Starting phenix.real_space_refine on Sat Feb 7 15:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkz_38432/02_2026/8xkz_38432.cif" } resolution = 2.55 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= 0.005 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 21778 2.51 5 N 5956 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34270 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 17120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2146, 17120 Classifications: {'peptide': 2146} Link IDs: {'PTRANS': 99, 'TRANS': 2046} Chain breaks: 4 Chain: "D" Number of atoms: 17120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2146, 17120 Classifications: {'peptide': 2146} Link IDs: {'PTRANS': 99, 'TRANS': 2046} Chain breaks: 4 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.39, per 1000 atoms: 0.22 Number of scatterers: 34270 At special positions: 0 Unit cell: (142.204, 196.069, 213.305, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 6336 8.00 N 5956 7.00 C 21778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8056 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 33 sheets defined 44.4% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 127 through 146 Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 166 through 172 removed outlier: 4.347A pdb=" N LYS C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 4.063A pdb=" N ASN C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 216 through 224 removed outlier: 4.469A pdb=" N GLU C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 297 through 305 removed outlier: 4.266A pdb=" N GLU C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.559A pdb=" N LEU C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 416 Processing helix chain 'C' and resid 446 through 452 removed outlier: 3.789A pdb=" N VAL C 452 " --> pdb=" O CYS C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 469 through 472 Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 566 through 581 Processing helix chain 'C' and resid 591 through 599 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 627 through 657 Processing helix chain 'C' and resid 849 through 865 removed outlier: 3.568A pdb=" N PHE C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS C 854 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 890 Processing helix chain 'C' and resid 893 through 905 Processing helix chain 'C' and resid 911 through 928 Processing helix chain 'C' and resid 937 through 952 Processing helix chain 'C' and resid 958 through 965 Processing helix chain 'C' and resid 965 through 975 Processing helix chain 'C' and resid 977 through 999 removed outlier: 3.988A pdb=" N GLY C 981 " --> pdb=" O SER C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1017 Processing helix chain 'C' and resid 1021 through 1033 removed outlier: 4.001A pdb=" N GLN C1033 " --> pdb=" O PHE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1047 Processing helix chain 'C' and resid 1058 through 1067 removed outlier: 3.749A pdb=" N ILE C1062 " --> pdb=" O GLU C1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1073 No H-bonds generated for 'chain 'C' and resid 1071 through 1073' Processing helix chain 'C' and resid 1074 through 1088 Processing helix chain 'C' and resid 1093 through 1107 Processing helix chain 'C' and resid 1115 through 1125 Processing helix chain 'C' and resid 1133 through 1137 Processing helix chain 'C' and resid 1144 through 1158 removed outlier: 3.586A pdb=" N ALA C1148 " --> pdb=" O VAL C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1248 removed outlier: 3.906A pdb=" N VAL C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C1248 " --> pdb=" O ASP C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1253 removed outlier: 3.619A pdb=" N MET C1253 " --> pdb=" O PHE C1249 " (cutoff:3.500A) Processing helix chain 'C' and resid 1300 through 1315 removed outlier: 3.553A pdb=" N PHE C1311 " --> pdb=" O MET C1307 " (cutoff:3.500A) Processing helix chain 'C' and resid 1316 through 1321 Processing helix chain 'C' and resid 1374 through 1378 Processing helix chain 'C' and resid 1382 through 1387 removed outlier: 3.650A pdb=" N ARG C1385 " --> pdb=" O GLU C1382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C1386 " --> pdb=" O LEU C1383 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C1387 " --> pdb=" O ASN C1384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1382 through 1387' Processing helix chain 'C' and resid 1438 through 1463 Processing helix chain 'C' and resid 1484 through 1499 removed outlier: 3.504A pdb=" N TYR C1499 " --> pdb=" O MET C1495 " (cutoff:3.500A) Processing helix chain 'C' and resid 1499 through 1506 Processing helix chain 'C' and resid 1586 through 1593 Processing helix chain 'C' and resid 1597 through 1599 No H-bonds generated for 'chain 'C' and resid 1597 through 1599' Processing helix chain 'C' and resid 1600 through 1616 Processing helix chain 'C' and resid 1617 through 1619 No H-bonds generated for 'chain 'C' and resid 1617 through 1619' Processing helix chain 'C' and resid 1627 through 1630 Processing helix chain 'C' and resid 1692 through 1710 Processing helix chain 'C' and resid 1727 through 1732 removed outlier: 3.753A pdb=" N HIS C1732 " --> pdb=" O GLU C1728 " (cutoff:3.500A) Processing helix chain 'C' and resid 1743 through 1746 removed outlier: 3.651A pdb=" N LYS C1746 " --> pdb=" O ASP C1743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1743 through 1746' Processing helix chain 'C' and resid 1754 through 1759 Processing helix chain 'C' and resid 1794 through 1811 removed outlier: 3.559A pdb=" N ARG C1798 " --> pdb=" O PRO C1794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1826 through 1834 Processing helix chain 'C' and resid 1850 through 1859 Processing helix chain 'C' and resid 1866 through 1871 Processing helix chain 'C' and resid 1871 through 1876 Processing helix chain 'C' and resid 1887 through 1900 Processing helix chain 'C' and resid 1933 through 1939 removed outlier: 4.293A pdb=" N MET C1937 " --> pdb=" O ASP C1933 " (cutoff:3.500A) Processing helix chain 'C' and resid 2019 through 2037 Processing helix chain 'C' and resid 2052 through 2058 Processing helix chain 'C' and resid 2059 through 2072 removed outlier: 3.594A pdb=" N PHE C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C2068 " --> pdb=" O GLY C2064 " (cutoff:3.500A) Processing helix chain 'C' and resid 2090 through 2095 removed outlier: 3.745A pdb=" N VAL C2095 " --> pdb=" O GLY C2091 " (cutoff:3.500A) Processing helix chain 'C' and resid 2119 through 2128 removed outlier: 3.853A pdb=" N ILE C2126 " --> pdb=" O GLY C2122 " (cutoff:3.500A) Processing helix chain 'C' and resid 2129 through 2138 Processing helix chain 'C' and resid 2141 through 2152 Processing helix chain 'C' and resid 2157 through 2175 Processing helix chain 'C' and resid 2175 through 2189 Processing helix chain 'C' and resid 2192 through 2200 removed outlier: 3.509A pdb=" N MET C2196 " --> pdb=" O THR C2192 " (cutoff:3.500A) Processing helix chain 'C' and resid 2210 through 2236 Processing helix chain 'C' and resid 2240 through 2257 Processing helix chain 'C' and resid 2258 through 2263 removed outlier: 4.264A pdb=" N TYR C2262 " --> pdb=" O VAL C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2280 removed outlier: 3.720A pdb=" N GLU C2280 " --> pdb=" O LYS C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2286 through 2311 removed outlier: 3.523A pdb=" N GLU C2290 " --> pdb=" O SER C2286 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2319 Processing helix chain 'C' and resid 2320 through 2324 Processing helix chain 'C' and resid 2327 through 2337 Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 127 through 146 Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 172 removed outlier: 4.345A pdb=" N LYS D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.012A pdb=" N ASN D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 216 through 224 removed outlier: 4.453A pdb=" N GLU D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 297 through 305 removed outlier: 4.275A pdb=" N GLU D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.568A pdb=" N LEU D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 416 Processing helix chain 'D' and resid 446 through 454 removed outlier: 3.837A pdb=" N VAL D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 473 through 480 Processing helix chain 'D' and resid 566 through 581 Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 600 through 605 Processing helix chain 'D' and resid 611 through 619 Processing helix chain 'D' and resid 627 through 657 Processing helix chain 'D' and resid 849 through 865 removed outlier: 3.590A pdb=" N PHE D 853 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS D 854 " --> pdb=" O HIS D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 890 Processing helix chain 'D' and resid 893 through 905 Processing helix chain 'D' and resid 911 through 928 Processing helix chain 'D' and resid 937 through 952 Processing helix chain 'D' and resid 958 through 965 Processing helix chain 'D' and resid 965 through 975 Processing helix chain 'D' and resid 977 through 999 removed outlier: 3.898A pdb=" N GLY D 981 " --> pdb=" O SER D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1017 Processing helix chain 'D' and resid 1021 through 1033 removed outlier: 4.002A pdb=" N GLN D1033 " --> pdb=" O PHE D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1047 Processing helix chain 'D' and resid 1058 through 1067 removed outlier: 3.673A pdb=" N ILE D1062 " --> pdb=" O GLU D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1071 through 1073 No H-bonds generated for 'chain 'D' and resid 1071 through 1073' Processing helix chain 'D' and resid 1074 through 1088 Processing helix chain 'D' and resid 1093 through 1107 Processing helix chain 'D' and resid 1115 through 1125 Processing helix chain 'D' and resid 1133 through 1137 Processing helix chain 'D' and resid 1144 through 1158 removed outlier: 3.586A pdb=" N ALA D1148 " --> pdb=" O VAL D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1242 through 1248 removed outlier: 3.920A pdb=" N VAL D1246 " --> pdb=" O PHE D1242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE D1248 " --> pdb=" O ASP D1244 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1253 removed outlier: 3.576A pdb=" N MET D1253 " --> pdb=" O PHE D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1300 through 1315 removed outlier: 3.601A pdb=" N PHE D1311 " --> pdb=" O MET D1307 " (cutoff:3.500A) Processing helix chain 'D' and resid 1316 through 1321 Processing helix chain 'D' and resid 1374 through 1378 Processing helix chain 'D' and resid 1382 through 1387 removed outlier: 3.611A pdb=" N ARG D1385 " --> pdb=" O GLU D1382 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D1386 " --> pdb=" O LEU D1383 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D1387 " --> pdb=" O ASN D1384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1382 through 1387' Processing helix chain 'D' and resid 1438 through 1463 Processing helix chain 'D' and resid 1484 through 1499 removed outlier: 3.526A pdb=" N TYR D1499 " --> pdb=" O MET D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1499 through 1506 Processing helix chain 'D' and resid 1586 through 1593 Processing helix chain 'D' and resid 1597 through 1599 No H-bonds generated for 'chain 'D' and resid 1597 through 1599' Processing helix chain 'D' and resid 1600 through 1616 Processing helix chain 'D' and resid 1617 through 1619 No H-bonds generated for 'chain 'D' and resid 1617 through 1619' Processing helix chain 'D' and resid 1627 through 1630 Processing helix chain 'D' and resid 1692 through 1710 Processing helix chain 'D' and resid 1727 through 1732 removed outlier: 3.739A pdb=" N HIS D1732 " --> pdb=" O GLU D1728 " (cutoff:3.500A) Processing helix chain 'D' and resid 1743 through 1746 removed outlier: 3.686A pdb=" N LYS D1746 " --> pdb=" O ASP D1743 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1743 through 1746' Processing helix chain 'D' and resid 1754 through 1759 Processing helix chain 'D' and resid 1760 through 1765 removed outlier: 5.492A pdb=" N ALA D1763 " --> pdb=" O ARG D1760 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D1765 " --> pdb=" O SER D1762 " (cutoff:3.500A) Processing helix chain 'D' and resid 1794 through 1811 removed outlier: 3.524A pdb=" N ARG D1798 " --> pdb=" O PRO D1794 " (cutoff:3.500A) Processing helix chain 'D' and resid 1826 through 1834 Processing helix chain 'D' and resid 1850 through 1859 Processing helix chain 'D' and resid 1866 through 1871 Processing helix chain 'D' and resid 1871 through 1876 Processing helix chain 'D' and resid 1887 through 1900 Processing helix chain 'D' and resid 1933 through 1939 removed outlier: 4.141A pdb=" N MET D1937 " --> pdb=" O ASP D1933 " (cutoff:3.500A) Processing helix chain 'D' and resid 2019 through 2037 Processing helix chain 'D' and resid 2052 through 2058 Processing helix chain 'D' and resid 2059 through 2072 removed outlier: 3.597A pdb=" N PHE D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL D2068 " --> pdb=" O GLY D2064 " (cutoff:3.500A) Processing helix chain 'D' and resid 2090 through 2095 removed outlier: 3.669A pdb=" N VAL D2095 " --> pdb=" O GLY D2091 " (cutoff:3.500A) Processing helix chain 'D' and resid 2119 through 2128 removed outlier: 3.852A pdb=" N ILE D2126 " --> pdb=" O GLY D2122 " (cutoff:3.500A) Processing helix chain 'D' and resid 2129 through 2138 Processing helix chain 'D' and resid 2141 through 2152 Processing helix chain 'D' and resid 2157 through 2175 Processing helix chain 'D' and resid 2175 through 2189 Processing helix chain 'D' and resid 2192 through 2200 removed outlier: 3.551A pdb=" N MET D2196 " --> pdb=" O THR D2192 " (cutoff:3.500A) Processing helix chain 'D' and resid 2210 through 2236 Processing helix chain 'D' and resid 2240 through 2257 Processing helix chain 'D' and resid 2258 through 2263 removed outlier: 4.253A pdb=" N TYR D2262 " --> pdb=" O VAL D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2266 through 2280 removed outlier: 3.683A pdb=" N GLU D2280 " --> pdb=" O LYS D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2286 through 2311 removed outlier: 3.511A pdb=" N GLU D2290 " --> pdb=" O SER D2286 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2319 Processing helix chain 'D' and resid 2320 through 2324 Processing helix chain 'D' and resid 2327 through 2337 Processing sheet with id=AA1, first strand: chain 'C' and resid 174 through 177 removed outlier: 4.140A pdb=" N MET C 156 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C 120 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N TRP C 206 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 122 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 290 through 291 removed outlier: 3.835A pdb=" N ILE C 346 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY C 320 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 432 through 439 removed outlier: 5.813A pdb=" N PHE C 433 " --> pdb=" O SER C 428 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 428 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N PHE C 435 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C 426 " --> pdb=" O PHE C 435 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 437 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N HIS C 357 " --> pdb=" O ASP C 377 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP C 377 " --> pdb=" O HIS C 357 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 359 " --> pdb=" O GLY C 375 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY C 375 " --> pdb=" O GLU C 359 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN C 361 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER C 379 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE C 388 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN C 381 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS C 386 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 387 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 558 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 548 through 549 removed outlier: 6.584A pdb=" N ARG C 584 " --> pdb=" O GLN C 527 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 529 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER C 582 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 670 through 676 Processing sheet with id=AA6, first strand: chain 'C' and resid 753 through 755 Processing sheet with id=AA7, first strand: chain 'C' and resid 787 through 792 removed outlier: 3.596A pdb=" N VAL C 784 " --> pdb=" O MET C 787 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 780 " --> pdb=" O LEU C 791 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR C 779 " --> pdb=" O TYR C 765 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR C 765 " --> pdb=" O TYR C 779 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLU C 781 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 807 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1162 through 1169 removed outlier: 5.521A pdb=" N LEU C1163 " --> pdb=" O MET C1183 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C1183 " --> pdb=" O LEU C1163 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N HIS C1287 " --> pdb=" O ARG C1326 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR C1328 " --> pdb=" O HIS C1287 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C1289 " --> pdb=" O THR C1328 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU C1330 " --> pdb=" O LEU C1289 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C1291 " --> pdb=" O LEU C1330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1389 through 1394 removed outlier: 4.301A pdb=" N LEU C1403 " --> pdb=" O ILE C1394 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N HIS C1472 " --> pdb=" O TYR C1419 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE C1421 " --> pdb=" O HIS C1472 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C1474 " --> pdb=" O PHE C1421 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C1423 " --> pdb=" O PHE C1474 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN C1476 " --> pdb=" O VAL C1423 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C1425 " --> pdb=" O ASN C1476 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL C1478 " --> pdb=" O ALA C1425 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE C1427 " --> pdb=" O VAL C1478 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR C1480 " --> pdb=" O ILE C1427 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN C1471 " --> pdb=" O GLN C1510 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLU C1512 " --> pdb=" O ASN C1471 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE C1473 " --> pdb=" O GLU C1512 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS C1514 " --> pdb=" O ILE C1473 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C1475 " --> pdb=" O LYS C1514 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ASN C1516 " --> pdb=" O LEU C1475 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N PHE C1477 " --> pdb=" O ASN C1516 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C1547 " --> pdb=" O PRO C1527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1645 through 1648 removed outlier: 4.223A pdb=" N ALA C1661 " --> pdb=" O LEU C1637 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU C1639 " --> pdb=" O MET C1659 " (cutoff:3.500A) removed outlier: 11.646A pdb=" N MET C1659 " --> pdb=" O LEU C1639 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE C1714 " --> pdb=" O ASP C1676 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE C1678 " --> pdb=" O ILE C1714 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL C1716 " --> pdb=" O ILE C1678 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C1680 " --> pdb=" O VAL C1716 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C1713 " --> pdb=" O ILE C1817 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU C1819 " --> pdb=" O ARG C1713 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C1715 " --> pdb=" O LEU C1819 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1735 through 1738 removed outlier: 3.766A pdb=" N TYR C1750 " --> pdb=" O ALA C1737 " (cutoff:3.500A) removed outlier: 16.405A pdb=" N ARG C1749 " --> pdb=" O ASP C1784 " (cutoff:3.500A) removed outlier: 11.842A pdb=" N ASP C1784 " --> pdb=" O ARG C1749 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU C1751 " --> pdb=" O ILE C1782 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER C1778 " --> pdb=" O ASP C1774 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP C1774 " --> pdb=" O SER C1778 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR C1780 " --> pdb=" O VAL C1772 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C1772 " --> pdb=" O TYR C1780 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE C1782 " --> pdb=" O GLU C1770 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU C1770 " --> pdb=" O ILE C1782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1823 through 1825 removed outlier: 6.167A pdb=" N ALA C1824 " --> pdb=" O ILE C1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 1940 through 1942 Processing sheet with id=AB5, first strand: chain 'C' and resid 1961 through 1962 removed outlier: 8.010A pdb=" N MET C2041 " --> pdb=" O PRO C1982 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY C1984 " --> pdb=" O MET C2041 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE C2043 " --> pdb=" O GLY C1984 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C1986 " --> pdb=" O PHE C2043 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C2040 " --> pdb=" O LEU C2079 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR C2081 " --> pdb=" O LEU C2040 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL C2042 " --> pdb=" O TYR C2081 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N ASP C2204 " --> pdb=" O MET C2105 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET C2107 " --> pdb=" O ASP C2204 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU C2206 " --> pdb=" O MET C2107 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA C2109 " --> pdb=" O LEU C2206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1993 through 1997 Processing sheet with id=AB7, first strand: chain 'C' and resid 2086 through 2089 removed outlier: 6.556A pdb=" N ALA C2086 " --> pdb=" O ARG C2114 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER C2116 " --> pdb=" O ALA C2086 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU C2088 " --> pdb=" O SER C2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 174 through 177 removed outlier: 4.148A pdb=" N MET D 156 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS D 120 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TRP D 206 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU D 122 " --> pdb=" O TRP D 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 290 through 291 removed outlier: 3.847A pdb=" N ILE D 346 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLY D 320 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 432 through 439 removed outlier: 5.871A pdb=" N PHE D 433 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER D 428 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE D 435 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU D 426 " --> pdb=" O PHE D 435 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 437 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS D 357 " --> pdb=" O ASP D 377 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP D 377 " --> pdb=" O HIS D 357 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU D 359 " --> pdb=" O GLY D 375 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY D 375 " --> pdb=" O GLU D 359 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN D 361 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER D 379 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE D 388 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN D 381 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS D 386 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE D 387 " --> pdb=" O ARG D 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 558 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 513 through 514 removed outlier: 3.888A pdb=" N LYS D 520 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 548 through 549 removed outlier: 6.571A pdb=" N ARG D 584 " --> pdb=" O GLN D 527 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 529 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER D 582 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 670 through 676 Processing sheet with id=AC5, first strand: chain 'D' and resid 753 through 755 Processing sheet with id=AC6, first strand: chain 'D' and resid 787 through 792 removed outlier: 3.734A pdb=" N ALA D 780 " --> pdb=" O LEU D 791 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N TYR D 779 " --> pdb=" O TYR D 765 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR D 765 " --> pdb=" O TYR D 779 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU D 781 " --> pdb=" O ILE D 763 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 807 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1162 through 1169 removed outlier: 5.482A pdb=" N LEU D1163 " --> pdb=" O MET D1183 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET D1183 " --> pdb=" O LEU D1163 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS D1287 " --> pdb=" O ARG D1326 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N THR D1328 " --> pdb=" O HIS D1287 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU D1289 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU D1330 " --> pdb=" O LEU D1289 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D1291 " --> pdb=" O LEU D1330 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1389 through 1394 removed outlier: 4.341A pdb=" N LEU D1403 " --> pdb=" O ILE D1394 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N HIS D1472 " --> pdb=" O TYR D1419 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE D1421 " --> pdb=" O HIS D1472 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE D1474 " --> pdb=" O PHE D1421 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL D1423 " --> pdb=" O PHE D1474 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASN D1476 " --> pdb=" O VAL D1423 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA D1425 " --> pdb=" O ASN D1476 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL D1478 " --> pdb=" O ALA D1425 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ILE D1427 " --> pdb=" O VAL D1478 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR D1480 " --> pdb=" O ILE D1427 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN D1471 " --> pdb=" O GLN D1510 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLU D1512 " --> pdb=" O ASN D1471 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE D1473 " --> pdb=" O GLU D1512 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LYS D1514 " --> pdb=" O ILE D1473 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D1475 " --> pdb=" O LYS D1514 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASN D1516 " --> pdb=" O LEU D1475 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N PHE D1477 " --> pdb=" O ASN D1516 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU D1547 " --> pdb=" O PRO D1527 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 1645 through 1648 removed outlier: 4.280A pdb=" N ALA D1661 " --> pdb=" O LEU D1637 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU D1639 " --> pdb=" O MET D1659 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N MET D1659 " --> pdb=" O LEU D1639 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE D1714 " --> pdb=" O ASP D1676 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D1678 " --> pdb=" O ILE D1714 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL D1716 " --> pdb=" O ILE D1678 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D1680 " --> pdb=" O VAL D1716 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG D1713 " --> pdb=" O ILE D1817 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D1819 " --> pdb=" O ARG D1713 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR D1715 " --> pdb=" O LEU D1819 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1735 through 1738 removed outlier: 6.524A pdb=" N HIS D1735 " --> pdb=" O LEU D1751 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU D1751 " --> pdb=" O HIS D1735 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA D1737 " --> pdb=" O ARG D1749 " (cutoff:3.500A) removed outlier: 16.377A pdb=" N ARG D1749 " --> pdb=" O ASP D1784 " (cutoff:3.500A) removed outlier: 11.837A pdb=" N ASP D1784 " --> pdb=" O ARG D1749 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU D1751 " --> pdb=" O ILE D1782 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER D1778 " --> pdb=" O ASP D1774 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP D1774 " --> pdb=" O SER D1778 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR D1780 " --> pdb=" O VAL D1772 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL D1772 " --> pdb=" O TYR D1780 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE D1782 " --> pdb=" O GLU D1770 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU D1770 " --> pdb=" O ILE D1782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1824 through 1825 removed outlier: 6.186A pdb=" N ALA D1824 " --> pdb=" O ILE D1847 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 1940 through 1942 Processing sheet with id=AD4, first strand: chain 'D' and resid 1961 through 1962 removed outlier: 7.989A pdb=" N MET D2041 " --> pdb=" O PRO D1982 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY D1984 " --> pdb=" O MET D2041 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE D2043 " --> pdb=" O GLY D1984 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D1986 " --> pdb=" O PHE D2043 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU D2040 " --> pdb=" O LEU D2079 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR D2081 " --> pdb=" O LEU D2040 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL D2042 " --> pdb=" O TYR D2081 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ASP D2204 " --> pdb=" O MET D2105 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N MET D2107 " --> pdb=" O ASP D2204 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU D2206 " --> pdb=" O MET D2107 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA D2109 " --> pdb=" O LEU D2206 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1993 through 1997 Processing sheet with id=AD6, first strand: chain 'D' and resid 2086 through 2089 removed outlier: 6.552A pdb=" N ALA D2086 " --> pdb=" O ARG D2114 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N SER D2116 " --> pdb=" O ALA D2086 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D2088 " --> pdb=" O SER D2116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 1613 hydrogen bonds defined for protein. 4623 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: 11.09 Time building geometry restraints manager: 4.02 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: 5903 1.32 - 1.44: 9144 1.44 - 1.57: 19622 1.57 - 1.69: 1 1.69 - 1.81: 342 Bond restraints: 35012 Sorted by residual: bond pdb=" C TRP D2018 " pdb=" N PHE D2019 " ideal model delta sigma weight residual 1.323 1.201 0.121 1.64e-02 3.72e+03 5.48e+01 bond pdb=" C TRP C2018 " pdb=" N PHE C2019 " ideal model delta sigma weight residual 1.323 1.211 0.111 1.64e-02 3.72e+03 4.59e+01 bond pdb=" CG1 ILE C 128 " pdb=" CD1 ILE C 128 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" CG1 ILE D 128 " pdb=" CD1 ILE D 128 " ideal model delta sigma weight residual 1.513 1.394 0.119 3.90e-02 6.57e+02 9.32e+00 bond pdb=" C2 BTN C2401 " pdb=" S1 BTN C2401 " ideal model delta sigma weight residual 1.824 1.765 0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 35007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 46423 2.38 - 4.75: 837 4.75 - 7.13: 142 7.13 - 9.50: 16 9.50 - 11.88: 6 Bond angle restraints: 47424 Sorted by residual: angle pdb=" C VAL D 418 " pdb=" N SER D 419 " pdb=" CA SER D 419 " ideal model delta sigma weight residual 121.54 133.42 -11.88 1.91e+00 2.74e-01 3.87e+01 angle pdb=" C VAL C 418 " pdb=" N SER C 419 " pdb=" CA SER C 419 " ideal model delta sigma weight residual 121.54 133.09 -11.55 1.91e+00 2.74e-01 3.66e+01 angle pdb=" C ARG D1240 " pdb=" N THR D1241 " pdb=" CA THR D1241 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C ARG C1240 " pdb=" N THR C1241 " pdb=" CA THR C1241 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C TYR D1139 " pdb=" N HIS D1140 " pdb=" CA HIS D1140 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 ... (remaining 47419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 20290 17.83 - 35.66: 584 35.66 - 53.49: 201 53.49 - 71.31: 76 71.31 - 89.14: 33 Dihedral angle restraints: 21184 sinusoidal: 8692 harmonic: 12492 Sorted by residual: dihedral pdb=" CA ARG C1687 " pdb=" C ARG C1687 " pdb=" N ILE C1688 " pdb=" CA ILE C1688 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA ARG D1687 " pdb=" C ARG D1687 " pdb=" N ILE D1688 " pdb=" CA ILE D1688 " ideal model delta harmonic sigma weight residual -180.00 -147.03 -32.97 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA HIS D1140 " pdb=" C HIS D1140 " pdb=" N SER D1141 " pdb=" CA SER D1141 " ideal model delta harmonic sigma weight residual 180.00 147.91 32.09 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 21181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3629 0.051 - 0.101: 1286 0.101 - 0.152: 310 0.152 - 0.203: 23 0.203 - 0.253: 8 Chirality restraints: 5256 Sorted by residual: chirality pdb=" CB ILE C 128 " pdb=" CA ILE C 128 " pdb=" CG1 ILE C 128 " pdb=" CG2 ILE C 128 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE C1688 " pdb=" CA ILE C1688 " pdb=" CG1 ILE C1688 " pdb=" CG2 ILE C1688 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE D1688 " pdb=" N ILE D1688 " pdb=" C ILE D1688 " pdb=" CB ILE D1688 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 5253 not shown) Planarity restraints: 6152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 419 " 0.035 2.00e-02 2.50e+03 6.88e-02 4.74e+01 pdb=" C SER D 419 " -0.119 2.00e-02 2.50e+03 pdb=" O SER D 419 " 0.043 2.00e-02 2.50e+03 pdb=" N ALA D 420 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 419 " 0.034 2.00e-02 2.50e+03 6.74e-02 4.55e+01 pdb=" C SER C 419 " -0.117 2.00e-02 2.50e+03 pdb=" O SER C 419 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA C 420 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C1579 " 0.030 2.00e-02 2.50e+03 6.07e-02 3.69e+01 pdb=" C THR C1579 " -0.105 2.00e-02 2.50e+03 pdb=" O THR C1579 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS C1580 " 0.036 2.00e-02 2.50e+03 ... (remaining 6149 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3844 2.75 - 3.28: 33516 3.28 - 3.82: 55339 3.82 - 4.36: 68297 4.36 - 4.90: 116061 Nonbonded interactions: 277057 Sorted by model distance: nonbonded pdb=" O THR D1579 " pdb=" OG1 THR D1579 " model vdw 2.207 3.040 nonbonded pdb=" O THR C1579 " pdb=" OG1 THR C1579 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR C 417 " pdb=" O ALA C 420 " model vdw 2.229 3.040 nonbonded pdb=" NH1 ARG C 139 " pdb=" OD1 ASN D 573 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN C 573 " pdb=" NH1 ARG D 139 " model vdw 2.237 3.120 ... (remaining 277052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.360 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.011 0.139 35014 Z= 0.448 Angle : 0.861 11.876 47424 Z= 0.482 Chirality : 0.053 0.253 5256 Planarity : 0.006 0.069 6152 Dihedral : 11.469 89.142 13128 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.92 % Favored : 93.77 % Rotamer: Outliers : 1.41 % Allowed : 0.77 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4272 helix: -0.30 (0.11), residues: 1680 sheet: 0.38 (0.17), residues: 874 loop : -1.78 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1935 TYR 0.019 0.002 TYR C 417 PHE 0.018 0.003 PHE D1242 TRP 0.013 0.002 TRP C 485 HIS 0.012 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.01062 (35012) covalent geometry : angle 0.86096 (47424) hydrogen bonds : bond 0.15144 ( 1613) hydrogen bonds : angle 6.49942 ( 4623) Misc. bond : bond 0.06773 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 688 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 MET cc_start: 0.7532 (mmp) cc_final: 0.6825 (mtp) REVERT: C 886 MET cc_start: 0.8800 (mmp) cc_final: 0.8507 (mmt) REVERT: C 980 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7193 (mtt180) REVERT: C 1358 PHE cc_start: 0.7930 (m-80) cc_final: 0.7523 (m-80) REVERT: C 1830 TYR cc_start: 0.8354 (m-80) cc_final: 0.8151 (m-80) REVERT: C 1849 THR cc_start: 0.8504 (m) cc_final: 0.8216 (p) REVERT: C 2147 LEU cc_start: 0.8504 (mt) cc_final: 0.8196 (tt) REVERT: D 139 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7636 (tmt170) REVERT: D 332 ASN cc_start: 0.8184 (m-40) cc_final: 0.7944 (m110) REVERT: D 574 MET cc_start: 0.8442 (tpp) cc_final: 0.8217 (tpt) REVERT: D 589 THR cc_start: 0.7704 (m) cc_final: 0.7449 (p) REVERT: D 593 TYR cc_start: 0.7763 (t80) cc_final: 0.6991 (t80) REVERT: D 1143 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7112 (pp30) REVERT: D 1151 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: D 1159 ILE cc_start: 0.6717 (tp) cc_final: 0.6460 (tp) REVERT: D 1308 PHE cc_start: 0.8018 (m-80) cc_final: 0.7627 (m-80) REVERT: D 1513 LEU cc_start: 0.8558 (tt) cc_final: 0.8324 (mm) outliers start: 53 outliers final: 15 residues processed: 736 average time/residue: 0.8403 time to fit residues: 717.8037 Evaluate side-chains 319 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 485 TRP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 149 ARG Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 441 ARG Chi-restraints excluded: chain D residue 485 TRP Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1151 GLU Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2128 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN C 443 GLN C 530 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 948 HIS C1174 ASN C1231 GLN C2146 HIS C2181 GLN C2303 GLN D 443 GLN D 530 ASN D 559 HIS D1074 ASN D1168 HIS D1174 ASN D2285 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.103768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.079846 restraints weight = 98397.802| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.58 r_work: 0.3520 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35014 Z= 0.142 Angle : 0.666 13.645 47424 Z= 0.345 Chirality : 0.046 0.189 5256 Planarity : 0.005 0.055 6152 Dihedral : 6.053 65.689 4789 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.75 % Allowed : 10.14 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 4272 helix: 0.74 (0.12), residues: 1752 sheet: 0.90 (0.18), residues: 796 loop : -1.57 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 607 TYR 0.018 0.001 TYR C 175 PHE 0.023 0.002 PHE C1311 TRP 0.013 0.001 TRP C 260 HIS 0.007 0.001 HIS D2285 Details of bonding type rmsd covalent geometry : bond 0.00308 (35012) covalent geometry : angle 0.66625 (47424) hydrogen bonds : bond 0.04859 ( 1613) hydrogen bonds : angle 5.19292 ( 4623) Misc. bond : bond 0.00051 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 361 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8098 (mttm) REVERT: C 728 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8215 (ttmt) REVERT: C 799 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7168 (pp) REVERT: C 922 MET cc_start: 0.7946 (ptm) cc_final: 0.7651 (mtm) REVERT: C 963 MET cc_start: 0.8504 (mmp) cc_final: 0.8179 (ppp) REVERT: C 980 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7161 (mtt180) REVERT: C 983 MET cc_start: 0.7134 (tmm) cc_final: 0.6883 (tmm) REVERT: C 1111 TYR cc_start: 0.1960 (t80) cc_final: 0.1520 (t80) REVERT: C 1139 TYR cc_start: 0.6749 (p90) cc_final: 0.5984 (p90) REVERT: C 1326 ARG cc_start: 0.6715 (ptt90) cc_final: 0.6353 (ttp-170) REVERT: C 1358 PHE cc_start: 0.8025 (m-80) cc_final: 0.7224 (m-80) REVERT: C 1401 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7744 (mtm) REVERT: C 1488 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (mp) REVERT: C 2321 HIS cc_start: 0.8082 (m90) cc_final: 0.7875 (m-70) REVERT: D 574 MET cc_start: 0.8289 (tpp) cc_final: 0.8032 (tpt) REVERT: D 593 TYR cc_start: 0.8094 (t80) cc_final: 0.7229 (t80) REVERT: D 613 LEU cc_start: 0.8745 (tp) cc_final: 0.8534 (tp) REVERT: D 732 ASP cc_start: 0.7838 (p0) cc_final: 0.7634 (t0) REVERT: D 1151 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6617 (tt0) REVERT: D 1153 TYR cc_start: 0.7879 (t80) cc_final: 0.7670 (t80) REVERT: D 1180 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: D 1236 MET cc_start: 0.6726 (tpp) cc_final: 0.6355 (tpp) REVERT: D 1399 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7063 (p90) REVERT: D 1431 ASP cc_start: 0.8041 (m-30) cc_final: 0.7468 (t0) REVERT: D 1513 LEU cc_start: 0.8778 (tt) cc_final: 0.8425 (mm) REVERT: D 1557 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7837 (pmt) REVERT: D 2129 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6629 (mtp180) REVERT: D 2254 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8134 (pp20) outliers start: 103 outliers final: 23 residues processed: 440 average time/residue: 0.7951 time to fit residues: 411.6971 Evaluate side-chains 294 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 980 ARG Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1123 LEU Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1401 MET Chi-restraints excluded: chain C residue 1488 ILE Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2092 SER Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 559 HIS Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1074 ASN Chi-restraints excluded: chain D residue 1151 GLU Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1240 ARG Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1583 LEU Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2128 PHE Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2254 GLU Chi-restraints excluded: chain D residue 2265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 363 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 234 optimal weight: 0.4980 chunk 202 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS C 707 HIS C 924 GLN C1168 HIS C1181 GLN C1231 GLN C1510 GLN C1843 ASN D 443 GLN D 559 HIS D1876 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.101096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.076050 restraints weight = 98568.253| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.47 r_work: 0.3469 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35014 Z= 0.169 Angle : 0.646 11.332 47424 Z= 0.332 Chirality : 0.046 0.206 5256 Planarity : 0.005 0.045 6152 Dihedral : 5.461 59.797 4767 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.76 % Favored : 94.22 % Rotamer: Outliers : 2.80 % Allowed : 11.56 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4272 helix: 0.87 (0.12), residues: 1792 sheet: 0.80 (0.18), residues: 828 loop : -1.46 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C2297 TYR 0.015 0.001 TYR D 142 PHE 0.021 0.002 PHE C1115 TRP 0.021 0.001 TRP C 260 HIS 0.025 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00388 (35012) covalent geometry : angle 0.64565 (47424) hydrogen bonds : bond 0.04694 ( 1613) hydrogen bonds : angle 5.02129 ( 4623) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 291 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: C 274 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5963 (p90) REVERT: C 728 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8384 (tttp) REVERT: C 922 MET cc_start: 0.8079 (ptm) cc_final: 0.7807 (mtm) REVERT: C 963 MET cc_start: 0.8642 (mmp) cc_final: 0.8227 (tmm) REVERT: C 983 MET cc_start: 0.7270 (tmm) cc_final: 0.6987 (tmm) REVERT: C 1021 MET cc_start: 0.8859 (mmt) cc_final: 0.8652 (mmt) REVERT: C 1139 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6322 (p90) REVERT: C 1147 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7130 (mpp) REVERT: C 1236 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7868 (mmm) REVERT: C 1326 ARG cc_start: 0.6844 (ptt90) cc_final: 0.6414 (ttp-170) REVERT: C 1327 LEU cc_start: 0.8456 (tt) cc_final: 0.8242 (tt) REVERT: C 1358 PHE cc_start: 0.8094 (m-80) cc_final: 0.7207 (m-80) REVERT: C 1466 VAL cc_start: 0.8276 (m) cc_final: 0.7886 (p) REVERT: C 1467 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7301 (mtp85) REVERT: D 152 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7509 (mmm160) REVERT: D 243 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8171 (mptt) REVERT: D 309 MET cc_start: 0.5329 (tpp) cc_final: 0.4961 (tpp) REVERT: D 347 PHE cc_start: 0.5966 (p90) cc_final: 0.5751 (p90) REVERT: D 414 MET cc_start: 0.8439 (tmm) cc_final: 0.8218 (OUTLIER) REVERT: D 593 TYR cc_start: 0.8437 (t80) cc_final: 0.7699 (t80) REVERT: D 732 ASP cc_start: 0.8075 (p0) cc_final: 0.7697 (t0) REVERT: D 754 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6441 (mtp) REVERT: D 1180 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7091 (m-10) REVERT: D 1236 MET cc_start: 0.7048 (tpp) cc_final: 0.6745 (tpt) REVERT: D 1370 TYR cc_start: 0.8335 (m-80) cc_final: 0.8094 (m-80) REVERT: D 1399 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7212 (p90) REVERT: D 1431 ASP cc_start: 0.8176 (m-30) cc_final: 0.7550 (t0) REVERT: D 1495 MET cc_start: 0.8167 (ptp) cc_final: 0.7837 (ptm) REVERT: D 1513 LEU cc_start: 0.8846 (tt) cc_final: 0.8428 (mm) REVERT: D 1557 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7902 (pmt) REVERT: D 2129 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6883 (mtp180) outliers start: 105 outliers final: 25 residues processed: 370 average time/residue: 0.7751 time to fit residues: 339.8079 Evaluate side-chains 270 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1139 TYR Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1604 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 754 MET Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1466 VAL Chi-restraints excluded: chain D residue 1536 SER Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1622 LEU Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2304 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 255 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 410 optimal weight: 10.0000 chunk 13 optimal weight: 0.0050 chunk 243 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 292 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 HIS C 559 HIS ** C1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1231 GLN C2059 GLN D 443 GLN D 559 HIS D 698 ASN D1074 ASN D1313 GLN D1402 HIS ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN D2303 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.099084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.073778 restraints weight = 98303.253| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.48 r_work: 0.3424 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35014 Z= 0.214 Angle : 0.670 11.089 47424 Z= 0.345 Chirality : 0.047 0.202 5256 Planarity : 0.005 0.067 6152 Dihedral : 5.373 53.356 4756 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 3.34 % Allowed : 11.88 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4272 helix: 0.90 (0.12), residues: 1788 sheet: 0.65 (0.18), residues: 836 loop : -1.52 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 382 TYR 0.017 0.002 TYR D 142 PHE 0.020 0.002 PHE C1115 TRP 0.018 0.001 TRP C 260 HIS 0.013 0.001 HIS C 384 Details of bonding type rmsd covalent geometry : bond 0.00497 (35012) covalent geometry : angle 0.66958 (47424) hydrogen bonds : bond 0.04787 ( 1613) hydrogen bonds : angle 5.02031 ( 4623) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 267 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASN cc_start: 0.8481 (t0) cc_final: 0.8184 (t0) REVERT: C 223 LEU cc_start: 0.8813 (pp) cc_final: 0.8568 (pt) REVERT: C 274 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6033 (p90) REVERT: C 622 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: C 728 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8432 (tttp) REVERT: C 836 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8071 (mt) REVERT: C 902 ILE cc_start: 0.9046 (mt) cc_final: 0.8744 (tt) REVERT: C 922 MET cc_start: 0.8117 (ptm) cc_final: 0.7905 (mtm) REVERT: C 963 MET cc_start: 0.8706 (mmp) cc_final: 0.8170 (tmm) REVERT: C 983 MET cc_start: 0.7305 (tmm) cc_final: 0.6966 (tmm) REVERT: C 1021 MET cc_start: 0.8930 (mmt) cc_final: 0.8705 (mmt) REVERT: C 1065 GLU cc_start: 0.8453 (tp30) cc_final: 0.8179 (tp30) REVERT: C 1139 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6250 (p90) REVERT: C 1236 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: C 1239 PHE cc_start: 0.6550 (m-80) cc_final: 0.5831 (m-80) REVERT: C 1326 ARG cc_start: 0.6792 (ptt90) cc_final: 0.6342 (ttp-170) REVERT: C 1358 PHE cc_start: 0.8088 (m-80) cc_final: 0.7365 (m-80) REVERT: C 2316 MET cc_start: 0.7706 (mmm) cc_final: 0.7387 (mpp) REVERT: D 152 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7524 (mmm160) REVERT: D 243 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8296 (mptt) REVERT: D 593 TYR cc_start: 0.8559 (t80) cc_final: 0.7976 (t80) REVERT: D 622 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (pp30) REVERT: D 732 ASP cc_start: 0.8102 (p0) cc_final: 0.7753 (t0) REVERT: D 1180 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: D 1236 MET cc_start: 0.6929 (tpp) cc_final: 0.6619 (tpt) REVERT: D 1370 TYR cc_start: 0.8401 (m-80) cc_final: 0.8110 (m-80) REVERT: D 1399 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7281 (p90) REVERT: D 1401 MET cc_start: 0.9067 (mtt) cc_final: 0.8862 (mtm) REVERT: D 1431 ASP cc_start: 0.8199 (m-30) cc_final: 0.7537 (t0) REVERT: D 1495 MET cc_start: 0.8303 (ptp) cc_final: 0.7991 (ptm) REVERT: D 1513 LEU cc_start: 0.8842 (tt) cc_final: 0.8322 (mm) REVERT: D 1557 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7848 (pmt) REVERT: D 2041 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8073 (mmm) outliers start: 125 outliers final: 38 residues processed: 358 average time/residue: 0.8010 time to fit residues: 340.3962 Evaluate side-chains 278 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1139 TYR Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1488 ILE Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2248 LEU Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 559 HIS Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 683 LEU Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1466 VAL Chi-restraints excluded: chain D residue 1536 SER Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1583 LEU Chi-restraints excluded: chain D residue 1622 LEU Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 390 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 422 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 369 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 315 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 439 ASN C 559 HIS C2234 ASN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS D 688 GLN D1136 ASN D1140 HIS D1143 GLN ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.099287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.073936 restraints weight = 98349.049| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.50 r_work: 0.3430 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35014 Z= 0.168 Angle : 0.627 10.712 47424 Z= 0.324 Chirality : 0.045 0.205 5256 Planarity : 0.004 0.065 6152 Dihedral : 5.208 49.999 4756 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.78 % Allowed : 12.60 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4272 helix: 0.99 (0.12), residues: 1800 sheet: 0.54 (0.18), residues: 850 loop : -1.46 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 607 TYR 0.015 0.001 TYR D 142 PHE 0.032 0.002 PHE D 347 TRP 0.019 0.001 TRP C 260 HIS 0.022 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00387 (35012) covalent geometry : angle 0.62728 (47424) hydrogen bonds : bond 0.04374 ( 1613) hydrogen bonds : angle 4.92084 ( 4623) Misc. bond : bond 0.00045 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 258 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASN cc_start: 0.8473 (t0) cc_final: 0.8220 (t0) REVERT: C 223 LEU cc_start: 0.8839 (pp) cc_final: 0.8576 (pt) REVERT: C 274 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.6176 (p90) REVERT: C 414 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8316 (ttp) REVERT: C 451 MET cc_start: 0.8141 (mmm) cc_final: 0.7939 (mmm) REVERT: C 622 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7174 (mm-40) REVERT: C 624 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5480 (mp0) REVERT: C 728 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8402 (tttp) REVERT: C 902 ILE cc_start: 0.9133 (mt) cc_final: 0.8722 (tt) REVERT: C 922 MET cc_start: 0.8078 (ptm) cc_final: 0.7724 (mtm) REVERT: C 962 PHE cc_start: 0.8473 (t80) cc_final: 0.8016 (t80) REVERT: C 963 MET cc_start: 0.8713 (mmp) cc_final: 0.8394 (tmm) REVERT: C 983 MET cc_start: 0.7276 (tmm) cc_final: 0.6929 (tmm) REVERT: C 1065 GLU cc_start: 0.8445 (tp30) cc_final: 0.8178 (tp30) REVERT: C 1236 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7882 (mmm) REVERT: C 1239 PHE cc_start: 0.6543 (m-80) cc_final: 0.5828 (m-80) REVERT: C 1358 PHE cc_start: 0.8041 (m-80) cc_final: 0.7346 (m-80) REVERT: C 2316 MET cc_start: 0.7670 (mmm) cc_final: 0.7425 (mpp) REVERT: D 152 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7637 (mmm160) REVERT: D 347 PHE cc_start: 0.6010 (p90) cc_final: 0.5384 (p90) REVERT: D 593 TYR cc_start: 0.8518 (t80) cc_final: 0.7965 (t80) REVERT: D 613 LEU cc_start: 0.8979 (tp) cc_final: 0.8674 (tp) REVERT: D 622 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7006 (pp30) REVERT: D 732 ASP cc_start: 0.8113 (p0) cc_final: 0.7685 (t0) REVERT: D 754 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6415 (mtt) REVERT: D 1180 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7061 (m-10) REVERT: D 1236 MET cc_start: 0.6911 (tpp) cc_final: 0.6624 (tpt) REVERT: D 1253 MET cc_start: 0.6909 (mtm) cc_final: 0.6444 (ppp) REVERT: D 1370 TYR cc_start: 0.8395 (m-80) cc_final: 0.8075 (m-80) REVERT: D 1431 ASP cc_start: 0.8147 (m-30) cc_final: 0.7492 (t0) REVERT: D 1495 MET cc_start: 0.8347 (ptp) cc_final: 0.8038 (ptm) REVERT: D 1513 LEU cc_start: 0.8822 (tt) cc_final: 0.8318 (mm) REVERT: D 1557 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7867 (pmt) REVERT: D 2041 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: D 2129 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6786 (mtp180) outliers start: 104 outliers final: 39 residues processed: 334 average time/residue: 0.7444 time to fit residues: 298.9075 Evaluate side-chains 286 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1139 TYR Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 152 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 754 MET Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1021 MET Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1466 VAL Chi-restraints excluded: chain D residue 1536 SER Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1583 LEU Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2056 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 411 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 218 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS C1188 HIS C2234 ASN D 443 GLN D1113 HIS ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.098866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.073636 restraints weight = 98297.652| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.46 r_work: 0.3424 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35014 Z= 0.170 Angle : 0.635 11.291 47424 Z= 0.325 Chirality : 0.045 0.273 5256 Planarity : 0.004 0.063 6152 Dihedral : 5.151 50.634 4754 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.86 % Allowed : 13.37 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4272 helix: 1.03 (0.12), residues: 1800 sheet: 0.52 (0.18), residues: 846 loop : -1.49 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 383 TYR 0.016 0.001 TYR D 142 PHE 0.028 0.002 PHE D 347 TRP 0.021 0.001 TRP C 260 HIS 0.012 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00394 (35012) covalent geometry : angle 0.63524 (47424) hydrogen bonds : bond 0.04277 ( 1613) hydrogen bonds : angle 4.89188 ( 4623) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 261 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASN cc_start: 0.8504 (t0) cc_final: 0.8262 (t0) REVERT: C 274 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6430 (p90) REVERT: C 309 MET cc_start: 0.5537 (tpp) cc_final: 0.5326 (tpp) REVERT: C 622 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7165 (mm-40) REVERT: C 728 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8409 (tttp) REVERT: C 902 ILE cc_start: 0.9095 (mt) cc_final: 0.8717 (tt) REVERT: C 922 MET cc_start: 0.8085 (ptm) cc_final: 0.7720 (mtm) REVERT: C 962 PHE cc_start: 0.8543 (t80) cc_final: 0.8071 (t80) REVERT: C 963 MET cc_start: 0.8721 (mmp) cc_final: 0.8412 (ppp) REVERT: C 983 MET cc_start: 0.7325 (tmm) cc_final: 0.6979 (tmm) REVERT: C 1065 GLU cc_start: 0.8448 (tp30) cc_final: 0.8182 (tp30) REVERT: C 1236 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7948 (mmm) REVERT: C 1239 PHE cc_start: 0.6644 (m-80) cc_final: 0.5809 (m-80) REVERT: C 1358 PHE cc_start: 0.7943 (m-80) cc_final: 0.7685 (m-80) REVERT: D 347 PHE cc_start: 0.6017 (p90) cc_final: 0.5449 (p90) REVERT: D 593 TYR cc_start: 0.8518 (t80) cc_final: 0.7956 (t80) REVERT: D 613 LEU cc_start: 0.8972 (tp) cc_final: 0.8662 (tp) REVERT: D 622 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7146 (pp30) REVERT: D 732 ASP cc_start: 0.8113 (p0) cc_final: 0.7769 (t0) REVERT: D 754 MET cc_start: 0.6676 (mtp) cc_final: 0.6404 (mtp) REVERT: D 787 MET cc_start: 0.7279 (mmm) cc_final: 0.7039 (mmp) REVERT: D 1155 ARG cc_start: 0.8867 (mtp85) cc_final: 0.8644 (mtt90) REVERT: D 1180 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: D 1236 MET cc_start: 0.6903 (tpp) cc_final: 0.6668 (tpt) REVERT: D 1253 MET cc_start: 0.7094 (mtm) cc_final: 0.6431 (ppp) REVERT: D 1370 TYR cc_start: 0.8388 (m-80) cc_final: 0.8123 (m-80) REVERT: D 1431 ASP cc_start: 0.8130 (m-30) cc_final: 0.7429 (t0) REVERT: D 1495 MET cc_start: 0.8368 (ptp) cc_final: 0.8123 (ptm) REVERT: D 1557 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7774 (pmt) REVERT: D 1616 MET cc_start: 0.8239 (mtp) cc_final: 0.7816 (mtm) REVERT: D 2041 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (mmm) REVERT: D 2129 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6755 (mtp180) outliers start: 107 outliers final: 47 residues processed: 340 average time/residue: 0.6907 time to fit residues: 281.8830 Evaluate side-chains 290 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 GLN Chi-restraints excluded: chain C residue 624 GLU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1140 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1604 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2092 SER Chi-restraints excluded: chain C residue 2278 LEU Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1021 MET Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1372 HIS Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1583 LEU Chi-restraints excluded: chain D residue 1759 LYS Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2056 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 204 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 357 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 331 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS C1402 HIS C2245 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 900 GLN ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.099162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.073634 restraints weight = 98472.522| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.62 r_work: 0.3423 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35014 Z= 0.147 Angle : 0.626 11.585 47424 Z= 0.318 Chirality : 0.044 0.176 5256 Planarity : 0.004 0.047 6152 Dihedral : 5.069 51.650 4754 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.46 % Allowed : 13.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4272 helix: 1.06 (0.12), residues: 1810 sheet: 0.58 (0.18), residues: 834 loop : -1.47 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 607 TYR 0.014 0.001 TYR D 142 PHE 0.043 0.002 PHE D1239 TRP 0.022 0.001 TRP C 260 HIS 0.010 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00337 (35012) covalent geometry : angle 0.62627 (47424) hydrogen bonds : bond 0.04074 ( 1613) hydrogen bonds : angle 4.81929 ( 4623) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 259 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASN cc_start: 0.8529 (t0) cc_final: 0.8292 (t0) REVERT: C 274 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6500 (p90) REVERT: C 728 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8391 (tttp) REVERT: C 838 ARG cc_start: 0.7624 (pmm150) cc_final: 0.7197 (pmm150) REVERT: C 902 ILE cc_start: 0.9005 (mt) cc_final: 0.8646 (tt) REVERT: C 962 PHE cc_start: 0.8548 (t80) cc_final: 0.7899 (t80) REVERT: C 963 MET cc_start: 0.8784 (mmp) cc_final: 0.8425 (ppp) REVERT: C 983 MET cc_start: 0.7351 (tmm) cc_final: 0.6992 (tmm) REVERT: C 1065 GLU cc_start: 0.8481 (tp30) cc_final: 0.8214 (tp30) REVERT: C 1236 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (mmm) REVERT: C 1239 PHE cc_start: 0.6658 (m-80) cc_final: 0.6440 (m-80) REVERT: C 1358 PHE cc_start: 0.8048 (m-80) cc_final: 0.7811 (m-80) REVERT: D 347 PHE cc_start: 0.5985 (p90) cc_final: 0.5500 (p90) REVERT: D 593 TYR cc_start: 0.8516 (t80) cc_final: 0.7978 (t80) REVERT: D 613 LEU cc_start: 0.8971 (tp) cc_final: 0.8660 (tp) REVERT: D 622 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (pp30) REVERT: D 732 ASP cc_start: 0.8108 (p0) cc_final: 0.7747 (t0) REVERT: D 754 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6332 (mtp) REVERT: D 787 MET cc_start: 0.7249 (mmm) cc_final: 0.7005 (mmp) REVERT: D 1155 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8471 (mtt90) REVERT: D 1180 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6879 (m-10) REVERT: D 1236 MET cc_start: 0.6911 (tpp) cc_final: 0.6683 (tpt) REVERT: D 1253 MET cc_start: 0.7083 (mtm) cc_final: 0.6430 (ppp) REVERT: D 1370 TYR cc_start: 0.8373 (m-80) cc_final: 0.8134 (m-80) REVERT: D 1386 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: D 1495 MET cc_start: 0.8370 (ptp) cc_final: 0.8156 (ptm) REVERT: D 1557 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7777 (pmt) REVERT: D 1616 MET cc_start: 0.8325 (mtp) cc_final: 0.7936 (mtm) REVERT: D 2041 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: D 2129 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6782 (mtp180) outliers start: 92 outliers final: 45 residues processed: 327 average time/residue: 0.7849 time to fit residues: 309.8878 Evaluate side-chains 285 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 905 SER Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1140 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1152 VAL Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2004 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2092 SER Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2278 LEU Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 754 MET Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1021 MET Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1386 MET Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1465 ASN Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1583 LEU Chi-restraints excluded: chain D residue 1726 LEU Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2056 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 17 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 288 optimal weight: 0.0370 chunk 352 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS C 622 GLN D 443 GLN D 698 ASN ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.098886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073429 restraints weight = 98519.427| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.62 r_work: 0.3417 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35014 Z= 0.158 Angle : 0.641 11.530 47424 Z= 0.326 Chirality : 0.045 0.176 5256 Planarity : 0.004 0.063 6152 Dihedral : 5.106 52.055 4754 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.54 % Allowed : 14.36 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4272 helix: 1.07 (0.12), residues: 1810 sheet: 0.58 (0.18), residues: 830 loop : -1.47 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C1240 TYR 0.015 0.001 TYR D 142 PHE 0.046 0.002 PHE D1239 TRP 0.022 0.001 TRP C 260 HIS 0.011 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00365 (35012) covalent geometry : angle 0.64129 (47424) hydrogen bonds : bond 0.04124 ( 1613) hydrogen bonds : angle 4.82036 ( 4623) Misc. bond : bond 0.00039 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 243 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASN cc_start: 0.8541 (t0) cc_final: 0.8317 (t0) REVERT: C 274 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6577 (p90) REVERT: C 728 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8339 (tttp) REVERT: C 838 ARG cc_start: 0.7835 (pmm150) cc_final: 0.7533 (pmm-80) REVERT: C 902 ILE cc_start: 0.9034 (mt) cc_final: 0.8662 (tt) REVERT: C 922 MET cc_start: 0.8211 (ptm) cc_final: 0.7714 (mtm) REVERT: C 962 PHE cc_start: 0.8587 (t80) cc_final: 0.7925 (t80) REVERT: C 963 MET cc_start: 0.8806 (mmp) cc_final: 0.8420 (ppp) REVERT: C 983 MET cc_start: 0.7371 (tmm) cc_final: 0.7018 (tmm) REVERT: C 1065 GLU cc_start: 0.8502 (tp30) cc_final: 0.8233 (tp30) REVERT: C 1236 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: C 1239 PHE cc_start: 0.7461 (m-80) cc_final: 0.6251 (m-80) REVERT: C 2316 MET cc_start: 0.7855 (mmm) cc_final: 0.7530 (mpp) REVERT: D 347 PHE cc_start: 0.5898 (p90) cc_final: 0.5458 (p90) REVERT: D 437 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7915 (pp20) REVERT: D 593 TYR cc_start: 0.8505 (t80) cc_final: 0.7947 (t80) REVERT: D 622 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7023 (pp30) REVERT: D 732 ASP cc_start: 0.8136 (p0) cc_final: 0.7775 (t0) REVERT: D 754 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6325 (mtp) REVERT: D 851 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8363 (tpp-160) REVERT: D 1180 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: D 1236 MET cc_start: 0.6789 (tpp) cc_final: 0.6545 (tpt) REVERT: D 1253 MET cc_start: 0.7054 (mtm) cc_final: 0.6477 (ppp) REVERT: D 1370 TYR cc_start: 0.8391 (m-80) cc_final: 0.8120 (m-80) REVERT: D 1386 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8365 (mmm) REVERT: D 1495 MET cc_start: 0.8410 (ptp) cc_final: 0.8194 (ptm) REVERT: D 1557 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7767 (pmt) REVERT: D 1616 MET cc_start: 0.8298 (mtp) cc_final: 0.8006 (mtm) REVERT: D 2041 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8191 (mmm) REVERT: D 2129 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6813 (mtp180) outliers start: 95 outliers final: 44 residues processed: 314 average time/residue: 0.7645 time to fit residues: 286.8101 Evaluate side-chains 281 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2004 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2092 SER Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2259 VAL Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 754 MET Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 1021 MET Chi-restraints excluded: chain D residue 1140 HIS Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1372 HIS Chi-restraints excluded: chain D residue 1386 MET Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1759 LYS Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1910 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2056 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 70 optimal weight: 0.7980 chunk 286 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 355 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1313 GLN ** D1943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2085 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.097195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.071613 restraints weight = 98815.135| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.61 r_work: 0.3387 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 35014 Z= 0.240 Angle : 0.720 12.135 47424 Z= 0.368 Chirality : 0.048 0.198 5256 Planarity : 0.005 0.060 6152 Dihedral : 5.393 50.306 4754 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.84 % Favored : 93.14 % Rotamer: Outliers : 2.06 % Allowed : 15.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4272 helix: 0.93 (0.12), residues: 1782 sheet: 0.33 (0.18), residues: 844 loop : -1.56 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 502 TYR 0.018 0.002 TYR D 142 PHE 0.027 0.002 PHE D1242 TRP 0.026 0.002 TRP D 260 HIS 0.017 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00562 (35012) covalent geometry : angle 0.72016 (47424) hydrogen bonds : bond 0.04809 ( 1613) hydrogen bonds : angle 5.03540 ( 4623) Misc. bond : bond 0.00057 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 274 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6615 (p90) REVERT: C 349 MET cc_start: 0.6043 (pmm) cc_final: 0.5815 (pmm) REVERT: C 441 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7669 (ppt170) REVERT: C 728 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8415 (tttp) REVERT: C 838 ARG cc_start: 0.7913 (pmm150) cc_final: 0.7029 (tmt-80) REVERT: C 922 MET cc_start: 0.8227 (ptm) cc_final: 0.7712 (mtm) REVERT: C 962 PHE cc_start: 0.8544 (t80) cc_final: 0.8034 (t80) REVERT: C 983 MET cc_start: 0.7459 (tmm) cc_final: 0.7056 (tmm) REVERT: C 1065 GLU cc_start: 0.8527 (tp30) cc_final: 0.8247 (tp30) REVERT: C 1105 LEU cc_start: 0.8272 (pp) cc_final: 0.7909 (mt) REVERT: C 1236 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7896 (mmm) REVERT: C 1239 PHE cc_start: 0.7564 (m-80) cc_final: 0.6363 (m-80) REVERT: C 1557 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7535 (pp-130) REVERT: C 1648 MET cc_start: 0.7568 (ptt) cc_final: 0.7348 (ptt) REVERT: C 2316 MET cc_start: 0.7732 (mmm) cc_final: 0.7439 (mpp) REVERT: D 347 PHE cc_start: 0.5807 (p90) cc_final: 0.5385 (p90) REVERT: D 593 TYR cc_start: 0.8592 (t80) cc_final: 0.7986 (t80) REVERT: D 622 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7048 (pp30) REVERT: D 732 ASP cc_start: 0.8161 (p0) cc_final: 0.7749 (t0) REVERT: D 851 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8339 (mmm-85) REVERT: D 1180 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6704 (m-10) REVERT: D 1236 MET cc_start: 0.6872 (tpp) cc_final: 0.6616 (tpt) REVERT: D 1253 MET cc_start: 0.7094 (mtm) cc_final: 0.6890 (mtm) REVERT: D 1370 TYR cc_start: 0.8417 (m-80) cc_final: 0.8165 (m-80) REVERT: D 1483 MET cc_start: 0.4016 (OUTLIER) cc_final: 0.3486 (mmt) REVERT: D 1495 MET cc_start: 0.8429 (ptp) cc_final: 0.8221 (ptm) REVERT: D 1557 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7727 (pmt) REVERT: D 1616 MET cc_start: 0.8383 (mtp) cc_final: 0.7988 (mtm) REVERT: D 2041 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8233 (mmm) REVERT: D 2129 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6877 (mtp180) outliers start: 77 outliers final: 47 residues processed: 294 average time/residue: 0.7166 time to fit residues: 252.2792 Evaluate side-chains 282 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 211 HIS Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 441 ARG Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1095 LEU Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1163 LEU Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1381 LEU Chi-restraints excluded: chain C residue 1557 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2004 LEU Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2092 SER Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2259 VAL Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain D residue 1140 HIS Chi-restraints excluded: chain D residue 1152 VAL Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1399 HIS Chi-restraints excluded: chain D residue 1483 MET Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1906 VAL Chi-restraints excluded: chain D residue 1910 VAL Chi-restraints excluded: chain D residue 1937 MET Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2056 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2176 ILE Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 232 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 236 optimal weight: 30.0000 chunk 225 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 129 optimal weight: 0.3980 chunk 350 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 559 HIS ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN D1136 ASN D1465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.099335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.074053 restraints weight = 98354.000| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.63 r_work: 0.3431 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35014 Z= 0.129 Angle : 0.666 17.877 47424 Z= 0.335 Chirality : 0.045 0.262 5256 Planarity : 0.004 0.047 6152 Dihedral : 5.059 52.297 4754 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.55 % Allowed : 15.88 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.13), residues: 4272 helix: 1.15 (0.13), residues: 1794 sheet: 0.41 (0.18), residues: 844 loop : -1.44 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1240 TYR 0.012 0.001 TYR D 142 PHE 0.039 0.002 PHE D1249 TRP 0.025 0.001 TRP C 260 HIS 0.007 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00289 (35012) covalent geometry : angle 0.66570 (47424) hydrogen bonds : bond 0.03853 ( 1613) hydrogen bonds : angle 4.81533 ( 4623) Misc. bond : bond 0.00024 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 349 MET cc_start: 0.6091 (pmm) cc_final: 0.5845 (pmm) REVERT: C 728 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8298 (tttp) REVERT: C 838 ARG cc_start: 0.7936 (pmm150) cc_final: 0.7176 (tmt-80) REVERT: C 902 ILE cc_start: 0.8989 (mt) cc_final: 0.8648 (tt) REVERT: C 962 PHE cc_start: 0.8663 (t80) cc_final: 0.7968 (t80) REVERT: C 983 MET cc_start: 0.7312 (tmm) cc_final: 0.6962 (tmm) REVERT: C 1065 GLU cc_start: 0.8497 (tp30) cc_final: 0.8244 (tp30) REVERT: C 1147 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7515 (mpp) REVERT: C 1236 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8061 (mmm) REVERT: C 2316 MET cc_start: 0.7728 (mmm) cc_final: 0.7425 (mpp) REVERT: D 593 TYR cc_start: 0.8474 (t80) cc_final: 0.7927 (t80) REVERT: D 622 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6948 (pp30) REVERT: D 732 ASP cc_start: 0.8014 (p0) cc_final: 0.7754 (t0) REVERT: D 785 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7745 (mmt) REVERT: D 851 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8149 (tpp-160) REVERT: D 1180 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: D 1308 PHE cc_start: 0.8245 (m-80) cc_final: 0.8009 (m-80) REVERT: D 1370 TYR cc_start: 0.8375 (m-80) cc_final: 0.8054 (m-80) REVERT: D 1557 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7638 (pmt) REVERT: D 1616 MET cc_start: 0.8279 (mtp) cc_final: 0.8029 (mtm) REVERT: D 2041 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8201 (mmm) REVERT: D 2129 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6808 (mtp180) outliers start: 58 outliers final: 26 residues processed: 284 average time/residue: 0.7644 time to fit residues: 260.4727 Evaluate side-chains 255 residues out of total 3746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 1132 ASP Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1180 PHE Chi-restraints excluded: chain C residue 1236 MET Chi-restraints excluded: chain C residue 1253 MET Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1909 SER Chi-restraints excluded: chain C residue 2018 TRP Chi-restraints excluded: chain C residue 2128 PHE Chi-restraints excluded: chain C residue 2259 VAL Chi-restraints excluded: chain C residue 2300 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 785 MET Chi-restraints excluded: chain D residue 836 LEU Chi-restraints excluded: chain D residue 905 SER Chi-restraints excluded: chain D residue 1140 HIS Chi-restraints excluded: chain D residue 1180 PHE Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1557 MET Chi-restraints excluded: chain D residue 1759 LYS Chi-restraints excluded: chain D residue 1808 SER Chi-restraints excluded: chain D residue 1910 VAL Chi-restraints excluded: chain D residue 2018 TRP Chi-restraints excluded: chain D residue 2041 MET Chi-restraints excluded: chain D residue 2129 ARG Chi-restraints excluded: chain D residue 2146 HIS Chi-restraints excluded: chain D residue 2322 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 338 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 364 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN C 559 HIS C 948 HIS ** C1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1465 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.099866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.074620 restraints weight = 97951.282| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.62 r_work: 0.3444 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35014 Z= 0.121 Angle : 0.652 13.319 47424 Z= 0.326 Chirality : 0.045 0.312 5256 Planarity : 0.004 0.047 6152 Dihedral : 4.888 54.678 4750 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.39 % Allowed : 16.02 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4272 helix: 1.24 (0.13), residues: 1794 sheet: 0.57 (0.18), residues: 834 loop : -1.40 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 532 TYR 0.011 0.001 TYR D 142 PHE 0.037 0.001 PHE D1249 TRP 0.022 0.001 TRP C 260 HIS 0.008 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00268 (35012) covalent geometry : angle 0.65229 (47424) hydrogen bonds : bond 0.03716 ( 1613) hydrogen bonds : angle 4.72493 ( 4623) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19932.83 seconds wall clock time: 338 minutes 12.14 seconds (20292.14 seconds total)