Starting phenix.real_space_refine on Tue Jul 29 14:44:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcb_18328/07_2025/8qcb_18328.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.004 sd= 0.148 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 49 5.16 5 C 7301 2.51 5 N 1927 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11423 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 704 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 85} Chain breaks: 4 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 4938 Classifications: {'peptide': 644} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 10, 'TRANS': 633} Chain breaks: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 12, 'ASN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2839 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 361} Chain breaks: 4 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2707 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 355} Chain breaks: 6 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 235 Classifications: {'peptide': 33} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'TRANS': 32} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.92, per 1000 atoms: 0.61 Number of scatterers: 11423 At special positions: 0 Unit cell: (91.9296, 113.21, 136.192, 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 49 16.00 O 2146 8.00 N 1927 7.00 C 7301 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=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 42.2% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.638A pdb=" N MET A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.563A pdb=" N LEU A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 799 removed outlier: 4.248A pdb=" N GLU B 799 " --> pdb=" O LYS B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 825 removed outlier: 3.865A pdb=" N GLN B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 847 Processing helix chain 'B' and resid 852 through 869 removed outlier: 4.164A pdb=" N LEU B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 removed outlier: 5.377A pdb=" N ASP B 874 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 876 " --> pdb=" O VAL B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 888 removed outlier: 3.646A pdb=" N SER B 888 " --> pdb=" O ILE B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 901 removed outlier: 3.817A pdb=" N ASP B 897 " --> pdb=" O SER B 893 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 899 " --> pdb=" O GLU B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 909 Processing helix chain 'B' and resid 914 through 929 Processing helix chain 'B' and resid 941 through 963 Processing helix chain 'B' and resid 964 through 980 removed outlier: 3.675A pdb=" N ARG B 968 " --> pdb=" O GLU B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1000 through 1007 Processing helix chain 'B' and resid 1009 through 1015 Processing helix chain 'B' and resid 1019 through 1032 Processing helix chain 'B' and resid 1034 through 1049 removed outlier: 3.541A pdb=" N ALA B1038 " --> pdb=" O ASP B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 4.275A pdb=" N TRP B1056 " --> pdb=" O ASP B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1083 Processing helix chain 'B' and resid 1087 through 1102 removed outlier: 3.679A pdb=" N GLN B1091 " --> pdb=" O SER B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1129 Processing helix chain 'B' and resid 1135 through 1149 Processing helix chain 'B' and resid 1151 through 1173 removed outlier: 3.560A pdb=" N ALA B1155 " --> pdb=" O HIS B1151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B1157 " --> pdb=" O GLU B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1197 removed outlier: 4.178A pdb=" N ASN B1181 " --> pdb=" O ARG B1177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B1195 " --> pdb=" O ARG B1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1214 Processing helix chain 'B' and resid 1218 through 1239 removed outlier: 3.990A pdb=" N LYS B1223 " --> pdb=" O GLU B1219 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B1224 " --> pdb=" O LYS B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1243 through 1257 Processing helix chain 'B' and resid 1259 through 1274 removed outlier: 3.813A pdb=" N GLY B1274 " --> pdb=" O LEU B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1275 through 1293 Processing helix chain 'B' and resid 1296 through 1311 removed outlier: 3.654A pdb=" N THR B1300 " --> pdb=" O ASP B1296 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1324 removed outlier: 4.193A pdb=" N SER B1317 " --> pdb=" O ARG B1313 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B1318 " --> pdb=" O GLU B1314 " (cutoff:3.500A) Processing helix chain 'B' and resid 1327 through 1334 Processing helix chain 'B' and resid 1337 through 1351 removed outlier: 3.593A pdb=" N TYR B1341 " --> pdb=" O LYS B1337 " (cutoff:3.500A) Processing helix chain 'B' and resid 1356 through 1367 removed outlier: 4.250A pdb=" N TRP B1360 " --> pdb=" O GLY B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1386 removed outlier: 3.601A pdb=" N ALA B1386 " --> pdb=" O GLN B1382 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1404 Processing helix chain 'B' and resid 1407 through 1418 Processing helix chain 'B' and resid 1421 through 1432 removed outlier: 3.820A pdb=" N PHE B1432 " --> pdb=" O LEU B1428 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.772A pdb=" N HIS C 122 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.021A pdb=" N ILE C 336 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.895A pdb=" N ILE C 342 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.568A pdb=" N LYS D 121 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS D 122 " --> pdb=" O MET D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 118 through 122' Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 77 through 86 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 11 removed outlier: 4.671A pdb=" N VAL C 4 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP C 390 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN C 10 " --> pdb=" O ILE C 388 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 388 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 359 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.748A pdb=" N SER C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 33 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 74 removed outlier: 3.796A pdb=" N HIS C 67 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 87 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N GLU C 80 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ARG C 100 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE C 95 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 124 through 130 removed outlier: 3.626A pdb=" N ALA C 126 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS C 139 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS C 154 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU C 175 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N HIS C 156 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 173 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 189 through 194 removed outlier: 6.475A pdb=" N GLY C 203 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL C 192 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 201 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 194 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU C 199 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 209 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN C 222 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 211 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 241 removed outlier: 6.694A pdb=" N ALA C 251 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 239 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA C 249 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE C 241 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU C 247 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 272 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 264 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG C 270 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 294 through 299 removed outlier: 6.588A pdb=" N ALA C 309 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 297 " --> pdb=" O CYS C 307 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS C 307 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C 299 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR C 305 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 315 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR C 328 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE C 317 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 11 removed outlier: 6.855A pdb=" N TRP D 390 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 10 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 388 " --> pdb=" O ASN D 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP D 359 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.953A pdb=" N SER D 21 " --> pdb=" O CYS D 32 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 74 removed outlier: 3.909A pdb=" N HIS D 67 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N GLU D 80 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ARG D 100 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N CYS D 82 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE D 95 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 130 removed outlier: 3.650A pdb=" N ALA D 126 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS D 139 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR D 150 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR D 178 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 152 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 158 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N SER D 170 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 189 through 194 removed outlier: 3.527A pdb=" N SER D 191 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR D 208 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 209 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN D 222 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 211 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 236 through 241 removed outlier: 6.756A pdb=" N ILE D 236 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP D 253 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE D 260 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 273 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU D 262 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 299 removed outlier: 6.579A pdb=" N ALA D 309 " --> pdb=" O MET D 295 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU D 297 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS D 307 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE D 299 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR D 305 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 315 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR D 328 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 317 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 324 " --> pdb=" O ASP D 319 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1668 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: 3.60 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3720 1.34 - 1.46: 2254 1.46 - 1.58: 5598 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 11642 Sorted by residual: bond pdb=" CG LEU B1246 " pdb=" CD1 LEU B1246 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.93e-01 bond pdb=" CA VAL D 276 " pdb=" CB VAL D 276 " ideal model delta sigma weight residual 1.537 1.546 -0.009 1.29e-02 6.01e+03 5.15e-01 bond pdb=" CB ASP D 145 " pdb=" CG ASP D 145 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 4.98e-01 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.539 1.530 0.009 1.36e-02 5.41e+03 4.58e-01 bond pdb=" CB VAL C 70 " pdb=" CG2 VAL C 70 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.46e-01 ... (remaining 11637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 15254 1.01 - 2.03: 424 2.03 - 3.04: 83 3.04 - 4.06: 15 4.06 - 5.07: 11 Bond angle restraints: 15787 Sorted by residual: angle pdb=" N ASP A 189 " pdb=" CA ASP A 189 " pdb=" C ASP A 189 " ideal model delta sigma weight residual 108.19 112.42 -4.23 1.29e+00 6.01e-01 1.07e+01 angle pdb=" C ASN C 255 " pdb=" CA ASN C 255 " pdb=" CB ASN C 255 " ideal model delta sigma weight residual 110.06 112.91 -2.85 1.39e+00 5.18e-01 4.20e+00 angle pdb=" C ASP A 189 " pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 114.10 109.89 4.21 2.11e+00 2.25e-01 3.98e+00 angle pdb=" N GLY D 356 " pdb=" CA GLY D 356 " pdb=" C GLY D 356 " ideal model delta sigma weight residual 113.18 117.75 -4.57 2.37e+00 1.78e-01 3.72e+00 angle pdb=" CA ILE B1103 " pdb=" C ILE B1103 " pdb=" N ASN B1104 " ideal model delta sigma weight residual 116.60 119.38 -2.78 1.45e+00 4.76e-01 3.67e+00 ... (remaining 15782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 6214 16.24 - 32.48: 545 32.48 - 48.71: 96 48.71 - 64.95: 15 64.95 - 81.19: 11 Dihedral angle restraints: 6881 sinusoidal: 2505 harmonic: 4376 Sorted by residual: dihedral pdb=" CA ASP C 253 " pdb=" C ASP C 253 " pdb=" N SER C 254 " pdb=" CA SER C 254 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASP D 253 " pdb=" C ASP D 253 " pdb=" N SER D 254 " pdb=" CA SER D 254 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA HIS C 227 " pdb=" C HIS C 227 " pdb=" N SER C 228 " pdb=" CA SER C 228 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1239 0.032 - 0.064: 433 0.064 - 0.096: 94 0.096 - 0.128: 64 0.128 - 0.160: 4 Chirality restraints: 1834 Sorted by residual: chirality pdb=" CG LEU C 136 " pdb=" CB LEU C 136 " pdb=" CD1 LEU C 136 " pdb=" CD2 LEU C 136 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA THR D 265 " pdb=" N THR D 265 " pdb=" C THR D 265 " pdb=" CB THR D 265 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE C 194 " pdb=" N ILE C 194 " pdb=" C ILE C 194 " pdb=" CB ILE C 194 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1831 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 354 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 355 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 355 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 355 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 196 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 197 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 255 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ASN C 255 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN C 255 " -0.007 2.00e-02 2.50e+03 pdb=" N SER C 256 " -0.007 2.00e-02 2.50e+03 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3055 2.81 - 3.33: 9885 3.33 - 3.86: 18001 3.86 - 4.38: 21783 4.38 - 4.90: 38591 Nonbonded interactions: 91315 Sorted by model distance: nonbonded pdb=" O PHE B 826 " pdb=" OG SER B 830 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP B 897 " pdb=" NZ LYS B 928 " model vdw 2.291 3.120 nonbonded pdb=" O ASP A 96 " pdb=" OH TYR B 949 " model vdw 2.303 3.040 nonbonded pdb=" ND2 ASN C 376 " pdb=" O GLU C 393 " model vdw 2.307 3.120 nonbonded pdb=" O GLN B1039 " pdb=" ND2 ASN B1043 " model vdw 2.314 3.120 ... (remaining 91310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 12 or (resid 13 through 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 25 or (resid 26 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 43 or (resi \ d 44 and (name N or name CA or name C or name O or name CB )) or resid 45 or (re \ sid 46 through 48 and (name N or name CA or name C or name O or name CB )) or re \ sid 49 through 73 or (resid 74 through 76 and (name N or name CA or name C or na \ me O or name CB )) or resid 79 or (resid 80 and (name N or name CA or name C or \ name O or name CB )) or resid 81 through 100 or (resid 101 through 106 and (name \ N or name CA or name C or name O or name CB )) or resid 107 through 133 or (res \ id 134 through 135 and (name N or name CA or name C or name O or name CB )) or r \ esid 136 or (resid 137 through 138 and (name N or name CA or name C or name O or \ name CB )) or resid 139 through 158 or (resid 168 and (name N or name CA or nam \ e C or name O or name CB )) or resid 169 through 195 or (resid 196 through 197 a \ nd (name N or name CA or name C or name O or name CB )) or resid 198 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 214 or (resid 215 and (name N or name CA or name C or name O or nam \ e CB )) or resid 216 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 223 or (resid 224 and (name N or na \ me CA or name C or name O or name CB )) or resid 225 or (resid 231 through 234 a \ nd (name N or name CA or name C or name O or name CB )) or resid 235 through 243 \ or (resid 244 and (name N or name CA or name C or name O or name CB )) or resid \ 245 or (resid 246 and (name N or name CA or name C or name O or name CB )) or r \ esid 247 through 253 or (resid 254 and (name N or name CA or name C or name O or \ name CB )) or resid 255 through 264 or (resid 265 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 or (resid 269 and (name N o \ r name CA or name C or name O or name CB )) or resid 270 through 277 or resid 28 \ 7 through 301 or (resid 302 and (name N or name CA or name C or name O or name C \ B )) or resid 303 through 320 or (resid 321 and (name N or name CA or name C or \ name O or name CB )) or resid 322 through 335 or (resid 336 and (name N or name \ CA or name C or name O or name CB )) or resid 340 through 368 or (resid 369 thro \ ugh 375 and (name N or name CA or name C or name O or name CB )) or resid 376 th \ rough 377 or (resid 378 and (name N or name CA or name C or name O or name CB )) \ or resid 379 through 391 or (resid 392 and (name N or name CA or name C or name \ O or name CB )) or resid 393 through 394)) selection = (chain 'D' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 20 or (resid 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 46 or (resid 47 throug \ h 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throug \ h 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) or \ resid 148 through 158 or resid 168 through 185 or (resid 186 and (name N or name \ CA or name C or name O or name CB )) or resid 187 through 353 or (resid 354 and \ (name N or name CA or name C or name O or name CB )) or resid 355 through 363 o \ r (resid 364 through 365 and (name N or name CA or name C or name O or name CB ) \ ) or resid 366 through 369 or resid 375 through 386 or (resid 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 394)) } 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.990 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.002 0.027 11642 Z= 0.103 Angle : 0.446 5.071 15787 Z= 0.248 Chirality : 0.039 0.160 1834 Planarity : 0.003 0.055 2002 Dihedral : 12.784 81.190 4019 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.22), residues: 1462 helix: 2.24 (0.22), residues: 565 sheet: 0.64 (0.28), residues: 365 loop : -1.04 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 153 HIS 0.004 0.001 HIS C 66 PHE 0.019 0.001 PHE B1189 TYR 0.011 0.001 TYR B 947 ARG 0.003 0.000 ARG D 368 Details of bonding type rmsd hydrogen bonds : bond 0.16731 ( 572) hydrogen bonds : angle 5.66723 ( 1668) covalent geometry : bond 0.00218 (11642) covalent geometry : angle 0.44630 (15787) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 16 SER cc_start: 0.7301 (m) cc_final: 0.7027 (m) REVERT: B 1376 ARG cc_start: 0.6799 (mpt180) cc_final: 0.6423 (mmt-90) REVERT: C 174 GLU cc_start: 0.7821 (tt0) cc_final: 0.7620 (tt0) REVERT: D 213 GLU cc_start: 0.7565 (tp30) cc_final: 0.7260 (tp30) REVERT: D 331 MET cc_start: 0.7342 (mmp) cc_final: 0.7120 (mmp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 1.3520 time to fit residues: 240.0286 Evaluate side-chains 116 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 984 ASN C 176 GLN C 210 GLN D 205 ASN D 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.114077 restraints weight = 13343.432| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.92 r_work: 0.3125 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11642 Z= 0.129 Angle : 0.487 5.114 15787 Z= 0.266 Chirality : 0.041 0.202 1834 Planarity : 0.003 0.055 2002 Dihedral : 4.251 25.308 1564 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.71 % Allowed : 6.85 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1462 helix: 2.07 (0.22), residues: 581 sheet: 0.80 (0.28), residues: 367 loop : -1.05 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 153 HIS 0.005 0.001 HIS C 66 PHE 0.025 0.001 PHE B 973 TYR 0.011 0.001 TYR B 947 ARG 0.005 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 572) hydrogen bonds : angle 4.08370 ( 1668) covalent geometry : bond 0.00296 (11642) covalent geometry : angle 0.48740 (15787) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.338 Fit side-chains REVERT: B 1312 LYS cc_start: 0.7927 (mttt) cc_final: 0.7336 (mtpt) REVERT: B 1376 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7484 (mmt-90) REVERT: C 54 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8227 (mmtp) REVERT: C 321 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (tmtm) REVERT: D 331 MET cc_start: 0.8376 (mmp) cc_final: 0.8046 (mmp) REVERT: D 368 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7783 (mmt180) outliers start: 20 outliers final: 8 residues processed: 140 average time/residue: 1.5183 time to fit residues: 230.8128 Evaluate side-chains 116 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 368 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1043 ASN C 176 GLN D 222 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111906 restraints weight = 13527.792| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.92 r_work: 0.3106 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11642 Z= 0.168 Angle : 0.536 6.524 15787 Z= 0.290 Chirality : 0.042 0.187 1834 Planarity : 0.004 0.056 2002 Dihedral : 4.489 28.142 1564 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.31 % Allowed : 9.76 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1462 helix: 1.91 (0.21), residues: 581 sheet: 0.76 (0.27), residues: 367 loop : -1.12 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 153 HIS 0.006 0.001 HIS C 66 PHE 0.025 0.002 PHE B 973 TYR 0.013 0.001 TYR B 947 ARG 0.005 0.001 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 572) hydrogen bonds : angle 4.08343 ( 1668) covalent geometry : bond 0.00401 (11642) covalent geometry : angle 0.53615 (15787) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: B 907 LEU cc_start: 0.6567 (tp) cc_final: 0.6308 (tp) REVERT: B 1207 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: B 1296 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7488 (t0) REVERT: B 1312 LYS cc_start: 0.7991 (mttt) cc_final: 0.7386 (mtpt) REVERT: B 1376 ARG cc_start: 0.7711 (mpt180) cc_final: 0.7381 (mmt-90) REVERT: C 54 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8225 (mmtp) REVERT: C 101 GLU cc_start: 0.6688 (mp0) cc_final: 0.6419 (pm20) REVERT: C 110 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: D 331 MET cc_start: 0.8381 (mmp) cc_final: 0.8075 (mmp) outliers start: 27 outliers final: 14 residues processed: 134 average time/residue: 1.4804 time to fit residues: 214.2124 Evaluate side-chains 126 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 368 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 142 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN D 222 ASN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112705 restraints weight = 13430.596| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.84 r_work: 0.3108 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11642 Z= 0.143 Angle : 0.504 8.169 15787 Z= 0.273 Chirality : 0.041 0.198 1834 Planarity : 0.003 0.054 2002 Dihedral : 4.392 28.203 1564 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.83 % Allowed : 10.45 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1462 helix: 1.99 (0.21), residues: 579 sheet: 0.74 (0.27), residues: 369 loop : -1.10 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 153 HIS 0.005 0.001 HIS C 66 PHE 0.022 0.001 PHE B 973 TYR 0.012 0.001 TYR B 947 ARG 0.005 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 572) hydrogen bonds : angle 3.94367 ( 1668) covalent geometry : bond 0.00338 (11642) covalent geometry : angle 0.50376 (15787) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: B 1207 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: B 1312 LYS cc_start: 0.7972 (mttt) cc_final: 0.7369 (mtpt) REVERT: B 1376 ARG cc_start: 0.7711 (mpt180) cc_final: 0.7381 (mmt-90) REVERT: C 54 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8217 (mmtp) REVERT: C 101 GLU cc_start: 0.6861 (mp0) cc_final: 0.6533 (pm20) REVERT: C 110 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: D 331 MET cc_start: 0.8388 (mmp) cc_final: 0.8089 (mmp) REVERT: D 352 LEU cc_start: 0.7753 (mt) cc_final: 0.7383 (mm) outliers start: 33 outliers final: 17 residues processed: 138 average time/residue: 1.7514 time to fit residues: 263.6505 Evaluate side-chains 129 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 368 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1043 ASN C 176 GLN E 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111037 restraints weight = 13408.129| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.96 r_work: 0.3071 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11642 Z= 0.172 Angle : 0.547 8.385 15787 Z= 0.294 Chirality : 0.043 0.236 1834 Planarity : 0.004 0.054 2002 Dihedral : 4.534 29.231 1564 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 10.70 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1462 helix: 1.88 (0.21), residues: 578 sheet: 0.71 (0.27), residues: 362 loop : -1.15 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 153 HIS 0.006 0.001 HIS C 66 PHE 0.019 0.002 PHE B 973 TYR 0.013 0.001 TYR B 947 ARG 0.005 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 572) hydrogen bonds : angle 4.02340 ( 1668) covalent geometry : bond 0.00411 (11642) covalent geometry : angle 0.54746 (15787) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: B 789 SER cc_start: 0.7560 (t) cc_final: 0.7346 (m) REVERT: B 1015 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 1207 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: B 1312 LYS cc_start: 0.7967 (mttt) cc_final: 0.7334 (mtpt) REVERT: B 1376 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7379 (mmt-90) REVERT: C 54 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8231 (mmtp) REVERT: C 101 GLU cc_start: 0.6862 (mp0) cc_final: 0.6443 (pm20) REVERT: C 110 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: D 331 MET cc_start: 0.8345 (mmp) cc_final: 0.8098 (mmp) REVERT: D 352 LEU cc_start: 0.7782 (mt) cc_final: 0.7411 (mm) REVERT: D 359 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8339 (t70) outliers start: 36 outliers final: 21 residues processed: 141 average time/residue: 1.9648 time to fit residues: 297.6208 Evaluate side-chains 140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain E residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110391 restraints weight = 13578.759| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.96 r_work: 0.3063 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11642 Z= 0.178 Angle : 0.557 8.577 15787 Z= 0.299 Chirality : 0.043 0.220 1834 Planarity : 0.004 0.054 2002 Dihedral : 4.580 29.803 1564 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.74 % Allowed : 11.90 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1462 helix: 1.79 (0.21), residues: 580 sheet: 0.69 (0.27), residues: 364 loop : -1.14 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 153 HIS 0.006 0.001 HIS C 66 PHE 0.018 0.002 PHE B 973 TYR 0.013 0.001 TYR B 947 ARG 0.005 0.000 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 572) hydrogen bonds : angle 4.03038 ( 1668) covalent geometry : bond 0.00428 (11642) covalent geometry : angle 0.55668 (15787) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: B 789 SER cc_start: 0.7706 (t) cc_final: 0.7467 (m) REVERT: B 1015 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7243 (tm-30) REVERT: B 1207 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7286 (m-30) REVERT: B 1312 LYS cc_start: 0.7874 (mttt) cc_final: 0.7265 (mtpt) REVERT: B 1376 ARG cc_start: 0.7707 (mpt180) cc_final: 0.7352 (mmt-90) REVERT: C 54 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8235 (mmtp) REVERT: C 101 GLU cc_start: 0.6908 (mp0) cc_final: 0.6401 (pm20) REVERT: C 110 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: D 331 MET cc_start: 0.8346 (mmp) cc_final: 0.8109 (mmp) REVERT: D 352 LEU cc_start: 0.7791 (mt) cc_final: 0.7408 (mm) outliers start: 32 outliers final: 24 residues processed: 142 average time/residue: 1.2329 time to fit residues: 190.7448 Evaluate side-chains 140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1296 ASP Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1043 ASN C 176 GLN E 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112590 restraints weight = 13602.816| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.95 r_work: 0.3106 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11642 Z= 0.128 Angle : 0.503 8.898 15787 Z= 0.271 Chirality : 0.040 0.188 1834 Planarity : 0.003 0.052 2002 Dihedral : 4.333 28.583 1564 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 12.24 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1462 helix: 2.04 (0.21), residues: 579 sheet: 0.77 (0.27), residues: 369 loop : -1.09 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 153 HIS 0.005 0.001 HIS C 66 PHE 0.017 0.001 PHE B 973 TYR 0.011 0.001 TYR B 947 ARG 0.004 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 572) hydrogen bonds : angle 3.86242 ( 1668) covalent geometry : bond 0.00299 (11642) covalent geometry : angle 0.50260 (15787) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: B 1015 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7198 (tm-30) REVERT: B 1207 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: B 1312 LYS cc_start: 0.7858 (mttt) cc_final: 0.7283 (mtpt) REVERT: B 1376 ARG cc_start: 0.7691 (mpt180) cc_final: 0.7326 (mmt-90) REVERT: C 54 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8212 (mmtp) REVERT: C 101 GLU cc_start: 0.6890 (mp0) cc_final: 0.6439 (pm20) REVERT: C 110 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: D 331 MET cc_start: 0.8334 (mmp) cc_final: 0.8088 (mmp) REVERT: D 359 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8192 (t70) outliers start: 33 outliers final: 23 residues processed: 141 average time/residue: 1.3211 time to fit residues: 203.5555 Evaluate side-chains 142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1189 PHE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain E residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 127 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115008 restraints weight = 13617.506| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.81 r_work: 0.3130 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11642 Z= 0.105 Angle : 0.474 9.085 15787 Z= 0.256 Chirality : 0.039 0.149 1834 Planarity : 0.003 0.053 2002 Dihedral : 4.087 26.662 1564 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.57 % Allowed : 12.84 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1462 helix: 2.22 (0.22), residues: 579 sheet: 0.84 (0.28), residues: 369 loop : -1.00 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 153 HIS 0.003 0.001 HIS C 66 PHE 0.030 0.001 PHE B 973 TYR 0.009 0.001 TYR B 947 ARG 0.003 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 572) hydrogen bonds : angle 3.72114 ( 1668) covalent geometry : bond 0.00237 (11642) covalent geometry : angle 0.47441 (15787) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: B 907 LEU cc_start: 0.6392 (tp) cc_final: 0.6104 (tp) REVERT: B 1015 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 1043 ASN cc_start: 0.7446 (m-40) cc_final: 0.7044 (m110) REVERT: B 1207 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: B 1288 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 1312 LYS cc_start: 0.7973 (mttt) cc_final: 0.7338 (mtpt) REVERT: B 1376 ARG cc_start: 0.7673 (mpt180) cc_final: 0.7289 (mmt-90) REVERT: C 101 GLU cc_start: 0.6849 (mp0) cc_final: 0.6406 (pm20) REVERT: C 110 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: C 196 GLU cc_start: 0.7614 (tp30) cc_final: 0.7294 (mm-30) REVERT: C 253 ASP cc_start: 0.8449 (m-30) cc_final: 0.8121 (m-30) REVERT: D 331 MET cc_start: 0.8344 (mmp) cc_final: 0.8104 (mmp) REVERT: D 368 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7655 (mmt180) outliers start: 30 outliers final: 19 residues processed: 142 average time/residue: 1.2100 time to fit residues: 187.0661 Evaluate side-chains 138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1189 PHE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 381 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 114 optimal weight: 0.0070 chunk 39 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114442 restraints weight = 13510.508| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11642 Z= 0.108 Angle : 0.479 9.006 15787 Z= 0.258 Chirality : 0.039 0.147 1834 Planarity : 0.003 0.056 2002 Dihedral : 4.065 26.363 1564 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.40 % Allowed : 13.10 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1462 helix: 2.28 (0.22), residues: 579 sheet: 0.87 (0.27), residues: 374 loop : -0.95 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 153 HIS 0.003 0.001 HIS D 15 PHE 0.030 0.001 PHE B 973 TYR 0.010 0.001 TYR B 947 ARG 0.003 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 572) hydrogen bonds : angle 3.75139 ( 1668) covalent geometry : bond 0.00245 (11642) covalent geometry : angle 0.47945 (15787) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: B 907 LEU cc_start: 0.6375 (tp) cc_final: 0.6059 (tp) REVERT: B 1015 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 1207 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: B 1288 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 1312 LYS cc_start: 0.7896 (mttt) cc_final: 0.7291 (mtpt) REVERT: B 1376 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7303 (mmt-90) REVERT: C 80 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 101 GLU cc_start: 0.6839 (mp0) cc_final: 0.6408 (pm20) REVERT: C 253 ASP cc_start: 0.8432 (m-30) cc_final: 0.8095 (m-30) REVERT: D 331 MET cc_start: 0.8352 (mmp) cc_final: 0.8104 (mmp) REVERT: D 359 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8138 (t70) REVERT: D 368 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7699 (mmt180) outliers start: 28 outliers final: 20 residues processed: 139 average time/residue: 1.5086 time to fit residues: 229.2157 Evaluate side-chains 142 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1188 GLN Chi-restraints excluded: chain B residue 1189 PHE Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 381 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1043 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109996 restraints weight = 13538.509| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.86 r_work: 0.3057 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11642 Z= 0.211 Angle : 0.603 8.662 15787 Z= 0.323 Chirality : 0.044 0.180 1834 Planarity : 0.004 0.056 2002 Dihedral : 4.641 29.900 1564 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.31 % Allowed : 13.27 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1462 helix: 1.81 (0.21), residues: 579 sheet: 0.75 (0.28), residues: 360 loop : -1.16 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 153 HIS 0.007 0.001 HIS C 66 PHE 0.028 0.002 PHE B 973 TYR 0.014 0.002 TYR B 947 ARG 0.007 0.001 ARG C 368 Details of bonding type rmsd hydrogen bonds : bond 0.05267 ( 572) hydrogen bonds : angle 4.11317 ( 1668) covalent geometry : bond 0.00512 (11642) covalent geometry : angle 0.60280 (15787) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: B 907 LEU cc_start: 0.6481 (tp) cc_final: 0.6272 (tp) REVERT: B 1015 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 1207 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7230 (m-30) REVERT: B 1312 LYS cc_start: 0.7860 (mttt) cc_final: 0.7233 (mtpt) REVERT: B 1376 ARG cc_start: 0.7630 (mpt180) cc_final: 0.7322 (mmt-90) REVERT: C 101 GLU cc_start: 0.6958 (mp0) cc_final: 0.6336 (pm20) REVERT: D 331 MET cc_start: 0.8357 (mmp) cc_final: 0.8099 (mmp) REVERT: D 352 LEU cc_start: 0.7811 (mt) cc_final: 0.7434 (mm) REVERT: D 359 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (t70) outliers start: 27 outliers final: 22 residues processed: 140 average time/residue: 1.2453 time to fit residues: 190.3710 Evaluate side-chains 141 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 793 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 862 VAL Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain B residue 1188 GLN Chi-restraints excluded: chain B residue 1207 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 381 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 116 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 31 optimal weight: 0.0000 chunk 72 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115615 restraints weight = 13514.076| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.89 r_work: 0.3147 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11642 Z= 0.096 Angle : 0.478 9.291 15787 Z= 0.258 Chirality : 0.039 0.146 1834 Planarity : 0.003 0.054 2002 Dihedral : 4.067 27.118 1564 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.97 % Allowed : 13.78 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1462 helix: 2.29 (0.22), residues: 573 sheet: 0.83 (0.27), residues: 374 loop : -1.01 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 153 HIS 0.002 0.001 HIS C 66 PHE 0.029 0.001 PHE B 973 TYR 0.008 0.001 TYR B 947 ARG 0.003 0.000 ARG D 140 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 572) hydrogen bonds : angle 3.73834 ( 1668) covalent geometry : bond 0.00209 (11642) covalent geometry : angle 0.47760 (15787) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8474.34 seconds wall clock time: 153 minutes 15.68 seconds (9195.68 seconds total)