing helix chain 'C' and resid 2289 through 2312 Processing helix chain 'C' and resid 2328 through 2341 removed outlier: 3.562A 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 2425 Proline residue: C2419 - end of helix Processing helix chain 'C' and resid 2490 through 2494 removed outlier: 4.065A pdb=" N ILE C2494 " --> pdb=" O LYS C2491 " (cutoff:3.500A) Processing helix chain 'C' and resid 2510 through 2522 Processing helix chain 'C' and resid 2560 through 2571 Processing helix chain 'C' and resid 2574 through 2578 Processing helix chain 'C' and resid 2607 through 2611 removed outlier: 3.706A pdb=" N PHE C2611 " --> pdb=" O GLU C2608 " (cutoff:3.500A) Processing helix chain 'C' and resid 2669 through 2691 removed outlier: 4.251A pdb=" N GLY C2691 " --> pdb=" O GLU C2687 " (cutoff:3.500A) Processing helix chain 'C' and resid 2705 through 2721 removed outlier: 3.580A pdb=" N GLY C2721 " --> pdb=" O VAL C2717 " (cutoff:3.500A) Processing helix chain 'C' and resid 2723 through 2738 removed outlier: 4.150A pdb=" N GLU C2727 " --> pdb=" O LEU C2723 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C2728 " --> pdb=" O GLU C2724 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 189 removed outlier: 4.109A pdb=" N ARG E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2450 through 2453 removed outlier: 6.612A pdb=" N LEU A2445 " --> pdb=" O PRO A2450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A2555 " --> pdb=" O VAL A2530 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A2534 " --> pdb=" O ASP A2551 " (cutoff:3.500A) removed outlier: 4.092A 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: 3.599A pdb=" N VAL A2652 " --> pdb=" O THR A2495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2581 through 2587 removed outlier: 5.399A pdb=" N THR A2582 " --> pdb=" O ILE A2616 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A2616 " --> pdb=" O THR A2582 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A2584 " --> pdb=" O ILE A2614 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A2614 " --> pdb=" O GLU A2584 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A2612 " --> pdb=" O ILE A2586 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A2615 " --> pdb=" O ASN A2634 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2450 through 2453 removed outlier: 6.613A pdb=" N LEU B2445 " --> pdb=" O PRO B2450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B2555 " --> pdb=" O VAL B2530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B2534 " --> pdb=" O ASP B2551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP B2551 " --> pdb=" O TRP B2534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2461 through 2462 removed outlier: 3.600A pdb=" N VAL B2652 " --> pdb=" O THR B2495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2581 through 2587 removed outlier: 5.399A pdb=" N THR B2582 " --> pdb=" O ILE B2616 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE B2616 " --> pdb=" O THR B2582 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU B2584 " --> pdb=" O ILE B2614 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE B2614 " --> pdb=" O GLU B2584 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET B2612 " --> pdb=" O ILE B2586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B2615 " --> pdb=" O ASN B2634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2450 through 2453 removed outlier: 6.613A pdb=" N LEU C2445 " --> pdb=" O PRO C2450 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C2555 " --> pdb=" O VAL C2530 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP C2534 " --> pdb=" O ASP C2551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP C2551 " --> pdb=" O TRP C2534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2461 through 2462 removed outlier: 3.599A pdb=" N VAL C2652 " --> pdb=" O THR C2495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2581 through 2587 removed outlier: 5.399A pdb=" N THR C2582 " --> pdb=" O ILE C2616 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE C2616 " --> pdb=" O THR C2582 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU C2584 " --> pdb=" O ILE C2614 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C2614 " --> pdb=" O GLU C2584 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET C2612 " --> pdb=" O ILE C2586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C2615 " --> pdb=" O ASN C2634 " (cutoff:3.500A) 2058 hydrogen bonds defined for protein. 6003 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: 6.66 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10480 1.34 - 1.46: 7310 1.46 - 1.58: 17652 1.58 - 1.70: 0 1.70 - 1.82: 384 Bond restraints: 35826 Sorted by residual: bond pdb=" C ILE B2509 " pdb=" N SER B2510 " ideal model delta sigma weight residual 1.330 1.235 0.095 1.47e-02 4.63e+03 4.20e+01 bond pdb=" C ILE C2509 " pdb=" N SER C2510 " ideal model delta sigma weight residual 1.330 1.235 0.095 1.47e-02 4.63e+03 4.15e+01 bond pdb=" C ILE A2509 " pdb=" N SER A2510 " ideal model delta sigma weight residual 1.330 1.235 0.095 1.47e-02 4.63e+03 4.14e+01 bond pdb=" C ARG C2738 " pdb=" N SER C2739 " ideal model delta sigma weight residual 1.332 1.300 0.033 1.14e-02 7.69e+03 8.20e+00 bond pdb=" C ARG B2738 " pdb=" N SER B2739 " ideal model delta sigma weight residual 1.332 1.301 0.032 1.14e-02 7.69e+03 7.74e+00 ... (remaining 35821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 47377 2.59 - 5.17: 1056 5.17 - 7.76: 113 7.76 - 10.34: 12 10.34 - 12.93: 6 Bond angle restraints: 48564 Sorted by residual: angle pdb=" C ILE C2509 " pdb=" N SER C2510 " pdb=" CA SER C2510 " ideal model delta sigma weight residual 120.68 133.61 -12.93 1.52e+00 4.33e-01 7.23e+01 angle pdb=" C ILE A2509 " pdb=" N SER A2510 " pdb=" CA SER A2510 " ideal model delta sigma weight residual 120.68 133.56 -12.88 1.52e+00 4.33e-01 7.18e+01 angle pdb=" C ILE B2509 " pdb=" N SER B2510 " pdb=" CA SER B2510 " ideal model delta sigma weight residual 120.68 133.56 -12.88 1.52e+00 4.33e-01 7.18e+01 angle pdb=" N ILE A2696 " pdb=" CA ILE A2696 " pdb=" C ILE A2696 " ideal model delta sigma weight residual 111.58 105.01 6.57 1.06e+00 8.90e-01 3.85e+01 angle pdb=" N ILE B2696 " pdb=" CA ILE B2696 " pdb=" C ILE B2696 " ideal model delta sigma weight residual 111.58 105.02 6.56 1.06e+00 8.90e-01 3.83e+01 ... (remaining 48559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18969 18.00 - 36.00: 1893 36.00 - 53.99: 240 53.99 - 71.99: 18 71.99 - 89.99: 27 Dihedral angle restraints: 21147 sinusoidal: 8550 harmonic: 12597 Sorted by residual: dihedral pdb=" CA ASN A2642 " pdb=" C ASN A2642 " pdb=" N PRO A2643 " pdb=" CA PRO A2643 " ideal model delta harmonic sigma weight residual 180.00 148.26 31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ASN C2642 " pdb=" C ASN C2642 " pdb=" N PRO C2643 " pdb=" CA PRO C2643 " ideal model delta harmonic sigma weight residual 180.00 148.40 31.60 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA ASN B2642 " pdb=" C ASN B2642 " pdb=" N PRO B2643 " pdb=" CA PRO B2643 " ideal model delta harmonic sigma weight residual 180.00 148.40 31.60 0 5.00e+00 4.00e-02 3.99e+01 ... (remaining 21144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3930 0.053 - 0.106: 1284 0.106 - 0.160: 204 0.160 - 0.213: 12 0.213 - 0.266: 9 Chirality restraints: 5439 Sorted by residual: chirality pdb=" CB ILE B2007 " pdb=" CA ILE B2007 " pdb=" CG1 ILE B2007 " pdb=" CG2 ILE B2007 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C2007 " pdb=" CA ILE C2007 " pdb=" CG1 ILE C2007 " pdb=" CG2 ILE C2007 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A2007 " pdb=" CA ILE A2007 " pdb=" CG1 ILE A2007 " pdb=" CG2 ILE A2007 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 5436 not shown) Planarity restraints: 5958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2630 " -0.032 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP A2630 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A2630 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A2630 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A2630 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A2630 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A2630 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2630 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2630 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A2630 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B2630 " 0.032 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP B2630 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B2630 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B2630 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B2630 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B2630 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B2630 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B2630 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B2630 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B2630 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C2630 " 0.032 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP C2630 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP C2630 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C2630 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C2630 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C2630 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C2630 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C2630 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C2630 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C2630 " 0.010 2.00e-02 2.50e+03 ... (remaining 5955 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 520 2.65 - 3.21: 35174 3.21 - 3.78: 55368 3.78 - 4.34: 71797 4.34 - 4.90: 117369 Nonbonded interactions: 280228 Sorted by model distance: nonbonded pdb=" OG SER B 959 " pdb=" OD1 ASN B 962 " model vdw 2.090 3.040 nonbonded pdb=" OG SER C 959 " pdb=" OD1 ASN C 962 " model vdw 2.091 3.040 nonbonded pdb=" OG SER A 959 " pdb=" OD1 ASN A 962 " model vdw 2.091 3.040 nonbonded pdb=" OG1 THR B2442 " pdb=" OG SER B2533 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C2442 " pdb=" OG SER C2533 " model vdw 2.107 3.040 ... (remaining 280223 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 'B' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 37.010 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 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 : 0.009 0.095 35832 Z= 0.398 Angle : 0.899 12.928 48576 Z= 0.497 Chirality : 0.050 0.266 5439 Planarity : 0.006 0.085 5958 Dihedral : 13.995 89.988 12957 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.76 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.37 (0.13), residues: 4191 helix: 0.22 (0.10), residues: 2574 sheet: -2.91 (0.47), residues: 117 loop : -2.75 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 189 TYR 0.036 0.002 TYR A2737 PHE 0.044 0.003 PHE C2211 TRP 0.062 0.003 TRP A2630 HIS 0.011 0.002 HIS B1934 Details of bonding type rmsd covalent geometry : bond 0.00931 (35826) covalent geometry : angle 0.89876 (48564) SS BOND : bond 0.00214 ( 6) SS BOND : angle 0.45806 ( 12) hydrogen bonds : bond 0.13648 ( 2058) hydrogen bonds : angle 6.12028 ( 6003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1967 MET cc_start: 0.8053 (tmm) cc_final: 0.7746 (tmm) REVERT: B 945 ILE cc_start: 0.7910 (mp) cc_final: 0.7710 (mt) REVERT: B 1967 MET cc_start: 0.7790 (tmm) cc_final: 0.7094 (tmm) REVERT: B 2244 MET cc_start: 0.7117 (mtt) cc_final: 0.6893 (mtt) REVERT: C 1967 MET cc_start: 0.7814 (tmm) cc_final: 0.7499 (tmm) REVERT: C 2563 LYS cc_start: 0.6856 (mmtt) cc_final: 0.6653 (mmtm) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.2149 time to fit residues: 126.3925 Evaluate side-chains 284 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 0.7980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2519 HIS B1709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.102789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.081084 restraints weight = 130169.950| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.92 r_work: 0.3422 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35832 Z= 0.159 Angle : 0.655 10.576 48576 Z= 0.345 Chirality : 0.042 0.178 5439 Planarity : 0.005 0.073 5958 Dihedral : 5.421 30.679 4617 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.47 % Favored : 92.39 % Rotamer: Outliers : 1.06 % Allowed : 8.15 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -0.81 (0.13), residues: 4191 helix: 0.65 (0.10), residues: 2607 sheet: -2.56 (0.48), residues: 111 loop : -2.59 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2620 TYR 0.025 0.002 TYR C1079 PHE 0.025 0.002 PHE B2211 TRP 0.039 0.002 TRP A 969 HIS 0.008 0.001 HIS A2519 Details of bonding type rmsd covalent geometry : bond 0.00348 (35826) covalent geometry : angle 0.65499 (48564) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.37489 ( 12) hydrogen bonds : bond 0.05144 ( 2058) hydrogen bonds : angle 5.03602 ( 6003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1063 MET cc_start: 0.6836 (ttm) cc_final: 0.6581 (ttm) REVERT: A 1144 MET cc_start: 0.7342 (mmp) cc_final: 0.6901 (mmp) REVERT: A 1967 MET cc_start: 0.8926 (tmm) cc_final: 0.8552 (tmm) REVERT: A 2470 ASN cc_start: 0.7332 (t0) cc_final: 0.7121 (m-40) REVERT: A 2483 MET cc_start: 0.8412 (mmt) cc_final: 0.7934 (mmt) REVERT: A 2530 VAL cc_start: 0.8671 (t) cc_final: 0.8408 (m) REVERT: A 2568 MET cc_start: 0.8530 (tpp) cc_final: 0.8274 (tpp) REVERT: B 1063 MET cc_start: 0.7246 (ttm) cc_final: 0.6900 (ttt) REVERT: B 1130 MET cc_start: 0.7187 (mmt) cc_final: 0.6985 (mmp) REVERT: B 1270 PHE cc_start: 0.7485 (t80) cc_final: 0.6887 (t80) REVERT: B 1542 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.6060 (m-70) REVERT: B 2404 MET cc_start: 0.7591 (mtm) cc_final: 0.7374 (ttp) REVERT: B 2568 MET cc_start: 0.8894 (tpp) cc_final: 0.8687 (tpt) REVERT: C 1712 MET cc_start: 0.7883 (mmp) cc_final: 0.7532 (mmm) REVERT: C 2464 MET cc_start: 0.7509 (tpp) cc_final: 0.7285 (tpp) REVERT: C 2483 MET cc_start: 0.8155 (mmp) cc_final: 0.7831 (mmt) REVERT: C 2520 GLU cc_start: 0.8663 (tt0) cc_final: 0.8319 (tt0) REVERT: C 2612 MET cc_start: 0.8861 (tpp) cc_final: 0.8616 (mtt) outliers start: 41 outliers final: 17 residues processed: 309 average time/residue: 0.2083 time to fit residues: 109.3351 Evaluate side-chains 290 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 272 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2437 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1542 HIS Chi-restraints excluded: chain B residue 2459 SER Chi-restraints excluded: chain B residue 2614 ILE Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1273 HIS Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 2404 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 381 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 272 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1876 HIS A2519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.092382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.070699 restraints weight = 130976.957| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.87 r_work: 0.3398 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35832 Z= 0.169 Angle : 0.617 10.133 48576 Z= 0.323 Chirality : 0.041 0.207 5439 Planarity : 0.005 0.069 5958 Dihedral : 5.140 30.660 4617 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 1.48 % Allowed : 10.97 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.53 (0.13), residues: 4191 helix: 0.84 (0.10), residues: 2616 sheet: -2.23 (0.49), residues: 105 loop : -2.45 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2738 TYR 0.029 0.001 TYR A2183 PHE 0.038 0.002 PHE C2211 TRP 0.045 0.002 TRP A 969 HIS 0.013 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00384 (35826) covalent geometry : angle 0.61739 (48564) SS BOND : bond 0.00173 ( 6) SS BOND : angle 0.33627 ( 12) hydrogen bonds : bond 0.04838 ( 2058) hydrogen bonds : angle 4.84028 ( 6003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1063 MET cc_start: 0.6770 (ttm) cc_final: 0.6223 (ttt) REVERT: A 1144 MET cc_start: 0.7378 (mmp) cc_final: 0.6918 (mmp) REVERT: A 1481 MET cc_start: 0.7961 (mtp) cc_final: 0.7673 (ttt) REVERT: A 1967 MET cc_start: 0.8879 (tmm) cc_final: 0.8549 (tmm) REVERT: A 2483 MET cc_start: 0.8341 (mmt) cc_final: 0.7846 (mmt) REVERT: A 2530 VAL cc_start: 0.8626 (t) cc_final: 0.8347 (m) REVERT: A 2568 MET cc_start: 0.8549 (tpp) cc_final: 0.8314 (tpp) REVERT: A 2611 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 1063 MET cc_start: 0.7214 (ttm) cc_final: 0.6855 (ttt) REVERT: B 1542 HIS cc_start: 0.6431 (OUTLIER) cc_final: 0.6157 (m-70) REVERT: B 1967 MET cc_start: 0.8759 (tmm) cc_final: 0.8008 (tmm) REVERT: B 2274 MET cc_start: 0.8829 (ttp) cc_final: 0.8599 (mtp) REVERT: B 2464 MET cc_start: 0.8055 (tpp) cc_final: 0.7771 (tpp) REVERT: B 2611 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7488 (t80) REVERT: C 934 MET cc_start: 0.8556 (ptp) cc_final: 0.8017 (ppp) REVERT: C 945 ILE cc_start: 0.7805 (tp) cc_final: 0.7563 (tt) REVERT: C 978 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6592 (pt) REVERT: C 1183 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (tt) REVERT: C 1712 MET cc_start: 0.7855 (mmp) cc_final: 0.7573 (mmm) REVERT: C 2464 MET cc_start: 0.7475 (tpp) cc_final: 0.7209 (tpp) REVERT: C 2483 MET cc_start: 0.8194 (mmp) cc_final: 0.7860 (mmt) REVERT: C 2520 GLU cc_start: 0.8633 (tt0) cc_final: 0.8303 (tt0) outliers start: 57 outliers final: 26 residues processed: 321 average time/residue: 0.2026 time to fit residues: 111.1169 Evaluate side-chains 305 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2459 SER Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2611 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1542 HIS Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2611 PHE Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain C residue 928 HIS Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2611 PHE Chi-restraints excluded: chain C residue 2703 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 93 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 382 optimal weight: 0.5980 chunk 370 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1876 HIS A2470 ASN A2474 GLN A2519 HIS A2537 GLN B1983 GLN ** C1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.099588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.076391 restraints weight = 119304.415| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.36 r_work: 0.3390 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35832 Z= 0.136 Angle : 0.578 9.762 48576 Z= 0.303 Chirality : 0.040 0.232 5439 Planarity : 0.004 0.065 5958 Dihedral : 4.959 30.937 4617 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.66 % Favored : 93.20 % Rotamer: Outliers : 1.86 % Allowed : 12.78 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.24 (0.13), residues: 4191 helix: 1.07 (0.10), residues: 2622 sheet: -1.96 (0.51), residues: 105 loop : -2.36 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2639 TYR 0.024 0.001 TYR C1079 PHE 0.027 0.001 PHE B2211 TRP 0.033 0.001 TRP C2209 HIS 0.013 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00294 (35826) covalent geometry : angle 0.57769 (48564) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.32454 ( 12) hydrogen bonds : bond 0.04500 ( 2058) hydrogen bonds : angle 4.65648 ( 6003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 ILE cc_start: 0.7613 (tp) cc_final: 0.7337 (pt) REVERT: A 1063 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6072 (ttt) REVERT: A 1073 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 1144 MET cc_start: 0.7383 (mmp) cc_final: 0.6918 (mmp) REVERT: A 1481 MET cc_start: 0.8093 (mtp) cc_final: 0.7805 (ttt) REVERT: A 1710 HIS cc_start: 0.5168 (m-70) cc_final: 0.4688 (m90) REVERT: A 1967 MET cc_start: 0.8902 (tmm) cc_final: 0.8567 (tmm) REVERT: A 2197 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7577 (t70) REVERT: A 2464 MET cc_start: 0.7236 (tpp) cc_final: 0.6324 (tpp) REVERT: A 2483 MET cc_start: 0.8432 (mmt) cc_final: 0.7965 (mmt) REVERT: A 2530 VAL cc_start: 0.8581 (t) cc_final: 0.8281 (m) REVERT: A 2568 MET cc_start: 0.8617 (tpp) cc_final: 0.8394 (tpt) REVERT: B 1063 MET cc_start: 0.7164 (ttm) cc_final: 0.6811 (ttt) REVERT: B 1069 PHE cc_start: 0.8399 (t80) cc_final: 0.8168 (t80) REVERT: B 1270 PHE cc_start: 0.7387 (t80) cc_final: 0.6957 (t80) REVERT: B 1542 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6235 (m-70) REVERT: B 1888 MET cc_start: 0.7323 (tpp) cc_final: 0.7062 (tpp) REVERT: B 1967 MET cc_start: 0.8758 (tmm) cc_final: 0.8139 (tmm) REVERT: B 2211 PHE cc_start: 0.7596 (t80) cc_final: 0.7282 (t80) REVERT: B 2464 MET cc_start: 0.8073 (tpp) cc_final: 0.7810 (tpp) REVERT: B 2483 MET cc_start: 0.8325 (mmm) cc_final: 0.8116 (mtt) REVERT: B 2611 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7219 (t80) REVERT: D 182 GLU cc_start: 0.4489 (tp30) cc_final: 0.3960 (tp30) REVERT: C 934 MET cc_start: 0.8674 (ptp) cc_final: 0.8101 (ppp) REVERT: C 945 ILE cc_start: 0.7739 (tp) cc_final: 0.7496 (tt) REVERT: C 978 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6502 (pt) REVERT: C 1063 MET cc_start: 0.6743 (ttm) cc_final: 0.6408 (ttt) REVERT: C 1073 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8482 (mm) REVERT: C 1183 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7876 (tt) REVERT: C 1712 MET cc_start: 0.7882 (mmp) cc_final: 0.7608 (mmm) REVERT: C 2197 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7599 (t70) REVERT: C 2464 MET cc_start: 0.7551 (tpp) cc_final: 0.7345 (tpp) REVERT: C 2483 MET cc_start: 0.8244 (mmp) cc_final: 0.7856 (mmt) REVERT: C 2520 GLU cc_start: 0.8617 (tt0) cc_final: 0.8296 (tt0) outliers start: 72 outliers final: 34 residues processed: 334 average time/residue: 0.1959 time to fit residues: 111.3269 Evaluate side-chains 317 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1542 HIS Chi-restraints excluded: chain B residue 1981 PHE Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2437 LEU Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2611 PHE Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 978 LEU Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1073 ILE Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2211 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2433 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2474 GLN Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2611 PHE Chi-restraints excluded: chain C residue 2703 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 280 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 413 optimal weight: 5.9990 chunk 394 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 147 optimal weight: 0.0870 chunk 297 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1146 HIS A1542 HIS A1710 HIS A2519 HIS B1146 HIS C1146 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.099090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.076154 restraints weight = 129769.242| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.18 r_work: 0.3250 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 35832 Z= 0.301 Angle : 0.690 10.891 48576 Z= 0.361 Chirality : 0.044 0.252 5439 Planarity : 0.005 0.067 5958 Dihedral : 5.086 30.295 4617 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.08 % Rotamer: Outliers : 2.43 % Allowed : 14.13 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.63 (0.13), residues: 4191 helix: 0.72 (0.10), residues: 2622 sheet: -2.19 (0.48), residues: 105 loop : -2.41 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C2738 TYR 0.036 0.002 TYR C2737 PHE 0.035 0.002 PHE B2211 TRP 0.036 0.002 TRP B2209 HIS 0.006 0.002 HIS C1281 Details of bonding type rmsd covalent geometry : bond 0.00715 (35826) covalent geometry : angle 0.69032 (48564) SS BOND : bond 0.00167 ( 6) SS BOND : angle 0.40877 ( 12) hydrogen bonds : bond 0.05078 ( 2058) hydrogen bonds : angle 4.78858 ( 6003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 298 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8666 (ptt) cc_final: 0.8162 (ppp) REVERT: A 945 ILE cc_start: 0.7615 (tp) cc_final: 0.7300 (pt) REVERT: A 1073 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 1270 PHE cc_start: 0.7690 (t80) cc_final: 0.7363 (t80) REVERT: A 1481 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7770 (ttt) REVERT: A 1710 HIS cc_start: 0.5088 (m170) cc_final: 0.4845 (m90) REVERT: A 1895 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: A 2197 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7692 (t70) REVERT: A 2454 MET cc_start: 0.7608 (tmm) cc_final: 0.6790 (tmm) REVERT: A 2568 MET cc_start: 0.8793 (tpp) cc_final: 0.8526 (tpt) REVERT: B 965 PHE cc_start: 0.7080 (m-10) cc_final: 0.6731 (m-10) REVERT: B 1063 MET cc_start: 0.6914 (ttm) cc_final: 0.6600 (ttt) REVERT: B 1144 MET cc_start: 0.7429 (mmp) cc_final: 0.6640 (tmm) REVERT: B 1542 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.6153 (m-70) REVERT: B 1888 MET cc_start: 0.7812 (tpp) cc_final: 0.6690 (mmm) REVERT: B 1895 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8515 (mm-30) REVERT: B 1967 MET cc_start: 0.8881 (tmm) cc_final: 0.8107 (tmm) REVERT: B 2197 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7183 (t0) REVERT: B 2211 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7409 (t80) REVERT: B 2404 MET cc_start: 0.7741 (ttm) cc_final: 0.7384 (ttm) REVERT: B 2448 TYR cc_start: 0.6788 (m-80) cc_final: 0.6235 (m-10) REVERT: B 2454 MET cc_start: 0.7697 (tmm) cc_final: 0.6962 (tmm) REVERT: B 2464 MET cc_start: 0.8263 (tpp) cc_final: 0.7923 (tpp) REVERT: D 182 GLU cc_start: 0.4830 (tp30) cc_final: 0.4396 (tp30) REVERT: C 934 MET cc_start: 0.8625 (ptp) cc_final: 0.8071 (ppp) REVERT: C 945 ILE cc_start: 0.7682 (tp) cc_final: 0.7446 (tt) REVERT: C 1183 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7787 (tt) REVERT: C 1712 MET cc_start: 0.7982 (mmp) cc_final: 0.7688 (mmm) REVERT: C 1895 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8247 (mm-30) REVERT: C 2197 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7594 (t70) REVERT: C 2464 MET cc_start: 0.7726 (tpp) cc_final: 0.7399 (tpp) REVERT: C 2483 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7952 (mmt) REVERT: C 2520 GLU cc_start: 0.8841 (tt0) cc_final: 0.8393 (tt0) REVERT: C 2603 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8359 (tptp) outliers start: 94 outliers final: 45 residues processed: 364 average time/residue: 0.1931 time to fit residues: 119.4341 Evaluate side-chains 345 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 1935 MET Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2711 CYS Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1464 LYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1542 HIS Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1945 LEU Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2351 MET Chi-restraints excluded: chain B residue 2437 LEU Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2694 HIS Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain B residue 2711 CYS Chi-restraints excluded: chain B residue 2734 ILE Chi-restraints excluded: chain C residue 928 HIS Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1292 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 2197 ASP Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2367 CYS Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2459 SER Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2483 MET Chi-restraints excluded: chain C residue 2703 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 199 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 402 optimal weight: 0.7980 chunk 303 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 274 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1876 HIS ** A1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.099599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075969 restraints weight = 117915.766| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.46 r_work: 0.3384 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35832 Z= 0.126 Angle : 0.580 11.605 48576 Z= 0.301 Chirality : 0.040 0.235 5439 Planarity : 0.004 0.065 5958 Dihedral : 4.887 29.793 4617 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 2.15 % Allowed : 15.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.16 (0.13), residues: 4191 helix: 1.16 (0.10), residues: 2616 sheet: -1.95 (0.49), residues: 105 loop : -2.37 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C2392 TYR 0.024 0.001 TYR C2183 PHE 0.033 0.001 PHE C2211 TRP 0.036 0.001 TRP C2209 HIS 0.014 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00271 (35826) covalent geometry : angle 0.57971 (48564) SS BOND : bond 0.00146 ( 6) SS BOND : angle 0.35322 ( 12) hydrogen bonds : bond 0.04410 ( 2058) hydrogen bonds : angle 4.55909 ( 6003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8606 (ptt) cc_final: 0.8106 (ppp) REVERT: A 945 ILE cc_start: 0.7541 (tp) cc_final: 0.7260 (pt) REVERT: A 1144 MET cc_start: 0.7260 (mmp) cc_final: 0.6800 (mmp) REVERT: A 1270 PHE cc_start: 0.7549 (t80) cc_final: 0.7286 (t80) REVERT: A 1481 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7721 (ttt) REVERT: A 1657 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7162 (mm) REVERT: A 1710 HIS cc_start: 0.5277 (m170) cc_final: 0.4990 (m90) REVERT: A 1895 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: A 1935 MET cc_start: 0.8367 (ttm) cc_final: 0.8091 (ttp) REVERT: A 2197 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7699 (t70) REVERT: A 2454 MET cc_start: 0.7456 (tmm) cc_final: 0.6700 (tmm) REVERT: A 2483 MET cc_start: 0.8446 (mmt) cc_final: 0.8000 (mmt) REVERT: A 2568 MET cc_start: 0.8656 (tpp) cc_final: 0.8443 (tpt) REVERT: B 1063 MET cc_start: 0.7011 (ttm) cc_final: 0.6662 (ttt) REVERT: B 1144 MET cc_start: 0.7448 (mmp) cc_final: 0.7232 (mmp) REVERT: B 1888 MET cc_start: 0.7304 (tpp) cc_final: 0.6352 (mmm) REVERT: B 1895 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: B 1967 MET cc_start: 0.8735 (tmm) cc_final: 0.8086 (tmm) REVERT: B 2197 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7289 (t0) REVERT: B 2211 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7125 (t80) REVERT: B 2404 MET cc_start: 0.7744 (ttm) cc_final: 0.7278 (ttm) REVERT: B 2454 MET cc_start: 0.7447 (tmm) cc_final: 0.6820 (tmm) REVERT: B 2464 MET cc_start: 0.8068 (tpp) cc_final: 0.7817 (tpp) REVERT: B 2483 MET cc_start: 0.8324 (mmm) cc_final: 0.8095 (mtt) REVERT: D 182 GLU cc_start: 0.4714 (tp30) cc_final: 0.4257 (tp30) REVERT: C 934 MET cc_start: 0.8631 (ptp) cc_final: 0.8089 (ppp) REVERT: C 945 ILE cc_start: 0.7756 (tp) cc_final: 0.7509 (tt) REVERT: C 1020 ASN cc_start: 0.6416 (m-40) cc_final: 0.6142 (t0) REVERT: C 1073 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8387 (tt) REVERT: C 1183 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (tt) REVERT: C 1712 MET cc_start: 0.8011 (mmp) cc_final: 0.7696 (mmm) REVERT: C 1895 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: C 2404 MET cc_start: 0.7871 (ttm) cc_final: 0.7642 (ttm) REVERT: C 2464 MET cc_start: 0.7465 (tpp) cc_final: 0.7216 (tpp) REVERT: C 2612 MET cc_start: 0.8841 (tpp) cc_final: 0.8551 (mtt) REVERT: E 182 GLU cc_start: 0.4957 (tt0) cc_final: 0.4684 (tp30) outliers start: 83 outliers final: 46 residues processed: 341 average time/residue: 0.1966 time to fit residues: 114.6880 Evaluate side-chains 327 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2367 CYS Chi-restraints excluded: chain A residue 2433 ILE Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2743 MET Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1455 PHE Chi-restraints excluded: chain B residue 1464 LYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1981 PHE Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2433 ILE Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2646 GLN Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 998 MET Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1073 ILE Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1463 VAL Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 2211 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2433 ILE Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2703 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 97 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 102 optimal weight: 0.6980 chunk 401 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 397 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2519 HIS A2604 GLN ** B1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1542 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.100568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078259 restraints weight = 129338.769| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.92 r_work: 0.3352 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 35832 Z= 0.204 Angle : 0.620 11.447 48576 Z= 0.321 Chirality : 0.041 0.240 5439 Planarity : 0.005 0.064 5958 Dihedral : 4.876 29.848 4617 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 2.69 % Allowed : 16.28 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.23 (0.13), residues: 4191 helix: 1.10 (0.10), residues: 2616 sheet: -1.94 (0.48), residues: 105 loop : -2.39 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C2738 TYR 0.025 0.001 TYR C2737 PHE 0.035 0.002 PHE C2211 TRP 0.039 0.001 TRP B2209 HIS 0.023 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00476 (35826) covalent geometry : angle 0.62006 (48564) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.34300 ( 12) hydrogen bonds : bond 0.04617 ( 2058) hydrogen bonds : angle 4.58352 ( 6003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 280 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8607 (ptt) cc_final: 0.8046 (ppp) REVERT: A 945 ILE cc_start: 0.7586 (tp) cc_final: 0.7281 (pt) REVERT: A 978 LEU cc_start: 0.7431 (mt) cc_final: 0.7197 (pt) REVERT: A 1270 PHE cc_start: 0.7571 (t80) cc_final: 0.7339 (t80) REVERT: A 1481 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7775 (ttt) REVERT: A 1657 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7182 (mm) REVERT: A 1710 HIS cc_start: 0.5320 (m170) cc_final: 0.5011 (m90) REVERT: A 1895 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8162 (mm-30) REVERT: A 2197 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7640 (t70) REVERT: A 2453 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 2454 MET cc_start: 0.7464 (tmm) cc_final: 0.6769 (tmm) REVERT: B 927 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7143 (p90) REVERT: B 965 PHE cc_start: 0.7034 (m-10) cc_final: 0.6753 (m-10) REVERT: B 1063 MET cc_start: 0.6999 (ttm) cc_final: 0.6712 (ttt) REVERT: B 1144 MET cc_start: 0.7481 (mmp) cc_final: 0.7229 (mmp) REVERT: B 1270 PHE cc_start: 0.7273 (t80) cc_final: 0.7042 (t80) REVERT: B 1888 MET cc_start: 0.7381 (tpp) cc_final: 0.6642 (mmm) REVERT: B 1895 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: B 1935 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8107 (mtp) REVERT: B 1967 MET cc_start: 0.8766 (tmm) cc_final: 0.7868 (tmm) REVERT: B 2197 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 2211 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 2404 MET cc_start: 0.7904 (ttm) cc_final: 0.7536 (ttm) REVERT: B 2453 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 2454 MET cc_start: 0.7643 (tmm) cc_final: 0.6982 (tmm) REVERT: B 2464 MET cc_start: 0.7992 (tpp) cc_final: 0.7766 (tpp) REVERT: D 182 GLU cc_start: 0.4520 (tp30) cc_final: 0.4028 (tp30) REVERT: C 934 MET cc_start: 0.8649 (ptp) cc_final: 0.8136 (ppp) REVERT: C 945 ILE cc_start: 0.7773 (tp) cc_final: 0.7527 (tt) REVERT: C 1020 ASN cc_start: 0.6461 (m-40) cc_final: 0.6222 (t0) REVERT: C 1030 ASN cc_start: 0.4606 (OUTLIER) cc_final: 0.3799 (t0) REVERT: C 1164 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: C 1183 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8031 (tt) REVERT: C 1712 MET cc_start: 0.8085 (mmp) cc_final: 0.7714 (mmm) REVERT: C 1895 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: C 1967 MET cc_start: 0.8751 (tmm) cc_final: 0.8400 (tmm) REVERT: C 2464 MET cc_start: 0.7482 (tpp) cc_final: 0.7244 (tpp) outliers start: 104 outliers final: 64 residues processed: 355 average time/residue: 0.1925 time to fit residues: 116.5134 Evaluate side-chains 353 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 274 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2367 CYS Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2453 THR Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2640 ILE Chi-restraints excluded: chain A residue 2697 MET Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2711 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2743 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1339 ILE Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1455 PHE Chi-restraints excluded: chain B residue 1464 LYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1935 MET Chi-restraints excluded: chain B residue 1945 LEU Chi-restraints excluded: chain B residue 2191 VAL Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2238 LEU Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2351 MET Chi-restraints excluded: chain B residue 2437 LEU Chi-restraints excluded: chain B residue 2439 VAL Chi-restraints excluded: chain B residue 2453 THR Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2640 ILE Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain B residue 2711 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1030 ASN Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1164 GLU Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1288 MET Chi-restraints excluded: chain C residue 1291 VAL Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1396 MET Chi-restraints excluded: chain C residue 1463 VAL Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 1948 LEU Chi-restraints excluded: chain C residue 2211 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2433 ILE Chi-restraints excluded: chain C residue 2439 VAL Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2640 ILE Chi-restraints excluded: chain C residue 2703 ASN Chi-restraints excluded: chain C residue 2716 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 394 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 404 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 315 optimal weight: 7.9990 chunk 283 optimal weight: 7.9990 chunk 405 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 288 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1876 HIS A2519 HIS ** B1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.098841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075077 restraints weight = 117920.225| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.30 r_work: 0.3355 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35832 Z= 0.175 Angle : 0.605 12.525 48576 Z= 0.315 Chirality : 0.041 0.243 5439 Planarity : 0.005 0.066 5958 Dihedral : 4.859 30.644 4617 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.68 % Favored : 93.18 % Rotamer: Outliers : 2.72 % Allowed : 16.51 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -0.17 (0.13), residues: 4191 helix: 1.13 (0.10), residues: 2619 sheet: -1.90 (0.49), residues: 105 loop : -2.36 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C2738 TYR 0.021 0.001 TYR C2183 PHE 0.034 0.002 PHE B2211 TRP 0.067 0.002 TRP B 969 HIS 0.017 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00405 (35826) covalent geometry : angle 0.60536 (48564) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.35558 ( 12) hydrogen bonds : bond 0.04511 ( 2058) hydrogen bonds : angle 4.53496 ( 6003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 275 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8466 (ptt) cc_final: 0.7987 (ppp) REVERT: A 945 ILE cc_start: 0.7585 (tp) cc_final: 0.7281 (pt) REVERT: A 1030 ASN cc_start: 0.4412 (OUTLIER) cc_final: 0.3807 (t0) REVERT: A 1164 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 1418 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7538 (m) REVERT: A 1481 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7737 (ttt) REVERT: A 1657 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7193 (mm) REVERT: A 1710 HIS cc_start: 0.5439 (m170) cc_final: 0.5148 (m90) REVERT: A 1895 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8206 (mm-30) REVERT: A 2197 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7627 (t70) REVERT: A 2453 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7773 (p) REVERT: A 2454 MET cc_start: 0.7468 (tmm) cc_final: 0.6792 (tmm) REVERT: A 2464 MET cc_start: 0.6781 (tpp) cc_final: 0.6579 (tpp) REVERT: A 2483 MET cc_start: 0.8465 (mmt) cc_final: 0.7986 (mmt) REVERT: B 927 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7164 (p90) REVERT: B 936 TRP cc_start: 0.7865 (t-100) cc_final: 0.7609 (t-100) REVERT: B 1030 ASN cc_start: 0.4608 (OUTLIER) cc_final: 0.4045 (t0) REVERT: B 1063 MET cc_start: 0.6920 (ttm) cc_final: 0.6701 (ttt) REVERT: B 1144 MET cc_start: 0.7476 (mmp) cc_final: 0.7218 (mmp) REVERT: B 1270 PHE cc_start: 0.7307 (t80) cc_final: 0.7036 (t80) REVERT: B 1418 CYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7502 (m) REVERT: B 1888 MET cc_start: 0.7492 (tpp) cc_final: 0.6857 (mmm) REVERT: B 1895 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: B 1935 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: B 1967 MET cc_start: 0.8770 (tmm) cc_final: 0.8465 (tmm) REVERT: B 2197 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7148 (t0) REVERT: B 2211 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7337 (t80) REVERT: B 2404 MET cc_start: 0.7895 (ttm) cc_final: 0.7528 (ttm) REVERT: B 2453 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7532 (p) REVERT: B 2454 MET cc_start: 0.7517 (tmm) cc_final: 0.6864 (tmm) REVERT: B 2464 MET cc_start: 0.7962 (tpp) cc_final: 0.7759 (tpp) REVERT: D 182 GLU cc_start: 0.4588 (tp30) cc_final: 0.4066 (tp30) REVERT: C 934 MET cc_start: 0.8672 (ptp) cc_final: 0.8138 (ppp) REVERT: C 945 ILE cc_start: 0.7786 (tp) cc_final: 0.7539 (tt) REVERT: C 965 PHE cc_start: 0.6351 (m-10) cc_final: 0.6047 (m-10) REVERT: C 1020 ASN cc_start: 0.6443 (m-40) cc_final: 0.6185 (t0) REVERT: C 1063 MET cc_start: 0.6728 (ttm) cc_final: 0.6440 (ttt) REVERT: C 1164 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: C 1183 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8037 (tt) REVERT: C 1712 MET cc_start: 0.8103 (mmp) cc_final: 0.7721 (mmm) REVERT: C 1895 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: C 2404 MET cc_start: 0.8098 (ttm) cc_final: 0.7772 (ttm) REVERT: C 2464 MET cc_start: 0.7449 (tpp) cc_final: 0.7203 (tpp) REVERT: E 182 GLU cc_start: 0.5035 (tt0) cc_final: 0.4685 (tp30) outliers start: 105 outliers final: 60 residues processed: 350 average time/residue: 0.1942 time to fit residues: 115.7644 Evaluate side-chains 352 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2367 CYS Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2453 THR Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2473 ILE Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2711 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2743 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1030 ASN Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1418 CYS Chi-restraints excluded: chain B residue 1421 PHE Chi-restraints excluded: chain B residue 1464 LYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1935 MET Chi-restraints excluded: chain B residue 2191 VAL Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2238 LEU Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2351 MET Chi-restraints excluded: chain B residue 2433 ILE Chi-restraints excluded: chain B residue 2439 VAL Chi-restraints excluded: chain B residue 2453 THR Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain B residue 2711 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2717 VAL Chi-restraints excluded: chain B residue 2734 ILE Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1164 GLU Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1288 MET Chi-restraints excluded: chain C residue 1339 ILE Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1396 MET Chi-restraints excluded: chain C residue 1463 VAL Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2439 VAL Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2703 ASN Chi-restraints excluded: chain C residue 2716 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 47 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 282 optimal weight: 40.0000 chunk 247 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 382 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 350 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1876 HIS ** B1361 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.100886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.078874 restraints weight = 128749.023| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.89 r_work: 0.3393 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35832 Z= 0.138 Angle : 0.591 13.232 48576 Z= 0.306 Chirality : 0.040 0.253 5439 Planarity : 0.004 0.065 5958 Dihedral : 4.803 31.722 4617 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.59 % Favored : 93.27 % Rotamer: Outliers : 2.36 % Allowed : 16.93 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: 0.03 (0.13), residues: 4191 helix: 1.30 (0.10), residues: 2622 sheet: -1.79 (0.49), residues: 105 loop : -2.29 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2392 TYR 0.028 0.001 TYR A2183 PHE 0.042 0.001 PHE A1889 TRP 0.041 0.001 TRP B2209 HIS 0.045 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00307 (35826) covalent geometry : angle 0.59115 (48564) SS BOND : bond 0.00118 ( 6) SS BOND : angle 0.32305 ( 12) hydrogen bonds : bond 0.04348 ( 2058) hydrogen bonds : angle 4.46709 ( 6003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 279 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8493 (ptt) cc_final: 0.8022 (ppp) REVERT: A 945 ILE cc_start: 0.7537 (tp) cc_final: 0.7252 (pt) REVERT: A 1164 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: A 1418 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7595 (m) REVERT: A 1481 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7736 (ttt) REVERT: A 1657 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 1710 HIS cc_start: 0.5643 (m170) cc_final: 0.5373 (m90) REVERT: A 1895 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: A 2197 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7662 (t70) REVERT: A 2453 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 2454 MET cc_start: 0.7375 (tmm) cc_final: 0.6731 (tmm) REVERT: A 2483 MET cc_start: 0.8294 (mmt) cc_final: 0.7948 (mmt) REVERT: A 2711 CYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7530 (m) REVERT: B 927 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7065 (p90) REVERT: B 952 TRP cc_start: 0.7670 (t60) cc_final: 0.7325 (t60) REVERT: B 965 PHE cc_start: 0.6816 (m-10) cc_final: 0.6537 (m-10) REVERT: B 1144 MET cc_start: 0.7472 (mmp) cc_final: 0.7187 (mmp) REVERT: B 1164 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: B 1270 PHE cc_start: 0.7269 (t80) cc_final: 0.7016 (t80) REVERT: B 1418 CYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7500 (m) REVERT: B 1888 MET cc_start: 0.7360 (tpp) cc_final: 0.6906 (mmm) REVERT: B 1895 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8467 (mm-30) REVERT: B 1935 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: B 1967 MET cc_start: 0.8726 (tmm) cc_final: 0.8446 (tmm) REVERT: B 2197 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7168 (t0) REVERT: B 2211 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7238 (t80) REVERT: B 2404 MET cc_start: 0.7894 (ttm) cc_final: 0.7560 (ttm) REVERT: B 2453 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7522 (p) REVERT: B 2454 MET cc_start: 0.7493 (tmm) cc_final: 0.6824 (tmm) REVERT: B 2464 MET cc_start: 0.7985 (tpp) cc_final: 0.7692 (tpp) REVERT: B 2711 CYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7673 (m) REVERT: D 182 GLU cc_start: 0.4629 (tp30) cc_final: 0.4053 (tp30) REVERT: C 934 MET cc_start: 0.8634 (ptp) cc_final: 0.8104 (ppp) REVERT: C 945 ILE cc_start: 0.7672 (tp) cc_final: 0.7441 (tt) REVERT: C 1030 ASN cc_start: 0.4718 (OUTLIER) cc_final: 0.4036 (t0) REVERT: C 1063 MET cc_start: 0.6585 (OUTLIER) cc_final: 0.6336 (ttt) REVERT: C 1164 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: C 1183 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7980 (tt) REVERT: C 1712 MET cc_start: 0.8027 (mmp) cc_final: 0.7616 (mmm) REVERT: C 1895 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: C 1906 ARG cc_start: 0.5828 (mpp-170) cc_final: 0.5614 (mpp-170) REVERT: C 2404 MET cc_start: 0.8032 (ttm) cc_final: 0.7703 (ttm) REVERT: C 2464 MET cc_start: 0.7450 (tpp) cc_final: 0.7134 (tpp) REVERT: E 182 GLU cc_start: 0.5065 (tt0) cc_final: 0.4767 (tp30) outliers start: 91 outliers final: 59 residues processed: 342 average time/residue: 0.1921 time to fit residues: 112.3107 Evaluate side-chains 356 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 275 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2367 CYS Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2453 THR Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2473 ILE Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2697 MET Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2711 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2743 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1418 CYS Chi-restraints excluded: chain B residue 1421 PHE Chi-restraints excluded: chain B residue 1464 LYS Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1935 MET Chi-restraints excluded: chain B residue 1981 PHE Chi-restraints excluded: chain B residue 2191 VAL Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2238 LEU Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2437 LEU Chi-restraints excluded: chain B residue 2439 VAL Chi-restraints excluded: chain B residue 2453 THR Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2611 PHE Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain B residue 2711 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2717 VAL Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1030 ASN Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1063 MET Chi-restraints excluded: chain C residue 1164 GLU Chi-restraints excluded: chain C residue 1183 ILE Chi-restraints excluded: chain C residue 1288 MET Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1396 MET Chi-restraints excluded: chain C residue 1463 VAL Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1657 LEU Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2439 VAL Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2703 ASN Chi-restraints excluded: chain C residue 2716 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 217 optimal weight: 0.9990 chunk 79 optimal weight: 0.0030 chunk 362 optimal weight: 0.0970 chunk 393 optimal weight: 6.9990 chunk 321 optimal weight: 0.6980 chunk 355 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 390 optimal weight: 0.8980 chunk 246 optimal weight: 0.2980 chunk 48 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1876 HIS A2519 HIS ** B1361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.102048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080178 restraints weight = 129507.397| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.23 r_work: 0.3420 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35832 Z= 0.115 Angle : 0.582 14.144 48576 Z= 0.298 Chirality : 0.039 0.258 5439 Planarity : 0.004 0.062 5958 Dihedral : 4.635 33.466 4617 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % Rotamer: Outliers : 2.04 % Allowed : 17.26 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.32 (0.13), residues: 4191 helix: 1.53 (0.10), residues: 2631 sheet: -1.66 (0.50), residues: 105 loop : -2.20 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 189 TYR 0.020 0.001 TYR C1080 PHE 0.031 0.001 PHE C2211 TRP 0.034 0.001 TRP B2209 HIS 0.018 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00244 (35826) covalent geometry : angle 0.58178 (48564) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.27053 ( 12) hydrogen bonds : bond 0.04063 ( 2058) hydrogen bonds : angle 4.32652 ( 6003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 934 MET cc_start: 0.8484 (ptt) cc_final: 0.8049 (ppp) REVERT: A 945 ILE cc_start: 0.7553 (tp) cc_final: 0.7282 (pt) REVERT: A 1144 MET cc_start: 0.7144 (mmp) cc_final: 0.6684 (mmp) REVERT: A 1164 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: A 1270 PHE cc_start: 0.7209 (t80) cc_final: 0.6896 (t80) REVERT: A 1418 CYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7524 (m) REVERT: A 1481 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (ttt) REVERT: A 1657 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7205 (mm) REVERT: A 1710 HIS cc_start: 0.5467 (m170) cc_final: 0.5184 (m90) REVERT: A 1895 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: A 2197 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7469 (t70) REVERT: A 2453 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 2454 MET cc_start: 0.7390 (tmm) cc_final: 0.6723 (tmm) REVERT: A 2470 ASN cc_start: 0.7764 (t0) cc_final: 0.7463 (m-40) REVERT: A 2483 MET cc_start: 0.8451 (mmt) cc_final: 0.8066 (mmt) REVERT: B 927 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7186 (p90) REVERT: B 1164 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: B 1270 PHE cc_start: 0.7225 (t80) cc_final: 0.7009 (t80) REVERT: B 1545 MET cc_start: 0.8327 (pmm) cc_final: 0.7963 (ptm) REVERT: B 1712 MET cc_start: 0.7722 (mmm) cc_final: 0.7128 (mmm) REVERT: B 1888 MET cc_start: 0.7470 (tpp) cc_final: 0.6954 (mmm) REVERT: B 1895 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: B 1967 MET cc_start: 0.8728 (tmm) cc_final: 0.8519 (tmm) REVERT: B 2197 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7154 (t0) REVERT: B 2211 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7106 (t80) REVERT: B 2404 MET cc_start: 0.7705 (ttm) cc_final: 0.7440 (ttm) REVERT: B 2453 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7492 (p) REVERT: B 2454 MET cc_start: 0.7239 (tmm) cc_final: 0.6602 (tmm) REVERT: B 2464 MET cc_start: 0.7883 (tpp) cc_final: 0.7635 (tpp) REVERT: B 2483 MET cc_start: 0.8401 (mmm) cc_final: 0.8099 (mtt) REVERT: C 934 MET cc_start: 0.8704 (ptp) cc_final: 0.8193 (ppp) REVERT: C 945 ILE cc_start: 0.7757 (tp) cc_final: 0.7513 (tt) REVERT: C 1164 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: C 1712 MET cc_start: 0.8191 (mmp) cc_final: 0.7749 (mmm) REVERT: C 1888 MET cc_start: 0.8010 (tpp) cc_final: 0.6685 (mmm) REVERT: C 1895 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8240 (mm-30) REVERT: C 2464 MET cc_start: 0.7248 (tpp) cc_final: 0.7030 (tpp) REVERT: C 2483 MET cc_start: 0.8104 (mmp) cc_final: 0.7740 (mtt) REVERT: E 182 GLU cc_start: 0.5020 (tt0) cc_final: 0.4655 (tp30) outliers start: 79 outliers final: 52 residues processed: 333 average time/residue: 0.1986 time to fit residues: 112.3537 Evaluate side-chains 339 residues out of total 3870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 272 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1288 MET Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1481 MET Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1876 HIS Chi-restraints excluded: chain A residue 1895 GLU Chi-restraints excluded: chain A residue 2197 ASP Chi-restraints excluded: chain A residue 2273 TRP Chi-restraints excluded: chain A residue 2341 VAL Chi-restraints excluded: chain A residue 2367 CYS Chi-restraints excluded: chain A residue 2399 VAL Chi-restraints excluded: chain A residue 2439 VAL Chi-restraints excluded: chain A residue 2453 THR Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2473 ILE Chi-restraints excluded: chain A residue 2531 VAL Chi-restraints excluded: chain A residue 2611 PHE Chi-restraints excluded: chain A residue 2703 ASN Chi-restraints excluded: chain A residue 2743 MET Chi-restraints excluded: chain B residue 927 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1035 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1273 HIS Chi-restraints excluded: chain B residue 1381 LEU Chi-restraints excluded: chain B residue 1421 PHE Chi-restraints excluded: chain B residue 1484 ILE Chi-restraints excluded: chain B residue 1895 GLU Chi-restraints excluded: chain B residue 1981 PHE Chi-restraints excluded: chain B residue 2197 ASP Chi-restraints excluded: chain B residue 2211 PHE Chi-restraints excluded: chain B residue 2238 LEU Chi-restraints excluded: chain B residue 2273 TRP Chi-restraints excluded: chain B residue 2341 VAL Chi-restraints excluded: chain B residue 2437 LEU Chi-restraints excluded: chain B residue 2453 THR Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2611 PHE Chi-restraints excluded: chain B residue 2697 MET Chi-restraints excluded: chain B residue 2703 ASN Chi-restraints excluded: chain B residue 2717 VAL Chi-restraints excluded: chain C residue 927 PHE Chi-restraints excluded: chain C residue 1001 GLN Chi-restraints excluded: chain C residue 1035 TYR Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1164 GLU Chi-restraints excluded: chain C residue 1288 MET Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1463 VAL Chi-restraints excluded: chain C residue 1481 MET Chi-restraints excluded: chain C residue 1653 TRP Chi-restraints excluded: chain C residue 1895 GLU Chi-restraints excluded: chain C residue 1981 PHE Chi-restraints excluded: chain C residue 2273 TRP Chi-restraints excluded: chain C residue 2341 VAL Chi-restraints excluded: chain C residue 2347 LEU Chi-restraints excluded: chain C residue 2441 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2531 VAL Chi-restraints excluded: chain C residue 2703 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 126 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 340 optimal weight: 0.0270 chunk 227 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 416 optimal weight: 0.1980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1876 HIS ** B1361 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.101853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.079801 restraints weight = 128743.477| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.17 r_work: 0.3430 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35832 Z= 0.120 Angle : 0.583 13.317 48576 Z= 0.298 Chirality : 0.039 0.252 5439 Planarity : 0.004 0.062 5958 Dihedral : 4.578 32.001 4617 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 1.92 % Allowed : 17.55 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.40 (0.13), residues: 4191 helix: 1.56 (0.10), residues: 2649 sheet: -1.59 (0.50), residues: 105 loop : -2.16 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1685 TYR 0.025 0.001 TYR A2183 PHE 0.045 0.001 PHE A1889 TRP 0.037 0.001 TRP B 936 HIS 0.021 0.001 HIS A1876 Details of bonding type rmsd covalent geometry : bond 0.00262 (35826) covalent geometry : angle 0.58306 (48564) SS BOND : bond 0.00073 ( 6) SS BOND : angle 0.24060 ( 12) hydrogen bonds : bond 0.04030 ( 2058) hydrogen bonds : angle 4.29850 ( 6003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8664.09 seconds wall clock time: 149 minutes 19.67 seconds (8959.67 seconds total)