Starting phenix.real_space_refine on Sun Jun 7 01:37:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7x_65735/06_2026/9w7x_65735.map" } resolution = 3.95 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= 0.022 sd= 0.084 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 177 5.16 5 C 21201 2.51 5 N 5130 2.21 5 O 5445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31971 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 10344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10344 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1263} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 8, 'ASN:plan1': 4, 'GLU:plan': 11, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 181 Chain: "A" Number of atoms: 10344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10344 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1263} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 8, 'ASN:plan1': 4, 'GLU:plan': 11, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 181 Chain: "C" Number of atoms: 10344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10344 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1263} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 8, 'ASN:plan1': 4, 'GLU:plan': 11, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 181 Chain: "B" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 261 Unusual residues: {'PEE': 1, 'PLX': 3} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 365 Unusual residues: {'PEE': 1, 'PLX': 5} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Chain: "C" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 313 Unusual residues: {'PEE': 1, 'PLX': 4} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Time building chain proxies: 7.88, per 1000 atoms: 0.25 Number of scatterers: 31971 At special positions: 0 Unit cell: (194.18, 204.82, 154.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 18 15.00 O 5445 8.00 N 5130 7.00 C 21201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B1227 " - pdb=" SG CYS B1248 " distance=2.03 Simple disulfide: pdb=" SG CYS B2394 " - pdb=" SG CYS B2411 " distance=2.02 Simple disulfide: pdb=" SG CYS A1227 " - pdb=" SG CYS A1248 " distance=2.03 Simple disulfide: pdb=" SG CYS A2394 " - pdb=" SG CYS A2411 " distance=2.07 Simple disulfide: pdb=" SG CYS C1227 " - pdb=" SG CYS C1248 " distance=2.03 Simple disulfide: pdb=" SG CYS C2394 " - pdb=" SG CYS C2411 " distance=2.02 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: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7494 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 9 sheets defined 70.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 766 through 823 removed outlier: 4.245A pdb=" N GLY B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 843 removed outlier: 3.540A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 850 removed outlier: 3.747A pdb=" N VAL B 850 " --> pdb=" O ARG B 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 847 through 850' Processing helix chain 'B' and resid 851 through 871 Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.010A pdb=" N VAL B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 924 " --> pdb=" O TYR B 920 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 925 " --> pdb=" O MET B 921 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 964 removed outlier: 3.583A pdb=" N LYS B 963 " --> pdb=" O ALA B 959 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 964 " --> pdb=" O ASP B 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 959 through 964' Processing helix chain 'B' and resid 964 through 997 removed outlier: 6.702A pdb=" N PHE B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR B 978 " --> pdb=" O ASN B 974 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 982 " --> pdb=" O TYR B 978 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU B 983 " --> pdb=" O LYS B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1013 Processing helix chain 'B' and resid 1015 through 1043 removed outlier: 3.822A pdb=" N LYS B1021 " --> pdb=" O SER B1017 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL B1025 " --> pdb=" O LYS B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1056 removed outlier: 4.208A pdb=" N GLU B1056 " --> pdb=" O PRO B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1058 No H-bonds generated for 'chain 'B' and resid 1057 through 1058' Processing helix chain 'B' and resid 1059 through 1067 removed outlier: 4.239A pdb=" N ARG B1065 " --> pdb=" O GLU B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1104 removed outlier: 3.526A pdb=" N LEU B1081 " --> pdb=" O HIS B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1170 removed outlier: 5.120A pdb=" N TYR B1157 " --> pdb=" O LEU B1153 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TRP B1158 " --> pdb=" O CYS B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1190 removed outlier: 3.555A pdb=" N TYR B1179 " --> pdb=" O LEU B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1196 removed outlier: 4.014A pdb=" N LEU B1195 " --> pdb=" O SER B1191 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B1196 " --> pdb=" O ASP B1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1191 through 1196' Processing helix chain 'B' and resid 1197 through 1229 removed outlier: 4.153A pdb=" N MET B1224 " --> pdb=" O THR B1220 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B1225 " --> pdb=" O SER B1221 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1237 Processing helix chain 'B' and resid 1237 through 1245 removed outlier: 4.091A pdb=" N HIS B1242 " --> pdb=" O CYS B1238 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B1243 " --> pdb=" O TRP B1239 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B1244 " --> pdb=" O LEU B1240 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1299 removed outlier: 4.436A pdb=" N TRP B1283 " --> pdb=" O VAL B1279 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP B1284 " --> pdb=" O VAL B1280 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1316 removed outlier: 3.669A pdb=" N HIS B1305 " --> pdb=" O HIS B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1317 through 1362 removed outlier: 3.611A pdb=" N ARG B1362 " --> pdb=" O GLN B1358 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1396 Processing helix chain 'B' and resid 1399 through 1404 removed outlier: 3.823A pdb=" N MET B1402 " --> pdb=" O ASP B1399 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B1404 " --> pdb=" O TYR B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1535 through 1570 removed outlier: 5.356A pdb=" N ASN B1551 " --> pdb=" O ARG B1547 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TYR B1552 " --> pdb=" O PHE B1548 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B1561 " --> pdb=" O ARG B1557 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B1562 " --> pdb=" O ILE B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1708 through 1724 removed outlier: 3.613A pdb=" N LEU B1714 " --> pdb=" O ILE B1710 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B1724 " --> pdb=" O ALA B1720 " (cutoff:3.500A) Processing helix chain 'B' and resid 1724 through 1741 removed outlier: 3.558A pdb=" N ILE B1728 " --> pdb=" O ASN B1724 " (cutoff:3.500A) Processing helix chain 'B' and resid 1746 through 1755 removed outlier: 3.739A pdb=" N ILE B1750 " --> pdb=" O LEU B1746 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1786 Processing helix chain 'B' and resid 1787 through 1791 removed outlier: 4.078A pdb=" N ILE B1790 " --> pdb=" O PHE B1787 " (cutoff:3.500A) Processing helix chain 'B' and resid 1817 through 1837 Processing helix chain 'B' and resid 1914 through 1924 Processing helix chain 'B' and resid 1932 through 1950 Processing helix chain 'B' and resid 1976 through 1999 Processing helix chain 'B' and resid 2000 through 2028 removed outlier: 4.699A pdb=" N VAL B2023 " --> pdb=" O MET B2019 " (cutoff:3.500A) Proline residue: B2024 - end of helix Processing helix chain 'B' and resid 2030 through 2033 Processing helix chain 'B' and resid 2034 through 2058 removed outlier: 3.568A pdb=" N ILE B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2070 removed outlier: 3.678A pdb=" N LYS B2070 " --> pdb=" O PHE B2067 " (cutoff:3.500A) Processing helix chain 'B' and resid 2073 through 2086 Processing helix chain 'B' and resid 2089 through 2101 removed outlier: 3.537A pdb=" N TRP B2098 " --> pdb=" O THR B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2106 through 2133 Processing helix chain 'B' and resid 2142 through 2170 Proline residue: B2164 - end of helix removed outlier: 3.581A pdb=" N LEU B2170 " --> pdb=" O CYS B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2208 through 2219 Processing helix chain 'B' and resid 2222 through 2230 Processing helix chain 'B' and resid 2253 through 2266 Processing helix chain 'B' and resid 2305 through 2314 Processing helix chain 'B' and resid 2365 through 2368 Processing helix chain 'B' and resid 2396 through 2402 removed outlier: 4.161A pdb=" N ASN B2400 " --> pdb=" O ASP B2396 " (cutoff:3.500A) Processing helix chain 'B' and resid 2403 through 2406 Processing helix chain 'B' and resid 2430 through 2435 removed outlier: 3.783A pdb=" N ALA B2434 " --> pdb=" O PHE B2431 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY B2435 " --> pdb=" O LEU B2432 " (cutoff:3.500A) Processing helix chain 'B' and resid 2436 through 2457 Processing helix chain 'B' and resid 2458 through 2467 removed outlier: 4.016A pdb=" N LYS B2462 " --> pdb=" O GLY B2458 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N MET B2464 " --> pdb=" O ASN B2460 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE B2465 " --> pdb=" O ARG B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2471 through 2487 Processing helix chain 'B' and resid 2489 through 2506 removed outlier: 3.694A pdb=" N GLU B2493 " --> pdb=" O GLU B2489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B2494 " --> pdb=" O PHE B2490 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP B2495 " --> pdb=" O ALA B2491 " (cutoff:3.500A) Processing helix chain 'B' and resid 2506 through 2514 Processing helix chain 'A' and resid 766 through 823 removed outlier: 4.244A pdb=" N GLY A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A 811 " --> pdb=" O ARG A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 843 removed outlier: 3.541A pdb=" N GLY A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 removed outlier: 3.749A pdb=" N VAL A 850 " --> pdb=" O ARG A 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 847 through 850' Processing helix chain 'A' and resid 851 through 871 Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.009A pdb=" N VAL A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE A 923 " --> pdb=" O ILE A 919 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 925 " --> pdb=" O MET A 921 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.593A pdb=" N LYS A 963 " --> pdb=" O ALA A 959 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP A 964 " --> pdb=" O ASP A 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 959 through 964' Processing helix chain 'A' and resid 964 through 997 removed outlier: 6.718A pdb=" N PHE A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A 978 " --> pdb=" O ASN A 974 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 982 " --> pdb=" O TYR A 978 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 983 " --> pdb=" O LYS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1013 Processing helix chain 'A' and resid 1015 through 1043 removed outlier: 3.838A pdb=" N LYS A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A1025 " --> pdb=" O LYS A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1056 removed outlier: 4.204A pdb=" N GLU A1056 " --> pdb=" O PRO A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1058 No H-bonds generated for 'chain 'A' and resid 1057 through 1058' Processing helix chain 'A' and resid 1059 through 1067 removed outlier: 4.426A pdb=" N ARG A1065 " --> pdb=" O GLU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1104 removed outlier: 3.529A pdb=" N LEU A1081 " --> pdb=" O HIS A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1170 removed outlier: 5.117A pdb=" N TYR A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP A1158 " --> pdb=" O CYS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 removed outlier: 3.566A pdb=" N TYR A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1196 removed outlier: 4.018A pdb=" N LEU A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A1196 " --> pdb=" O ASP A1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1191 through 1196' Processing helix chain 'A' and resid 1197 through 1229 removed outlier: 4.153A pdb=" N MET A1224 " --> pdb=" O THR A1220 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1237 Processing helix chain 'A' and resid 1237 through 1245 removed outlier: 4.119A pdb=" N HIS A1242 " --> pdb=" O CYS A1238 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET A1243 " --> pdb=" O TRP A1239 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1244 " --> pdb=" O LEU A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1299 removed outlier: 4.426A pdb=" N TRP A1283 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A1284 " --> pdb=" O VAL A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1316 removed outlier: 3.666A pdb=" N HIS A1305 " --> pdb=" O HIS A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1362 removed outlier: 3.615A pdb=" N ARG A1362 " --> pdb=" O GLN A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1399 through 1404 removed outlier: 3.779A pdb=" N MET A1402 " --> pdb=" O ASP A1399 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A1404 " --> pdb=" O TYR A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1570 removed outlier: 5.368A pdb=" N ASN A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR A1552 " --> pdb=" O PHE A1548 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A1561 " --> pdb=" O ARG A1557 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A1562 " --> pdb=" O ILE A1558 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1724 removed outlier: 3.612A pdb=" N LEU A1714 " --> pdb=" O ILE A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1724 through 1741 removed outlier: 3.565A pdb=" N ILE A1728 " --> pdb=" O ASN A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1755 removed outlier: 3.721A pdb=" N ILE A1750 " --> pdb=" O LEU A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1786 Processing helix chain 'A' and resid 1817 through 1837 Processing helix chain 'A' and resid 1914 through 1924 Processing helix chain 'A' and resid 1932 through 1950 Processing helix chain 'A' and resid 1976 through 1999 Processing helix chain 'A' and resid 2000 through 2028 removed outlier: 4.699A pdb=" N VAL A2023 " --> pdb=" O MET A2019 " (cutoff:3.500A) Proline residue: A2024 - end of helix Processing helix chain 'A' and resid 2030 through 2033 Processing helix chain 'A' and resid 2034 through 2058 removed outlier: 3.554A pdb=" N ILE A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2070 removed outlier: 3.672A pdb=" N LYS A2070 " --> pdb=" O PHE A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2086 Processing helix chain 'A' and resid 2089 through 2101 removed outlier: 3.522A pdb=" N TRP A2098 " --> pdb=" O THR A2094 " (cutoff:3.500A) Processing helix chain 'A' and resid 2106 through 2133 Processing helix chain 'A' and resid 2142 through 2170 Proline residue: A2164 - end of helix removed outlier: 3.584A pdb=" N LEU A2170 " --> pdb=" O CYS A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2219 removed outlier: 3.546A pdb=" N TYR A2219 " --> pdb=" O MET A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2230 Processing helix chain 'A' and resid 2253 through 2266 Processing helix chain 'A' and resid 2305 through 2314 Processing helix chain 'A' and resid 2365 through 2368 Processing helix chain 'A' and resid 2396 through 2402 removed outlier: 4.180A pdb=" N ASN A2400 " --> pdb=" O ASP A2396 " (cutoff:3.500A) Processing helix chain 'A' and resid 2403 through 2406 Processing helix chain 'A' and resid 2430 through 2435 removed outlier: 3.784A pdb=" N ALA A2434 " --> pdb=" O PHE A2431 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A2435 " --> pdb=" O LEU A2432 " (cutoff:3.500A) Processing helix chain 'A' and resid 2436 through 2457 Processing helix chain 'A' and resid 2458 through 2467 removed outlier: 4.015A pdb=" N LYS A2462 " --> pdb=" O GLY A2458 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET A2464 " --> pdb=" O ASN A2460 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N PHE A2465 " --> pdb=" O ARG A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2471 through 2487 Processing helix chain 'A' and resid 2489 through 2506 removed outlier: 3.670A pdb=" N GLU A2493 " --> pdb=" O GLU A2489 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A2494 " --> pdb=" O PHE A2490 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A2495 " --> pdb=" O ALA A2491 " (cutoff:3.500A) Processing helix chain 'A' and resid 2506 through 2514 Processing helix chain 'C' and resid 766 through 823 removed outlier: 4.245A pdb=" N GLY C 770 " --> pdb=" O GLU C 766 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 811 " --> pdb=" O ARG C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.541A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 850 removed outlier: 3.750A pdb=" N VAL C 850 " --> pdb=" O ARG C 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 847 through 850' Processing helix chain 'C' and resid 851 through 871 Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.009A pdb=" N VAL C 922 " --> pdb=" O ILE C 918 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL C 924 " --> pdb=" O TYR C 920 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR C 925 " --> pdb=" O MET C 921 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 removed outlier: 3.594A pdb=" N LYS C 963 " --> pdb=" O ALA C 959 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP C 964 " --> pdb=" O ASP C 960 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 959 through 964' Processing helix chain 'C' and resid 964 through 997 removed outlier: 6.717A pdb=" N PHE C 977 " --> pdb=" O LEU C 973 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR C 978 " --> pdb=" O ASN C 974 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 982 " --> pdb=" O TYR C 978 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU C 983 " --> pdb=" O LYS C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1013 Processing helix chain 'C' and resid 1015 through 1043 removed outlier: 3.823A pdb=" N LYS C1021 " --> pdb=" O SER C1017 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL C1025 " --> pdb=" O LYS C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1056 removed outlier: 4.206A pdb=" N GLU C1056 " --> pdb=" O PRO C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1058 No H-bonds generated for 'chain 'C' and resid 1057 through 1058' Processing helix chain 'C' and resid 1059 through 1067 removed outlier: 4.418A pdb=" N ARG C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1104 removed outlier: 3.526A pdb=" N LEU C1081 " --> pdb=" O HIS C1077 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1170 removed outlier: 5.117A pdb=" N TYR C1157 " --> pdb=" O LEU C1153 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP C1158 " --> pdb=" O CYS C1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1190 removed outlier: 3.579A pdb=" N TYR C1179 " --> pdb=" O LEU C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1196 removed outlier: 4.046A pdb=" N LEU C1195 " --> pdb=" O SER C1191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C1196 " --> pdb=" O ASP C1192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1191 through 1196' Processing helix chain 'C' and resid 1197 through 1229 removed outlier: 4.236A pdb=" N MET C1224 " --> pdb=" O THR C1220 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA C1225 " --> pdb=" O SER C1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 1229 through 1237 Processing helix chain 'C' and resid 1237 through 1245 removed outlier: 4.101A pdb=" N HIS C1242 " --> pdb=" O CYS C1238 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET C1243 " --> pdb=" O TRP C1239 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C1244 " --> pdb=" O LEU C1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1299 removed outlier: 4.407A pdb=" N TRP C1283 " --> pdb=" O VAL C1279 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP C1284 " --> pdb=" O VAL C1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1316 removed outlier: 3.666A pdb=" N HIS C1305 " --> pdb=" O HIS C1301 " (cutoff:3.500A) Processing helix chain 'C' and resid 1317 through 1362 removed outlier: 3.614A pdb=" N ARG C1362 " --> pdb=" O GLN C1358 " (cutoff:3.500A) Processing helix chain 'C' and resid 1390 through 1396 Processing helix chain 'C' and resid 1399 through 1404 removed outlier: 3.796A pdb=" N MET C1402 " --> pdb=" O ASP C1399 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C1404 " --> pdb=" O TYR C1401 " (cutoff:3.500A) Processing helix chain 'C' and resid 1535 through 1570 removed outlier: 5.343A pdb=" N ASN C1551 " --> pdb=" O ARG C1547 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N TYR C1552 " --> pdb=" O PHE C1548 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C1561 " --> pdb=" O ARG C1557 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU C1562 " --> pdb=" O ILE C1558 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1724 removed outlier: 3.605A pdb=" N LEU C1714 " --> pdb=" O ILE C1710 " (cutoff:3.500A) Processing helix chain 'C' and resid 1724 through 1741 removed outlier: 3.562A pdb=" N ILE C1728 " --> pdb=" O ASN C1724 " (cutoff:3.500A) Processing helix chain 'C' and resid 1746 through 1755 removed outlier: 3.724A pdb=" N ILE C1750 " --> pdb=" O LEU C1746 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1786 Processing helix chain 'C' and resid 1817 through 1837 Processing helix chain 'C' and resid 1914 through 1924 Processing helix chain 'C' and resid 1932 through 1950 Processing helix chain 'C' and resid 1976 through 1999 Processing helix chain 'C' and resid 2000 through 2028 removed outlier: 4.591A pdb=" N VAL C2023 " --> pdb=" O MET C2019 " (cutoff:3.500A) Proline residue: C2024 - end of helix Processing helix chain 'C' and resid 2030 through 2033 Processing helix chain 'C' and resid 2034 through 2058 removed outlier: 3.560A pdb=" N ILE C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) Processing helix chain 'C' and resid 2066 through 2070 removed outlier: 3.674A pdb=" N LYS C2070 " --> pdb=" O PHE C2067 " (cutoff:3.500A) Processing helix chain 'C' and resid 2073 through 2086 Processing helix chain 'C' and resid 2089 through 2101 removed outlier: 3.538A pdb=" N TRP C2098 " --> pdb=" O THR C2094 " (cutoff:3.500A) Processing helix chain 'C' and resid 2106 through 2133 Processing helix chain 'C' and resid 2142 through 2170 Proline residue: C2164 - end of helix removed outlier: 3.575A pdb=" N LEU C2170 " --> pdb=" O CYS C2166 " (cutoff:3.500A) Processing helix chain 'C' and resid 2208 through 2219 removed outlier: 3.550A pdb=" N TYR C2219 " --> pdb=" O MET C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2222 through 2230 Processing helix chain 'C' and resid 2253 through 2266 Processing helix chain 'C' and resid 2305 through 2314 Processing helix chain 'C' and resid 2365 through 2368 Processing helix chain 'C' and resid 2396 through 2402 removed outlier: 4.187A pdb=" N ASN C2400 " --> pdb=" O ASP C2396 " (cutoff:3.500A) Processing helix chain 'C' and resid 2403 through 2406 Processing helix chain 'C' and resid 2410 through 2414 removed outlier: 4.105A pdb=" N GLY C2414 " --> pdb=" O CYS C2411 " (cutoff:3.500A) Processing helix chain 'C' and resid 2430 through 2435 removed outlier: 3.784A pdb=" N ALA C2434 " --> pdb=" O PHE C2431 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C2435 " --> pdb=" O LEU C2432 " (cutoff:3.500A) Processing helix chain 'C' and resid 2436 through 2457 Processing helix chain 'C' and resid 2458 through 2467 removed outlier: 4.017A pdb=" N LYS C2462 " --> pdb=" O GLY C2458 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET C2464 " --> pdb=" O ASN C2460 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE C2465 " --> pdb=" O ARG C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2471 through 2487 Processing helix chain 'C' and resid 2489 through 2506 removed outlier: 3.680A pdb=" N GLU C2493 " --> pdb=" O GLU C2489 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C2494 " --> pdb=" O PHE C2490 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP C2495 " --> pdb=" O ALA C2491 " (cutoff:3.500A) Processing helix chain 'C' and resid 2506 through 2514 Processing sheet with id=AA1, first strand: chain 'B' and resid 2194 through 2200 removed outlier: 6.460A pdb=" N ILE B2189 " --> pdb=" O PRO B2194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2204 through 2206 removed outlier: 3.748A pdb=" N ASP B2356 " --> pdb=" O LEU B2352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2339 through 2346 removed outlier: 5.444A pdb=" N VAL B2340 " --> pdb=" O ILE B2375 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B2375 " --> pdb=" O VAL B2340 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B2373 " --> pdb=" O PRO B2342 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ARG B2371 " --> pdb=" O MET B2344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 2194 through 2200 removed outlier: 6.453A pdb=" N ILE A2189 " --> pdb=" O PRO A2194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2204 through 2206 removed outlier: 3.801A pdb=" N ASP A2356 " --> pdb=" O LEU A2352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2339 through 2346 removed outlier: 3.680A pdb=" N GLY A2343 " --> pdb=" O ARG A2371 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG A2371 " --> pdb=" O GLY A2343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2194 through 2200 removed outlier: 6.455A pdb=" N ILE C2189 " --> pdb=" O PRO C2194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2204 through 2206 removed outlier: 3.783A pdb=" N ASP C2356 " --> pdb=" O LEU C2352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2339 through 2346 removed outlier: 3.766A pdb=" N GLY C2343 " --> pdb=" O ARG C2371 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ARG C2371 " --> pdb=" O GLY C2343 " (cutoff:3.500A) 2078 hydrogen bonds defined for protein. 6132 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: 6.58 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4748 1.32 - 1.44: 9047 1.44 - 1.57: 18580 1.57 - 1.70: 37 1.70 - 1.83: 279 Bond restraints: 32691 Sorted by residual: bond pdb=" C38 PEE C2605 " pdb=" C39 PEE C2605 " ideal model delta sigma weight residual 1.523 1.296 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C38 PEE A2606 " pdb=" C39 PEE A2606 " ideal model delta sigma weight residual 1.523 1.298 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C38 PEE B2604 " pdb=" C39 PEE B2604 " ideal model delta sigma weight residual 1.523 1.301 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C18 PEE B2604 " pdb=" C19 PEE B2604 " ideal model delta sigma weight residual 1.523 1.308 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C18 PEE C2605 " pdb=" C19 PEE C2605 " ideal model delta sigma weight residual 1.523 1.313 0.210 2.00e-02 2.50e+03 1.10e+02 ... (remaining 32686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 43916 4.10 - 8.20: 206 8.20 - 12.30: 25 12.30 - 16.40: 9 16.40 - 20.50: 1 Bond angle restraints: 44157 Sorted by residual: angle pdb=" CA CYS A2394 " pdb=" CB CYS A2394 " pdb=" SG CYS A2394 " ideal model delta sigma weight residual 114.40 134.90 -20.50 2.30e+00 1.89e-01 7.95e+01 angle pdb=" CA LYS B1788 " pdb=" CB LYS B1788 " pdb=" CG LYS B1788 " ideal model delta sigma weight residual 114.10 125.10 -11.00 2.00e+00 2.50e-01 3.03e+01 angle pdb=" CB MET B2211 " pdb=" CG MET B2211 " pdb=" SD MET B2211 " ideal model delta sigma weight residual 112.70 96.55 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C38 PEE B2604 " pdb=" C39 PEE B2604 " pdb=" C40 PEE B2604 " ideal model delta sigma weight residual 112.47 126.67 -14.20 3.00e+00 1.11e-01 2.24e+01 angle pdb=" CG MET C2215 " pdb=" SD MET C2215 " pdb=" CE MET C2215 " ideal model delta sigma weight residual 100.90 90.58 10.32 2.20e+00 2.07e-01 2.20e+01 ... (remaining 44152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 18782 34.20 - 68.40: 766 68.40 - 102.60: 55 102.60 - 136.80: 32 136.80 - 171.00: 15 Dihedral angle restraints: 19650 sinusoidal: 8130 harmonic: 11520 Sorted by residual: dihedral pdb=" CB CYS B2394 " pdb=" SG CYS B2394 " pdb=" SG CYS B2411 " pdb=" CB CYS B2411 " ideal model delta sinusoidal sigma weight residual 93.00 166.06 -73.06 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" N PEE C2605 " pdb=" C4 PEE C2605 " pdb=" C5 PEE C2605 " pdb=" O4P PEE C2605 " ideal model delta sinusoidal sigma weight residual -56.97 114.03 -171.00 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C38 P5S C2606 " pdb=" C39 P5S C2606 " pdb=" C40 P5S C2606 " pdb=" C41 P5S C2606 " ideal model delta sinusoidal sigma weight residual 64.51 -98.88 163.39 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 19647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 4907 0.100 - 0.200: 149 0.200 - 0.300: 13 0.300 - 0.399: 3 0.399 - 0.499: 1 Chirality restraints: 5073 Sorted by residual: chirality pdb=" CG LEU B1014 " pdb=" CB LEU B1014 " pdb=" CD1 LEU B1014 " pdb=" CD2 LEU B1014 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" C6 PLX B2602 " pdb=" C7 PLX B2602 " pdb=" O6 PLX B2602 " pdb=" O7 PLX B2602 " both_signs ideal model delta sigma weight residual False 2.01 2.31 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU A2373 " pdb=" CB LEU A2373 " pdb=" CD1 LEU A2373 " pdb=" CD2 LEU A2373 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 5070 not shown) Planarity restraints: 5292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A2411 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C CYS A2411 " -0.077 2.00e-02 2.50e+03 pdb=" O CYS A2411 " 0.029 2.00e-02 2.50e+03 pdb=" N THR A2412 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B1010 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C VAL B1010 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B1010 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B1011 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2265 " 0.215 9.50e-02 1.11e+02 9.66e-02 5.82e+00 pdb=" NE ARG B2265 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B2265 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B2265 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B2265 " 0.009 2.00e-02 2.50e+03 ... (remaining 5289 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 145 2.50 - 3.10: 23200 3.10 - 3.70: 48788 3.70 - 4.30: 67309 4.30 - 4.90: 110938 Nonbonded interactions: 250380 Sorted by model distance: nonbonded pdb=" OH TYR C2399 " pdb=" O SER C2409 " model vdw 1.895 3.040 nonbonded pdb=" OH TYR B2399 " pdb=" O SER B2409 " model vdw 1.935 3.040 nonbonded pdb=" OH TYR A2399 " pdb=" O SER A2409 " model vdw 1.967 3.040 nonbonded pdb=" O15 P5S A2607 " pdb=" O18 P5S A2607 " model vdw 1.978 3.040 nonbonded pdb=" OG SER A2506 " pdb=" OG1 THR A2509 " model vdw 2.136 3.040 ... (remaining 250375 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 765 through 2603) selection = (chain 'B' and resid 765 through 2603) selection = (chain 'C' and resid 765 through 2603) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 29.040 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 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 : 0.006 0.227 32697 Z= 0.281 Angle : 0.749 20.504 44169 Z= 0.348 Chirality : 0.043 0.499 5073 Planarity : 0.004 0.097 5292 Dihedral : 19.135 171.001 12138 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 22.36 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.14), residues: 3831 helix: 2.25 (0.10), residues: 2493 sheet: 0.79 (0.34), residues: 213 loop : -0.83 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B2371 TYR 0.023 0.001 TYR B2368 PHE 0.037 0.001 PHE B2406 TRP 0.007 0.001 TRP B2388 HIS 0.008 0.001 HIS C 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 (32691) covalent geometry : angle 0.74054 / 0.34 (44157) SS BOND : bond 0.01839 / 0.93 ( 6) SS BOND : angle 6.95555 / 4.18 ( 12) hydrogen bonds : bond 0.09635 / 6.24 ( 2078) hydrogen bonds : angle 4.70814 / 3.47 ( 6132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 921 MET cc_start: 0.2598 (mmm) cc_final: 0.2050 (mmt) REVERT: B 937 MET cc_start: 0.1845 (ptm) cc_final: 0.1457 (ttm) REVERT: B 973 LEU cc_start: 0.7858 (mt) cc_final: 0.7581 (mt) REVERT: B 2115 ASP cc_start: 0.8502 (t0) cc_final: 0.8164 (t0) REVERT: B 2423 LYS cc_start: 0.7035 (mmmt) cc_final: 0.6355 (tppt) REVERT: A 921 MET cc_start: 0.2680 (mmm) cc_final: 0.1975 (mmt) REVERT: A 937 MET cc_start: 0.1195 (ptm) cc_final: 0.0058 (tmm) REVERT: A 1402 MET cc_start: 0.8260 (mtt) cc_final: 0.7913 (mtt) REVERT: A 2192 TYR cc_start: 0.7078 (m-80) cc_final: 0.6778 (m-80) REVERT: A 2423 LYS cc_start: 0.6640 (mmmt) cc_final: 0.6139 (tppt) REVERT: C 921 MET cc_start: 0.3046 (mmm) cc_final: 0.2517 (mmt) REVERT: C 2352 LEU cc_start: 0.9149 (mm) cc_final: 0.8722 (mt) REVERT: C 2423 LYS cc_start: 0.7025 (mmmt) cc_final: 0.6241 (tppt) outliers start: 49 outliers final: 44 residues processed: 288 average time/residue: 0.1762 time to fit residues: 86.7221 Evaluate side-chains 297 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1220 THR Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1746 LEU Chi-restraints excluded: chain B residue 2018 TRP Chi-restraints excluded: chain B residue 2030 THR Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2411 CYS Chi-restraints excluded: chain B residue 2415 ILE Chi-restraints excluded: chain B residue 2438 ILE Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1144 TYR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1302 TYR Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1416 HIS Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2105 MET Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2373 LEU Chi-restraints excluded: chain A residue 2403 LEU Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2443 THR Chi-restraints excluded: chain C residue 1195 LEU Chi-restraints excluded: chain C residue 1302 TYR Chi-restraints excluded: chain C residue 1305 HIS Chi-restraints excluded: chain C residue 1402 MET Chi-restraints excluded: chain C residue 1541 LEU Chi-restraints excluded: chain C residue 1983 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2032 ASN Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2240 VAL Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2312 MET Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2373 LEU Chi-restraints excluded: chain C residue 2443 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1027 GLN B1092 ASN B1301 HIS B1696 ASN ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1985 GLN A1027 GLN A1037 GLN A1092 ASN A1696 ASN C1027 GLN C1092 ASN C1301 HIS C1985 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.123285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106933 restraints weight = 81721.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.103957 restraints weight = 113964.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.102119 restraints weight = 108873.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101149 restraints weight = 113442.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100306 restraints weight = 106830.715| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32697 Z= 0.133 Angle : 0.534 7.805 44169 Z= 0.271 Chirality : 0.039 0.152 5073 Planarity : 0.004 0.044 5292 Dihedral : 16.214 175.609 5257 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.14 % Allowed : 21.08 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.13 (0.14), residues: 3831 helix: 2.33 (0.10), residues: 2493 sheet: 0.94 (0.35), residues: 219 loop : -0.66 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2371 TYR 0.014 0.001 TYR C2399 PHE 0.021 0.001 PHE C1098 TRP 0.011 0.001 TRP A2018 HIS 0.006 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (32691) covalent geometry : angle 0.53334 / 0.27 (44157) SS BOND : bond 0.00385 / 0.20 ( 6) SS BOND : angle 0.98847 / 0.60 ( 12) hydrogen bonds : bond 0.03878 / 2.60 ( 2078) hydrogen bonds : angle 4.07513 / 2.98 ( 6132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 279 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 921 MET cc_start: 0.3680 (mmm) cc_final: 0.2784 (mmt) REVERT: B 937 MET cc_start: 0.2094 (ptm) cc_final: 0.0559 (tpt) REVERT: B 973 LEU cc_start: 0.7940 (mt) cc_final: 0.7631 (mt) REVERT: B 1388 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7932 (mt) REVERT: B 2115 ASP cc_start: 0.8531 (t0) cc_final: 0.8139 (t0) REVERT: A 921 MET cc_start: 0.3828 (mmm) cc_final: 0.3177 (mmt) REVERT: A 937 MET cc_start: 0.2141 (ptm) cc_final: 0.0847 (tpt) REVERT: A 2115 ASP cc_start: 0.8305 (t0) cc_final: 0.8089 (t70) REVERT: A 2299 LEU cc_start: 0.7928 (mp) cc_final: 0.7368 (tt) REVERT: C 921 MET cc_start: 0.3891 (mmm) cc_final: 0.2737 (mmt) REVERT: C 937 MET cc_start: 0.2627 (ttm) cc_final: 0.1188 (tmm) REVERT: C 1985 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8736 (tp40) REVERT: C 2074 MET cc_start: 0.7855 (tpp) cc_final: 0.7595 (tpp) REVERT: C 2299 LEU cc_start: 0.7544 (mp) cc_final: 0.7284 (tt) REVERT: C 2352 LEU cc_start: 0.8232 (mm) cc_final: 0.7946 (mt) REVERT: C 2373 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6399 (tt) outliers start: 70 outliers final: 20 residues processed: 337 average time/residue: 0.1820 time to fit residues: 103.1875 Evaluate side-chains 273 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 2030 THR Chi-restraints excluded: chain B residue 2309 LEU Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1305 HIS Chi-restraints excluded: chain A residue 1416 HIS Chi-restraints excluded: chain A residue 1719 TYR Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2374 VAL Chi-restraints excluded: chain C residue 1305 HIS Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1985 GLN Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2373 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 212 optimal weight: 0.0170 chunk 306 optimal weight: 5.9990 chunk 343 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 319 optimal weight: 1.9990 chunk 289 optimal weight: 0.0170 chunk 228 optimal weight: 6.9990 chunk 238 optimal weight: 0.0270 chunk 331 optimal weight: 1.9990 overall best weight: 0.1672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1815 HIS C1985 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.107546 restraints weight = 81676.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104747 restraints weight = 112644.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101868 restraints weight = 109056.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100921 restraints weight = 118139.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100173 restraints weight = 106245.367| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32697 Z= 0.101 Angle : 0.493 7.982 44169 Z= 0.250 Chirality : 0.038 0.149 5073 Planarity : 0.004 0.044 5292 Dihedral : 15.548 178.803 5189 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % Rotamer: Outliers : 1.68 % Allowed : 21.48 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.16 (0.14), residues: 3831 helix: 2.37 (0.10), residues: 2496 sheet: 1.14 (0.36), residues: 219 loop : -0.71 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2265 TYR 0.021 0.001 TYR A2368 PHE 0.015 0.001 PHE C1098 TRP 0.013 0.001 TRP A2018 HIS 0.005 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (32691) covalent geometry : angle 0.49277 / 0.25 (44157) SS BOND : bond 0.00281 / 0.14 ( 6) SS BOND : angle 0.47568 / 0.30 ( 12) hydrogen bonds : bond 0.03571 / 2.40 ( 2078) hydrogen bonds : angle 3.90847 / 2.86 ( 6132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 921 MET cc_start: 0.3887 (mmm) cc_final: 0.3074 (mmt) REVERT: B 937 MET cc_start: 0.1861 (ptm) cc_final: 0.0392 (tpt) REVERT: B 973 LEU cc_start: 0.7948 (mt) cc_final: 0.7634 (mt) REVERT: B 1196 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6709 (mtt90) REVERT: B 2115 ASP cc_start: 0.8448 (t0) cc_final: 0.8116 (t0) REVERT: B 2192 TYR cc_start: 0.6357 (m-80) cc_final: 0.6034 (m-80) REVERT: A 921 MET cc_start: 0.3772 (mmm) cc_final: 0.3205 (mmt) REVERT: A 937 MET cc_start: 0.2119 (ptm) cc_final: 0.0836 (tpt) REVERT: A 1010 VAL cc_start: 0.6988 (OUTLIER) cc_final: 0.6651 (t) REVERT: A 1816 TYR cc_start: 0.5283 (p90) cc_final: 0.5024 (p90) REVERT: A 2084 MET cc_start: 0.9092 (mmm) cc_final: 0.8889 (mmp) REVERT: A 2115 ASP cc_start: 0.8298 (t0) cc_final: 0.8022 (t70) REVERT: A 2215 MET cc_start: 0.6872 (mmp) cc_final: 0.6643 (mmp) REVERT: A 2299 LEU cc_start: 0.7768 (mp) cc_final: 0.7217 (tt) REVERT: C 921 MET cc_start: 0.4041 (mmm) cc_final: 0.2923 (mmt) REVERT: C 937 MET cc_start: 0.2355 (ttm) cc_final: 0.0876 (tmm) REVERT: C 2074 MET cc_start: 0.7907 (tpp) cc_final: 0.7624 (tpp) REVERT: C 2192 TYR cc_start: 0.6629 (m-80) cc_final: 0.6205 (m-80) REVERT: C 2423 LYS cc_start: 0.4163 (OUTLIER) cc_final: 0.3689 (tppt) outliers start: 55 outliers final: 24 residues processed: 305 average time/residue: 0.1841 time to fit residues: 95.3714 Evaluate side-chains 272 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2309 LEU Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2517 LYS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1719 TYR Chi-restraints excluded: chain A residue 1815 HIS Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2373 LEU Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2374 VAL Chi-restraints excluded: chain C residue 2423 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 159 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 347 optimal weight: 0.0970 chunk 174 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 374 optimal weight: 0.0370 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1696 ASN ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2258 GLN C1815 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.122430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105935 restraints weight = 81521.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102954 restraints weight = 111985.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.101420 restraints weight = 103548.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.100766 restraints weight = 107258.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099469 restraints weight = 106360.060| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32697 Z= 0.118 Angle : 0.495 8.656 44169 Z= 0.250 Chirality : 0.039 0.170 5073 Planarity : 0.004 0.043 5292 Dihedral : 14.969 179.964 5180 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.84 % Rotamer: Outliers : 1.83 % Allowed : 21.57 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.24 (0.14), residues: 3831 helix: 2.44 (0.10), residues: 2481 sheet: 1.14 (0.36), residues: 219 loop : -0.66 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1993 TYR 0.015 0.001 TYR B1933 PHE 0.017 0.001 PHE B2228 TRP 0.014 0.001 TRP A2018 HIS 0.028 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (32691) covalent geometry : angle 0.49515 / 0.25 (44157) SS BOND : bond 0.00202 / 0.10 ( 6) SS BOND : angle 0.37877 / 0.22 ( 12) hydrogen bonds : bond 0.03516 / 2.38 ( 2078) hydrogen bonds : angle 3.85639 / 2.81 ( 6132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 921 MET cc_start: 0.3946 (mmm) cc_final: 0.3234 (mmt) REVERT: B 937 MET cc_start: 0.1923 (ptm) cc_final: 0.0442 (tpt) REVERT: B 973 LEU cc_start: 0.8045 (mt) cc_final: 0.7747 (mt) REVERT: B 1388 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7752 (mt) REVERT: B 2048 MET cc_start: 0.7584 (mtm) cc_final: 0.7376 (mtm) REVERT: B 2115 ASP cc_start: 0.8220 (t0) cc_final: 0.7829 (t0) REVERT: A 921 MET cc_start: 0.3516 (mmm) cc_final: 0.3145 (mmm) REVERT: A 937 MET cc_start: 0.1897 (ptm) cc_final: 0.0799 (tpt) REVERT: A 1010 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.6983 (t) REVERT: A 1388 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 2084 MET cc_start: 0.9179 (mmm) cc_final: 0.8975 (mmp) REVERT: A 2299 LEU cc_start: 0.7756 (mp) cc_final: 0.7230 (tt) REVERT: C 911 MET cc_start: 0.6365 (ppp) cc_final: 0.4434 (tpt) REVERT: C 921 MET cc_start: 0.4029 (mmm) cc_final: 0.3140 (mmt) REVERT: C 937 MET cc_start: 0.2499 (ttm) cc_final: 0.1050 (tmm) REVERT: C 1815 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5227 (m-70) REVERT: C 1816 TYR cc_start: 0.4772 (p90) cc_final: 0.4432 (p90) REVERT: C 2074 MET cc_start: 0.7976 (tpp) cc_final: 0.7699 (tpp) REVERT: C 2192 TYR cc_start: 0.6673 (m-80) cc_final: 0.6288 (m-80) outliers start: 60 outliers final: 33 residues processed: 328 average time/residue: 0.1938 time to fit residues: 105.5704 Evaluate side-chains 282 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1092 ASN Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1719 TYR Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2277 SER Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2373 LEU Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1541 LEU Chi-restraints excluded: chain C residue 1815 HIS Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 384 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 229 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 207 optimal weight: 0.0050 chunk 230 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.6806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1815 HIS A1985 GLN C2032 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.122194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.105652 restraints weight = 81296.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102724 restraints weight = 114976.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100110 restraints weight = 109353.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098862 restraints weight = 122422.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098480 restraints weight = 103833.634| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32697 Z= 0.108 Angle : 0.486 8.532 44169 Z= 0.246 Chirality : 0.038 0.162 5073 Planarity : 0.004 0.062 5292 Dihedral : 14.626 178.379 5180 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.89 % Rotamer: Outliers : 1.92 % Allowed : 21.57 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.26 (0.14), residues: 3831 helix: 2.46 (0.10), residues: 2484 sheet: 0.91 (0.35), residues: 225 loop : -0.63 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1553 TYR 0.016 0.001 TYR B 978 PHE 0.013 0.001 PHE A2088 TRP 0.014 0.001 TRP A2018 HIS 0.019 0.001 HIS C1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (32691) covalent geometry : angle 0.48591 / 0.25 (44157) SS BOND : bond 0.00253 / 0.12 ( 6) SS BOND : angle 0.43161 / 0.24 ( 12) hydrogen bonds : bond 0.03448 / 2.33 ( 2078) hydrogen bonds : angle 3.79240 / 2.76 ( 6132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5745 (OUTLIER) cc_final: 0.5528 (t) REVERT: B 921 MET cc_start: 0.3878 (mmm) cc_final: 0.3149 (mmt) REVERT: B 937 MET cc_start: 0.1883 (ptm) cc_final: 0.0429 (tpt) REVERT: B 973 LEU cc_start: 0.8067 (mt) cc_final: 0.7768 (mt) REVERT: B 1388 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7760 (mt) REVERT: B 2048 MET cc_start: 0.7485 (mtm) cc_final: 0.7263 (mtm) REVERT: A 853 VAL cc_start: 0.5460 (OUTLIER) cc_final: 0.5220 (t) REVERT: A 921 MET cc_start: 0.3453 (mmm) cc_final: 0.2656 (mmt) REVERT: A 937 MET cc_start: 0.2043 (ptm) cc_final: 0.1005 (tpt) REVERT: A 1010 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7096 (t) REVERT: A 1388 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7725 (mt) REVERT: A 1985 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8793 (tp40) REVERT: A 2074 MET cc_start: 0.7838 (tpp) cc_final: 0.7537 (tpp) REVERT: A 2115 ASP cc_start: 0.8268 (t0) cc_final: 0.8041 (t70) REVERT: A 2192 TYR cc_start: 0.6619 (m-80) cc_final: 0.6284 (m-80) REVERT: A 2299 LEU cc_start: 0.7762 (mp) cc_final: 0.7248 (tt) REVERT: C 911 MET cc_start: 0.6380 (ppp) cc_final: 0.4450 (tpt) REVERT: C 921 MET cc_start: 0.4123 (mmm) cc_final: 0.3370 (mmt) REVERT: C 937 MET cc_start: 0.2442 (ttm) cc_final: 0.0816 (tmm) REVERT: C 2074 MET cc_start: 0.8027 (tpp) cc_final: 0.7746 (tpp) REVERT: C 2192 TYR cc_start: 0.6645 (m-80) cc_final: 0.6282 (m-80) REVERT: C 2299 LEU cc_start: 0.7523 (mp) cc_final: 0.7300 (tt) outliers start: 63 outliers final: 39 residues processed: 316 average time/residue: 0.1828 time to fit residues: 97.7612 Evaluate side-chains 292 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1719 TYR Chi-restraints excluded: chain A residue 1815 HIS Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 1985 GLN Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1416 HIS Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2374 VAL Chi-restraints excluded: chain C residue 2464 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 353 optimal weight: 0.6980 chunk 311 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 328 optimal weight: 0.0270 chunk 322 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 ASN ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 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 = 0.3983 r_free = 0.3983 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.105587 restraints weight = 80985.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102714 restraints weight = 115822.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099785 restraints weight = 111204.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098195 restraints weight = 120495.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097426 restraints weight = 118157.222| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32697 Z= 0.103 Angle : 0.483 8.657 44169 Z= 0.244 Chirality : 0.038 0.139 5073 Planarity : 0.004 0.050 5292 Dihedral : 14.393 178.259 5180 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 1.86 % Allowed : 21.91 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.29 (0.14), residues: 3831 helix: 2.50 (0.10), residues: 2484 sheet: 1.00 (0.37), residues: 207 loop : -0.66 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1553 TYR 0.024 0.001 TYR A2368 PHE 0.019 0.001 PHE A2228 TRP 0.013 0.001 TRP A2018 HIS 0.022 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (32691) covalent geometry : angle 0.48262 / 0.24 (44157) SS BOND : bond 0.00141 / 0.07 ( 6) SS BOND : angle 0.35957 / 0.18 ( 12) hydrogen bonds : bond 0.03416 / 2.31 ( 2078) hydrogen bonds : angle 3.76845 / 2.74 ( 6132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5740 (OUTLIER) cc_final: 0.5524 (t) REVERT: B 921 MET cc_start: 0.3821 (mmm) cc_final: 0.3180 (mmt) REVERT: B 937 MET cc_start: 0.1907 (ptm) cc_final: 0.0447 (tpt) REVERT: B 973 LEU cc_start: 0.8086 (mt) cc_final: 0.7791 (mt) REVERT: B 1388 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7742 (mt) REVERT: B 1931 ASP cc_start: 0.7491 (t0) cc_final: 0.7271 (t0) REVERT: B 2048 MET cc_start: 0.7542 (mtm) cc_final: 0.7314 (mtm) REVERT: A 853 VAL cc_start: 0.5476 (OUTLIER) cc_final: 0.5244 (t) REVERT: A 921 MET cc_start: 0.3483 (mmm) cc_final: 0.2718 (mmt) REVERT: A 937 MET cc_start: 0.1973 (ptm) cc_final: 0.0936 (tpt) REVERT: A 1010 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.7168 (t) REVERT: A 1388 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 2074 MET cc_start: 0.7944 (tpp) cc_final: 0.7721 (tpp) REVERT: A 2115 ASP cc_start: 0.8240 (t0) cc_final: 0.7816 (t70) REVERT: A 2299 LEU cc_start: 0.7777 (mp) cc_final: 0.7284 (tt) REVERT: C 911 MET cc_start: 0.6360 (ppp) cc_final: 0.4389 (tpt) REVERT: C 921 MET cc_start: 0.4077 (mmm) cc_final: 0.3408 (mmt) REVERT: C 937 MET cc_start: 0.2423 (ttm) cc_final: 0.0782 (tmm) REVERT: C 1104 TYR cc_start: 0.5486 (m-80) cc_final: 0.3531 (t80) REVERT: C 2074 MET cc_start: 0.8036 (tpp) cc_final: 0.7743 (tpp) REVERT: C 2192 TYR cc_start: 0.6755 (m-80) cc_final: 0.6402 (m-80) REVERT: C 2215 MET cc_start: 0.6642 (mmp) cc_final: 0.6413 (mmp) outliers start: 61 outliers final: 38 residues processed: 311 average time/residue: 0.1748 time to fit residues: 93.3821 Evaluate side-chains 291 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1541 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2464 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 306 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 367 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 326 optimal weight: 0.7980 chunk 243 optimal weight: 20.0000 chunk 346 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 334 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 ASN B1546 ASN ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1985 GLN ** C1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.106552 restraints weight = 80437.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.103958 restraints weight = 116432.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101867 restraints weight = 104288.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100990 restraints weight = 109987.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100012 restraints weight = 104459.918| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32697 Z= 0.125 Angle : 0.506 10.227 44169 Z= 0.255 Chirality : 0.039 0.212 5073 Planarity : 0.004 0.050 5292 Dihedral : 13.886 179.895 5178 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.29 % Allowed : 21.85 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.21 (0.14), residues: 3831 helix: 2.45 (0.10), residues: 2499 sheet: 0.96 (0.36), residues: 207 loop : -0.77 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B2391 TYR 0.018 0.001 TYR C 978 PHE 0.014 0.001 PHE A1937 TRP 0.016 0.001 TRP A2018 HIS 0.007 0.001 HIS B2378 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (32691) covalent geometry : angle 0.50564 / 0.26 (44157) SS BOND : bond 0.00152 / 0.08 ( 6) SS BOND : angle 0.29457 / 0.15 ( 12) hydrogen bonds : bond 0.03527 / 2.38 ( 2078) hydrogen bonds : angle 3.79410 / 2.76 ( 6132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 262 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5778 (OUTLIER) cc_final: 0.5551 (t) REVERT: B 921 MET cc_start: 0.4013 (mmm) cc_final: 0.3527 (mmt) REVERT: B 937 MET cc_start: 0.2000 (ptm) cc_final: 0.0577 (tpt) REVERT: B 973 LEU cc_start: 0.8077 (mt) cc_final: 0.7788 (mt) REVERT: B 1388 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 2048 MET cc_start: 0.7566 (mtm) cc_final: 0.7305 (mtm) REVERT: B 2168 PHE cc_start: 0.4732 (OUTLIER) cc_final: 0.2960 (t80) REVERT: A 853 VAL cc_start: 0.5520 (OUTLIER) cc_final: 0.5270 (t) REVERT: A 911 MET cc_start: 0.5905 (ppp) cc_final: 0.3995 (tpt) REVERT: A 921 MET cc_start: 0.3727 (mmm) cc_final: 0.3191 (mmt) REVERT: A 937 MET cc_start: 0.2004 (ptm) cc_final: 0.0954 (tpt) REVERT: A 1010 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7336 (t) REVERT: A 1388 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 1841 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.5550 (pptt) REVERT: A 2074 MET cc_start: 0.7927 (tpp) cc_final: 0.7698 (tpp) REVERT: A 2192 TYR cc_start: 0.6805 (m-80) cc_final: 0.6567 (m-80) REVERT: A 2299 LEU cc_start: 0.7125 (mp) cc_final: 0.6804 (tt) REVERT: C 911 MET cc_start: 0.5940 (ppp) cc_final: 0.4363 (tpt) REVERT: C 921 MET cc_start: 0.4134 (mmm) cc_final: 0.3603 (mmt) REVERT: C 937 MET cc_start: 0.2477 (ttm) cc_final: 0.0792 (tmm) REVERT: C 1104 TYR cc_start: 0.5265 (m-80) cc_final: 0.3499 (t80) REVERT: C 1360 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6471 (ptp) REVERT: C 2074 MET cc_start: 0.7961 (tpp) cc_final: 0.7679 (tpp) REVERT: C 2168 PHE cc_start: 0.4493 (OUTLIER) cc_final: 0.3080 (t80) REVERT: C 2192 TYR cc_start: 0.6741 (m-80) cc_final: 0.6360 (m-80) REVERT: C 2215 MET cc_start: 0.6341 (mmp) cc_final: 0.6110 (mmp) REVERT: C 2344 MET cc_start: 0.6948 (tpp) cc_final: 0.6733 (tpt) outliers start: 75 outliers final: 46 residues processed: 324 average time/residue: 0.1834 time to fit residues: 99.9008 Evaluate side-chains 300 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1987 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2168 PHE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2344 MET Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1416 HIS Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2168 PHE Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2375 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 48 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 334 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2258 GLN ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1546 ASN A1985 GLN ** C1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.107099 restraints weight = 80679.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104382 restraints weight = 113227.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.103096 restraints weight = 101540.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101846 restraints weight = 110126.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100014 restraints weight = 122172.571| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32697 Z= 0.108 Angle : 0.488 9.117 44169 Z= 0.246 Chirality : 0.039 0.175 5073 Planarity : 0.004 0.044 5292 Dihedral : 13.561 178.710 5178 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 1.92 % Allowed : 22.36 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.25 (0.14), residues: 3831 helix: 2.44 (0.10), residues: 2532 sheet: 0.81 (0.36), residues: 213 loop : -0.72 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2391 TYR 0.029 0.001 TYR A2368 PHE 0.024 0.001 PHE A2228 TRP 0.013 0.001 TRP A2018 HIS 0.006 0.001 HIS C2378 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (32691) covalent geometry : angle 0.48831 / 0.25 (44157) SS BOND : bond 0.00137 / 0.07 ( 6) SS BOND : angle 0.28312 / 0.15 ( 12) hydrogen bonds : bond 0.03426 / 2.32 ( 2078) hydrogen bonds : angle 3.75271 / 2.73 ( 6132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 247 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5770 (OUTLIER) cc_final: 0.5544 (t) REVERT: B 921 MET cc_start: 0.4176 (mmm) cc_final: 0.3800 (mmt) REVERT: B 937 MET cc_start: 0.2001 (ptm) cc_final: 0.0522 (tpt) REVERT: B 1388 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 2048 MET cc_start: 0.7520 (mtm) cc_final: 0.7270 (mtm) REVERT: B 2168 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.2870 (t80) REVERT: B 2215 MET cc_start: 0.6434 (mmp) cc_final: 0.5937 (mmp) REVERT: A 853 VAL cc_start: 0.5519 (OUTLIER) cc_final: 0.5253 (t) REVERT: A 911 MET cc_start: 0.5942 (ppp) cc_final: 0.4044 (tpt) REVERT: A 921 MET cc_start: 0.3754 (mmm) cc_final: 0.3290 (mmm) REVERT: A 937 MET cc_start: 0.1979 (ptm) cc_final: 0.0950 (tpt) REVERT: A 1010 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7259 (t) REVERT: A 1388 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7708 (mt) REVERT: A 1841 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5564 (pptt) REVERT: A 1985 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8491 (tp40) REVERT: A 2074 MET cc_start: 0.7988 (tpp) cc_final: 0.7761 (tpp) REVERT: A 2115 ASP cc_start: 0.8225 (t0) cc_final: 0.7773 (t70) REVERT: A 2299 LEU cc_start: 0.6918 (mp) cc_final: 0.6664 (tt) REVERT: C 853 VAL cc_start: 0.5651 (OUTLIER) cc_final: 0.5390 (m) REVERT: C 911 MET cc_start: 0.5947 (ppp) cc_final: 0.4381 (tpt) REVERT: C 921 MET cc_start: 0.4105 (mmm) cc_final: 0.3626 (mmt) REVERT: C 1104 TYR cc_start: 0.5282 (m-80) cc_final: 0.3522 (t80) REVERT: C 2074 MET cc_start: 0.8003 (tpp) cc_final: 0.7717 (tpp) REVERT: C 2192 TYR cc_start: 0.6748 (m-80) cc_final: 0.6436 (m-80) REVERT: C 2215 MET cc_start: 0.6206 (mmp) cc_final: 0.6002 (mmp) REVERT: C 2344 MET cc_start: 0.7007 (tpp) cc_final: 0.6727 (tpt) REVERT: C 2377 MET cc_start: 0.7687 (tpt) cc_final: 0.6863 (tpt) outliers start: 63 outliers final: 44 residues processed: 298 average time/residue: 0.1830 time to fit residues: 91.5781 Evaluate side-chains 294 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1987 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2168 PHE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1388 ILE Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 1985 GLN Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2179 VAL Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2344 MET Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1416 HIS Chi-restraints excluded: chain C residue 1984 VAL Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2416 VAL Chi-restraints excluded: chain C residue 2501 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 295 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 349 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 352 optimal weight: 0.6980 chunk 56 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1815 HIS ** C1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.106574 restraints weight = 80381.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103923 restraints weight = 111953.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101643 restraints weight = 95427.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100957 restraints weight = 117862.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100210 restraints weight = 97845.348| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32697 Z= 0.121 Angle : 0.505 9.105 44169 Z= 0.253 Chirality : 0.039 0.173 5073 Planarity : 0.004 0.047 5292 Dihedral : 13.361 179.410 5178 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.71 % Rotamer: Outliers : 1.99 % Allowed : 22.30 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 2.22 (0.14), residues: 3831 helix: 2.42 (0.10), residues: 2526 sheet: 0.81 (0.36), residues: 213 loop : -0.70 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1553 TYR 0.016 0.001 TYR B1933 PHE 0.016 0.001 PHE B2406 TRP 0.015 0.001 TRP A2018 HIS 0.007 0.001 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (32691) covalent geometry : angle 0.50505 / 0.25 (44157) SS BOND : bond 0.00109 / 0.06 ( 6) SS BOND : angle 0.29827 / 0.15 ( 12) hydrogen bonds : bond 0.03493 / 2.36 ( 2078) hydrogen bonds : angle 3.78905 / 2.75 ( 6132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 248 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5790 (OUTLIER) cc_final: 0.5555 (t) REVERT: B 921 MET cc_start: 0.4162 (mmm) cc_final: 0.3848 (mmt) REVERT: B 937 MET cc_start: 0.2217 (ptm) cc_final: 0.0743 (tpt) REVERT: B 1388 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7803 (mt) REVERT: B 2048 MET cc_start: 0.7533 (mtm) cc_final: 0.7280 (mtm) REVERT: B 2168 PHE cc_start: 0.4775 (OUTLIER) cc_final: 0.2879 (t80) REVERT: A 853 VAL cc_start: 0.5515 (OUTLIER) cc_final: 0.5236 (t) REVERT: A 911 MET cc_start: 0.5925 (ppp) cc_final: 0.4041 (tpt) REVERT: A 921 MET cc_start: 0.4147 (mmm) cc_final: 0.3676 (mmm) REVERT: A 937 MET cc_start: 0.1556 (ptm) cc_final: 0.0542 (tpt) REVERT: A 1010 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7307 (t) REVERT: A 1360 MET cc_start: 0.7276 (ttp) cc_final: 0.6744 (ttm) REVERT: A 1841 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5592 (pptt) REVERT: A 2074 MET cc_start: 0.7972 (tpp) cc_final: 0.7741 (tpp) REVERT: A 2115 ASP cc_start: 0.8133 (t0) cc_final: 0.7723 (t70) REVERT: A 2299 LEU cc_start: 0.6892 (mp) cc_final: 0.6647 (tt) REVERT: C 853 VAL cc_start: 0.5665 (OUTLIER) cc_final: 0.5391 (m) REVERT: C 911 MET cc_start: 0.5944 (ppp) cc_final: 0.4389 (tpt) REVERT: C 921 MET cc_start: 0.4007 (mmm) cc_final: 0.3549 (mmt) REVERT: C 1104 TYR cc_start: 0.5271 (m-80) cc_final: 0.3602 (t80) REVERT: C 2074 MET cc_start: 0.7941 (tpp) cc_final: 0.7673 (tpp) REVERT: C 2168 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.3102 (t80) REVERT: C 2192 TYR cc_start: 0.6772 (m-80) cc_final: 0.6494 (m-80) REVERT: C 2344 MET cc_start: 0.6982 (tpp) cc_final: 0.6773 (tpt) outliers start: 65 outliers final: 52 residues processed: 300 average time/residue: 0.1870 time to fit residues: 94.2062 Evaluate side-chains 302 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1987 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2168 PHE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1815 HIS Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2344 MET Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1416 HIS Chi-restraints excluded: chain C residue 1724 ASN Chi-restraints excluded: chain C residue 1752 VAL Chi-restraints excluded: chain C residue 1984 VAL Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2160 CYS Chi-restraints excluded: chain C residue 2168 PHE Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2416 VAL Chi-restraints excluded: chain C residue 2464 MET Chi-restraints excluded: chain C residue 2488 LEU Chi-restraints excluded: chain C residue 2501 LEU Chi-restraints excluded: chain C residue 2506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 287 optimal weight: 0.6980 chunk 289 optimal weight: 0.0470 chunk 207 optimal weight: 2.9990 chunk 363 optimal weight: 20.0000 chunk 362 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 223 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 304 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 103 optimal weight: 30.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.121040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.106711 restraints weight = 80375.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.104005 restraints weight = 111536.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.102448 restraints weight = 110386.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101561 restraints weight = 117937.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100232 restraints weight = 109031.692| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 32697 Z= 0.156 Angle : 0.646 59.199 44169 Z= 0.359 Chirality : 0.041 0.752 5073 Planarity : 0.005 0.202 5292 Dihedral : 13.361 179.438 5178 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.96 % Allowed : 22.58 % Favored : 75.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.50 % 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: 2.23 (0.14), residues: 3831 helix: 2.43 (0.10), residues: 2526 sheet: 0.80 (0.36), residues: 213 loop : -0.71 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2259 TYR 0.016 0.001 TYR B1933 PHE 0.019 0.001 PHE B2406 TRP 0.015 0.001 TRP A2018 HIS 0.323 0.003 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (32691) covalent geometry : angle 0.64584 / 0.36 (44157) SS BOND : bond 0.00100 / 0.05 ( 6) SS BOND : angle 0.28727 / 0.14 ( 12) hydrogen bonds : bond 0.03526 / 2.38 ( 2078) hydrogen bonds : angle 3.79106 / 2.76 ( 6132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7662 Ramachandran restraints generated. 3831 Oldfield, 0 Emsley, 3831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 853 VAL cc_start: 0.5789 (OUTLIER) cc_final: 0.5558 (t) REVERT: B 921 MET cc_start: 0.4155 (mmm) cc_final: 0.3847 (mmt) REVERT: B 937 MET cc_start: 0.2213 (ptm) cc_final: 0.0735 (tpt) REVERT: B 1301 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7563 (m170) REVERT: B 1388 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 2048 MET cc_start: 0.7527 (mtm) cc_final: 0.7272 (mtm) REVERT: B 2168 PHE cc_start: 0.4783 (OUTLIER) cc_final: 0.2895 (t80) REVERT: A 853 VAL cc_start: 0.5519 (OUTLIER) cc_final: 0.5246 (t) REVERT: A 911 MET cc_start: 0.5931 (ppp) cc_final: 0.4046 (tpt) REVERT: A 921 MET cc_start: 0.4141 (mmm) cc_final: 0.3667 (mmm) REVERT: A 937 MET cc_start: 0.1550 (ptm) cc_final: 0.0527 (tpt) REVERT: A 1010 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7302 (t) REVERT: A 1360 MET cc_start: 0.7246 (ttp) cc_final: 0.6741 (ttm) REVERT: A 1841 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5595 (pptt) REVERT: A 2074 MET cc_start: 0.8021 (tpp) cc_final: 0.7780 (tpp) REVERT: A 2115 ASP cc_start: 0.8243 (t0) cc_final: 0.7822 (t70) REVERT: A 2299 LEU cc_start: 0.6911 (mp) cc_final: 0.6663 (tt) REVERT: C 853 VAL cc_start: 0.5661 (OUTLIER) cc_final: 0.5391 (m) REVERT: C 911 MET cc_start: 0.5959 (ppp) cc_final: 0.4400 (tpt) REVERT: C 921 MET cc_start: 0.4021 (mmm) cc_final: 0.3549 (mmt) REVERT: C 1104 TYR cc_start: 0.5408 (m-80) cc_final: 0.3588 (t80) REVERT: C 2074 MET cc_start: 0.8001 (tpp) cc_final: 0.7719 (tpp) REVERT: C 2168 PHE cc_start: 0.4461 (OUTLIER) cc_final: 0.3116 (t80) REVERT: C 2192 TYR cc_start: 0.6805 (m-80) cc_final: 0.6528 (m-80) REVERT: C 2344 MET cc_start: 0.7039 (tpp) cc_final: 0.6801 (tpt) outliers start: 64 outliers final: 51 residues processed: 294 average time/residue: 0.1879 time to fit residues: 92.7574 Evaluate side-chains 295 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1150 ASN Chi-restraints excluded: chain B residue 1301 HIS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1388 ILE Chi-restraints excluded: chain B residue 1406 MET Chi-restraints excluded: chain B residue 1541 LEU Chi-restraints excluded: chain B residue 1987 LEU Chi-restraints excluded: chain B residue 2075 VAL Chi-restraints excluded: chain B residue 2168 PHE Chi-restraints excluded: chain B residue 2270 LEU Chi-restraints excluded: chain B residue 2277 SER Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2443 THR Chi-restraints excluded: chain B residue 2484 VAL Chi-restraints excluded: chain B residue 2506 SER Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1068 MET Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1541 LEU Chi-restraints excluded: chain A residue 1718 TRP Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 2075 VAL Chi-restraints excluded: chain A residue 2242 LEU Chi-restraints excluded: chain A residue 2341 ILE Chi-restraints excluded: chain A residue 2344 MET Chi-restraints excluded: chain A residue 2438 ILE Chi-restraints excluded: chain A residue 2506 SER Chi-restraints excluded: chain C residue 850 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 989 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1217 LEU Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1360 MET Chi-restraints excluded: chain C residue 1416 HIS Chi-restraints excluded: chain C residue 1752 VAL Chi-restraints excluded: chain C residue 1984 VAL Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2075 VAL Chi-restraints excluded: chain C residue 2107 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2160 CYS Chi-restraints excluded: chain C residue 2168 PHE Chi-restraints excluded: chain C residue 2183 VAL Chi-restraints excluded: chain C residue 2197 THR Chi-restraints excluded: chain C residue 2309 LEU Chi-restraints excluded: chain C residue 2341 ILE Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2416 VAL Chi-restraints excluded: chain C residue 2464 MET Chi-restraints excluded: chain C residue 2488 LEU Chi-restraints excluded: chain C residue 2501 LEU Chi-restraints excluded: chain C residue 2506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 351 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 213 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 362 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105300 restraints weight = 81301.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103116 restraints weight = 124758.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101128 restraints weight = 107134.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099612 restraints weight = 124503.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.098943 restraints weight = 117972.906| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 32697 Z= 0.156 Angle : 0.646 59.199 44169 Z= 0.359 Chirality : 0.041 0.752 5073 Planarity : 0.005 0.202 5292 Dihedral : 13.361 179.438 5178 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.83 % Allowed : 22.73 % Favored : 75.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.50 % 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: 2.23 (0.14), residues: 3831 helix: 2.43 (0.10), residues: 2526 sheet: 0.80 (0.36), residues: 213 loop : -0.71 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2259 TYR 0.016 0.001 TYR B1933 PHE 0.019 0.001 PHE B2406 TRP 0.015 0.001 TRP A2018 HIS 0.323 0.003 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (32691) covalent geometry : angle 0.64583 / 0.36 (44157) SS BOND : bond 0.00100 / 0.05 ( 6) SS BOND : angle 0.28727 / 0.14 ( 12) hydrogen bonds : bond 0.03526 / 2.38 ( 2078) hydrogen bonds : angle 3.79106 / 2.76 ( 6132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4594.36 seconds wall clock time: 80 minutes 49.22 seconds (4849.22 seconds total)