Starting phenix.real_space_refine on Fri Feb 14 16:11:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.map" model { file = "/net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6msm_9230/02_2025/6msm_9230.cif" } resolution = 3.2 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= 0.002 sd= 0.056 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6343 2.51 5 N 1596 2.21 5 O 1709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9703 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9466 Classifications: {'peptide': 1181} Link IDs: {'PTRANS': 32, 'TRANS': 1148} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 6.58, per 1000 atoms: 0.68 Number of scatterers: 9703 At special positions: 0 Unit cell: (81.37, 88.58, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1709 8.00 N 1596 7.00 C 6343 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: 2.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 69.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.998A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.711A pdb=" N LEU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.679A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.730A pdb=" N LEU A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 166 removed outlier: 3.543A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.628A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.897A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 199 through 219 Proline residue: A 205 - end of helix removed outlier: 3.639A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.630A pdb=" N CYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.720A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.717A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 308 removed outlier: 4.244A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 4.204A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.706A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.916A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 352 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.729A pdb=" N GLN A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.906A pdb=" N GLY A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 532 removed outlier: 3.566A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.688A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.208A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 4.040A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 922 removed outlier: 3.526A pdb=" N TYR A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.630A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 927' Processing helix chain 'A' and resid 933 through 958 Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.634A pdb=" N LEU A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.565A pdb=" N ILE A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.563A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1047 removed outlier: 4.012A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.541A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.560A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.688A pdb=" N LEU A1065 " --> pdb=" O GLY A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.596A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1168 removed outlier: 3.995A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.617A pdb=" N PHE A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1322 removed outlier: 3.562A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.603A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.568A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1391 removed outlier: 3.966A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 3.580A pdb=" N ALA A1406 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 4.200A pdb=" N LEU A1430 " --> pdb=" O SER A1426 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1440 Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 4.139A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.756A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.463A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A 479 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.355A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 5.845A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A1232 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS A1213 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A1234 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N THR A1211 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 6.797A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1569 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: 3.27 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1310 1.46 - 1.58: 5629 1.58 - 1.70: 10 1.70 - 1.82: 79 Bond restraints: 9903 Sorted by residual: bond pdb=" N LEU A 935 " pdb=" CA LEU A 935 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.22e+01 bond pdb=" N ILE A1277 " pdb=" CA ILE A1277 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.09e-02 8.42e+03 1.13e+01 bond pdb=" N VAL A1318 " pdb=" CA VAL A1318 " ideal model delta sigma weight residual 1.460 1.500 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" C5 ATP A1504 " pdb=" C6 ATP A1504 " ideal model delta sigma weight residual 1.409 1.442 -0.033 1.00e-02 1.00e+04 1.11e+01 ... (remaining 9898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 12991 3.38 - 6.76: 389 6.76 - 10.14: 5 10.14 - 13.52: 1 13.52 - 16.90: 4 Bond angle restraints: 13390 Sorted by residual: angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 121.68 15.15 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 125.08 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 123.00 13.83 1.00e+00 1.00e+00 1.91e+02 angle pdb=" C THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta sigma weight residual 111.86 123.12 -11.26 1.34e+00 5.57e-01 7.06e+01 ... (remaining 13385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 5521 19.02 - 38.03: 348 38.03 - 57.05: 95 57.05 - 76.06: 11 76.06 - 95.08: 4 Dihedral angle restraints: 5979 sinusoidal: 2497 harmonic: 3482 Sorted by residual: dihedral pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N LEU A 188 " pdb=" CA LEU A 188 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C THR A 390 " pdb=" N THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta harmonic sigma weight residual -122.00 -132.90 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 583 0.042 - 0.084: 464 0.084 - 0.127: 346 0.127 - 0.169: 132 0.169 - 0.211: 20 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL A 855 " pdb=" N VAL A 855 " pdb=" C VAL A 855 " pdb=" CB VAL A 855 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR A 351 " pdb=" N THR A 351 " pdb=" C THR A 351 " pdb=" CB THR A 351 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1542 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1126 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLU A1126 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A1126 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A1127 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 390 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C THR A 390 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 391 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 348 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C MET A 348 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 348 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 349 " 0.013 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 26 2.54 - 3.13: 6907 3.13 - 3.72: 14356 3.72 - 4.31: 20158 4.31 - 4.90: 34225 Nonbonded interactions: 75672 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.955 2.170 nonbonded pdb=" O ASP A 112 " pdb=" OD1 ASP A 112 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.053 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.142 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.187 2.170 ... (remaining 75667 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.012 0.044 9903 Z= 0.761 Angle : 1.511 16.903 13390 Z= 1.118 Chirality : 0.078 0.211 1545 Planarity : 0.005 0.058 1628 Dihedral : 13.911 95.076 3727 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.39 % Allowed : 5.11 % Favored : 94.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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: -2.75 (0.20), residues: 1171 helix: -1.39 (0.16), residues: 732 sheet: -1.94 (0.61), residues: 69 loop : -2.39 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1274 HIS 0.008 0.002 HIS A 146 PHE 0.014 0.003 PHE A 337 TYR 0.031 0.003 TYR A 161 ARG 0.011 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8416 (mptt) cc_final: 0.7940 (tppt) REVERT: A 15 LEU cc_start: 0.8680 (tp) cc_final: 0.8404 (tt) REVERT: A 26 LYS cc_start: 0.8242 (tptp) cc_final: 0.7999 (tttp) REVERT: A 31 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7446 (ttt90) REVERT: A 51 GLU cc_start: 0.8301 (tp30) cc_final: 0.8092 (tp30) REVERT: A 68 LYS cc_start: 0.8211 (mttt) cc_final: 0.7939 (mtpp) REVERT: A 129 LEU cc_start: 0.8313 (tt) cc_final: 0.8099 (mm) REVERT: A 224 PHE cc_start: 0.7534 (m-80) cc_final: 0.6940 (t80) REVERT: A 235 LEU cc_start: 0.8815 (mt) cc_final: 0.8537 (mm) REVERT: A 246 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7745 (tmtt) REVERT: A 315 PHE cc_start: 0.8192 (t80) cc_final: 0.7713 (t80) REVERT: A 351 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 362 TYR cc_start: 0.8183 (m-80) cc_final: 0.7983 (m-80) REVERT: A 373 ASP cc_start: 0.8027 (t70) cc_final: 0.7817 (t0) REVERT: A 383 LEU cc_start: 0.7771 (tt) cc_final: 0.7087 (tt) REVERT: A 448 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 476 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8998 (pm20) REVERT: A 504 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 532 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8448 (ttmt) REVERT: A 905 VAL cc_start: 0.8528 (t) cc_final: 0.8238 (p) REVERT: A 958 GLN cc_start: 0.7794 (pt0) cc_final: 0.7581 (pt0) REVERT: A 985 ASP cc_start: 0.8299 (m-30) cc_final: 0.8063 (m-30) REVERT: A 1046 GLU cc_start: 0.7994 (tt0) cc_final: 0.7502 (tp30) REVERT: A 1060 LYS cc_start: 0.8190 (tttt) cc_final: 0.7850 (ttpt) REVERT: A 1137 MET cc_start: 0.8567 (mmm) cc_final: 0.8280 (mmp) REVERT: A 1224 ASN cc_start: 0.7629 (m110) cc_final: 0.7201 (t0) REVERT: A 1330 GLN cc_start: 0.8461 (tt0) cc_final: 0.8138 (mt0) REVERT: A 1341 ASP cc_start: 0.8253 (t0) cc_final: 0.7949 (t0) REVERT: A 1416 ILE cc_start: 0.8511 (mt) cc_final: 0.8161 (tt) REVERT: A 1444 SER cc_start: 0.7816 (m) cc_final: 0.7304 (t) outliers start: 4 outliers final: 0 residues processed: 270 average time/residue: 0.2804 time to fit residues: 100.2203 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 949 HIS A1088 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099223 restraints weight = 16743.570| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.84 r_work: 0.3105 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.214 Angle : 0.596 6.769 13390 Z= 0.312 Chirality : 0.041 0.171 1545 Planarity : 0.004 0.036 1628 Dihedral : 9.153 77.672 1470 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.83 % Allowed : 11.28 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.23), residues: 1171 helix: 0.59 (0.18), residues: 752 sheet: -1.49 (0.60), residues: 67 loop : -1.72 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 882 HIS 0.005 0.001 HIS A 199 PHE 0.027 0.001 PHE A 236 TYR 0.016 0.001 TYR A 304 ARG 0.006 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8492 (mptt) cc_final: 0.8062 (tppt) REVERT: A 31 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7418 (ttm170) REVERT: A 51 GLU cc_start: 0.8674 (tp30) cc_final: 0.8401 (tp30) REVERT: A 68 LYS cc_start: 0.8675 (mttt) cc_final: 0.8412 (mtpp) REVERT: A 286 GLU cc_start: 0.8210 (tt0) cc_final: 0.7938 (mt-10) REVERT: A 362 TYR cc_start: 0.8342 (m-80) cc_final: 0.8074 (m-80) REVERT: A 469 MET cc_start: 0.8131 (mmm) cc_final: 0.7881 (mmp) REVERT: A 504 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7978 (mt-10) REVERT: A 532 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8407 (tppt) REVERT: A 636 LEU cc_start: 0.9104 (tt) cc_final: 0.8738 (mt) REVERT: A 1046 GLU cc_start: 0.8242 (tt0) cc_final: 0.7870 (tp30) REVERT: A 1060 LYS cc_start: 0.8562 (tttt) cc_final: 0.8320 (ttpt) REVERT: A 1065 LEU cc_start: 0.8636 (mp) cc_final: 0.8408 (mt) REVERT: A 1224 ASN cc_start: 0.7933 (m110) cc_final: 0.7421 (t0) REVERT: A 1280 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 1341 ASP cc_start: 0.8448 (t0) cc_final: 0.8156 (t0) outliers start: 19 outliers final: 12 residues processed: 200 average time/residue: 0.2337 time to fit residues: 65.2584 Evaluate side-chains 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1404 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 27 optimal weight: 0.0370 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 GLN A1238 GLN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098190 restraints weight = 17089.110| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.80 r_work: 0.3090 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9903 Z= 0.191 Angle : 0.542 6.868 13390 Z= 0.279 Chirality : 0.039 0.156 1545 Planarity : 0.003 0.034 1628 Dihedral : 7.911 84.407 1467 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 13.50 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.24), residues: 1171 helix: 1.19 (0.19), residues: 747 sheet: -1.69 (0.58), residues: 69 loop : -1.37 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 882 HIS 0.004 0.001 HIS A1085 PHE 0.021 0.001 PHE A 236 TYR 0.013 0.001 TYR A 919 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8466 (mptt) cc_final: 0.8038 (tppt) REVERT: A 15 LEU cc_start: 0.8910 (tp) cc_final: 0.8545 (tt) REVERT: A 31 ARG cc_start: 0.7574 (ttm170) cc_final: 0.7329 (ttm170) REVERT: A 51 GLU cc_start: 0.8699 (tp30) cc_final: 0.8436 (tp30) REVERT: A 68 LYS cc_start: 0.8710 (mttt) cc_final: 0.8478 (mtpp) REVERT: A 78 PHE cc_start: 0.8480 (t80) cc_final: 0.7948 (t80) REVERT: A 217 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 362 TYR cc_start: 0.8351 (m-80) cc_final: 0.8094 (m-80) REVERT: A 504 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 532 LYS cc_start: 0.8747 (ttmt) cc_final: 0.8310 (tppt) REVERT: A 636 LEU cc_start: 0.9080 (tt) cc_final: 0.8781 (mt) REVERT: A 873 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 1059 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 1101 MET cc_start: 0.8499 (ttt) cc_final: 0.8286 (ttt) REVERT: A 1224 ASN cc_start: 0.7881 (m110) cc_final: 0.7363 (t0) REVERT: A 1280 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 1341 ASP cc_start: 0.8421 (t0) cc_final: 0.8151 (t0) outliers start: 27 outliers final: 18 residues processed: 168 average time/residue: 0.2078 time to fit residues: 50.7475 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1404 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 0.0070 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.117199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098853 restraints weight = 16920.539| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.79 r_work: 0.3097 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9903 Z= 0.174 Angle : 0.513 6.807 13390 Z= 0.264 Chirality : 0.038 0.155 1545 Planarity : 0.003 0.032 1628 Dihedral : 6.869 70.045 1467 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.99 % Allowed : 13.60 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.24), residues: 1171 helix: 1.40 (0.19), residues: 757 sheet: -1.48 (0.56), residues: 71 loop : -1.26 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A1085 PHE 0.018 0.001 PHE A 931 TYR 0.010 0.001 TYR A 517 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8549 (mptt) cc_final: 0.8114 (tppt) REVERT: A 15 LEU cc_start: 0.8910 (tp) cc_final: 0.8547 (tt) REVERT: A 31 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7405 (ttm170) REVERT: A 51 GLU cc_start: 0.8690 (tp30) cc_final: 0.8426 (tp30) REVERT: A 68 LYS cc_start: 0.8748 (mttt) cc_final: 0.8539 (mtpp) REVERT: A 78 PHE cc_start: 0.8430 (t80) cc_final: 0.7872 (t80) REVERT: A 217 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 249 ASP cc_start: 0.8621 (m-30) cc_final: 0.8357 (p0) REVERT: A 362 TYR cc_start: 0.8337 (m-80) cc_final: 0.8123 (m-80) REVERT: A 504 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 532 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8297 (tppt) REVERT: A 926 LEU cc_start: 0.8901 (mt) cc_final: 0.8461 (mt) REVERT: A 1101 MET cc_start: 0.8438 (ttt) cc_final: 0.8197 (ttt) REVERT: A 1224 ASN cc_start: 0.7842 (m110) cc_final: 0.7247 (t0) REVERT: A 1280 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7568 (tm-30) REVERT: A 1341 ASP cc_start: 0.8277 (t0) cc_final: 0.7995 (t0) outliers start: 31 outliers final: 18 residues processed: 165 average time/residue: 0.1971 time to fit residues: 47.3486 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092715 restraints weight = 17399.958| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.82 r_work: 0.3002 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9903 Z= 0.374 Angle : 0.616 7.762 13390 Z= 0.315 Chirality : 0.042 0.173 1545 Planarity : 0.004 0.032 1628 Dihedral : 6.993 64.798 1467 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.09 % Allowed : 15.14 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.24), residues: 1171 helix: 1.06 (0.19), residues: 762 sheet: -1.41 (0.56), residues: 72 loop : -1.17 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1089 HIS 0.007 0.001 HIS A1054 PHE 0.023 0.002 PHE A 131 TYR 0.017 0.002 TYR A 919 ARG 0.005 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8675 (mptt) cc_final: 0.8215 (tppt) REVERT: A 31 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7637 (ttm170) REVERT: A 68 LYS cc_start: 0.8766 (mttt) cc_final: 0.8537 (mtpp) REVERT: A 217 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 279 GLU cc_start: 0.8093 (mp0) cc_final: 0.7675 (mp0) REVERT: A 362 TYR cc_start: 0.8521 (m-80) cc_final: 0.8303 (m-80) REVERT: A 469 MET cc_start: 0.8183 (mmp) cc_final: 0.7748 (mmp) REVERT: A 504 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 532 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8379 (ttmm) REVERT: A 1224 ASN cc_start: 0.7865 (m110) cc_final: 0.7257 (t0) REVERT: A 1280 GLN cc_start: 0.8101 (tm-30) cc_final: 0.7566 (tm-30) outliers start: 32 outliers final: 27 residues processed: 151 average time/residue: 0.2001 time to fit residues: 43.9992 Evaluate side-chains 144 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096721 restraints weight = 17177.791| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.79 r_work: 0.3070 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.183 Angle : 0.515 6.858 13390 Z= 0.262 Chirality : 0.038 0.149 1545 Planarity : 0.003 0.032 1628 Dihedral : 6.436 57.061 1467 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.99 % Allowed : 16.01 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.24), residues: 1171 helix: 1.31 (0.19), residues: 761 sheet: -1.31 (0.54), residues: 74 loop : -1.08 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.035 0.001 PHE A 626 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8644 (mptt) cc_final: 0.8237 (tppt) REVERT: A 31 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7450 (ttm170) REVERT: A 68 LYS cc_start: 0.8777 (mttt) cc_final: 0.8544 (mttm) REVERT: A 78 PHE cc_start: 0.8486 (t80) cc_final: 0.7947 (t80) REVERT: A 217 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 279 GLU cc_start: 0.8034 (mp0) cc_final: 0.7775 (mp0) REVERT: A 362 TYR cc_start: 0.8381 (m-80) cc_final: 0.8180 (m-80) REVERT: A 469 MET cc_start: 0.8118 (mmp) cc_final: 0.7759 (mmp) REVERT: A 476 GLU cc_start: 0.8835 (mp0) cc_final: 0.8579 (mp0) REVERT: A 532 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8392 (ttmm) REVERT: A 1224 ASN cc_start: 0.7871 (m110) cc_final: 0.7309 (t0) REVERT: A 1280 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 1330 GLN cc_start: 0.8640 (mt0) cc_final: 0.8351 (mt0) REVERT: A 1341 ASP cc_start: 0.8281 (t0) cc_final: 0.8005 (t0) outliers start: 31 outliers final: 20 residues processed: 156 average time/residue: 0.2037 time to fit residues: 46.7679 Evaluate side-chains 144 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 1 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A1038 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099675 restraints weight = 17116.232| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.83 r_work: 0.3118 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9903 Z= 0.139 Angle : 0.496 7.135 13390 Z= 0.251 Chirality : 0.037 0.149 1545 Planarity : 0.003 0.032 1628 Dihedral : 6.048 51.785 1467 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.22 % Allowed : 17.26 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.25), residues: 1171 helix: 1.50 (0.19), residues: 759 sheet: -1.25 (0.52), residues: 77 loop : -1.00 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.006 0.001 HIS A 199 PHE 0.024 0.001 PHE A 626 TYR 0.009 0.001 TYR A1381 ARG 0.004 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8513 (mptt) cc_final: 0.8157 (tppt) REVERT: A 31 ARG cc_start: 0.7678 (ttm170) cc_final: 0.7426 (ttm170) REVERT: A 68 LYS cc_start: 0.8793 (mttt) cc_final: 0.8556 (mttm) REVERT: A 78 PHE cc_start: 0.8310 (t80) cc_final: 0.7766 (t80) REVERT: A 217 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 249 ASP cc_start: 0.8490 (m-30) cc_final: 0.8253 (p0) REVERT: A 279 GLU cc_start: 0.7964 (mp0) cc_final: 0.7690 (mp0) REVERT: A 469 MET cc_start: 0.8119 (mmp) cc_final: 0.7740 (mmp) REVERT: A 476 GLU cc_start: 0.8908 (mp0) cc_final: 0.8566 (pm20) REVERT: A 532 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8339 (ttmm) REVERT: A 1224 ASN cc_start: 0.7887 (m110) cc_final: 0.7304 (t0) REVERT: A 1277 ILE cc_start: 0.8700 (tp) cc_final: 0.8211 (tt) REVERT: A 1280 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 1330 GLN cc_start: 0.8609 (mt0) cc_final: 0.8326 (mt0) REVERT: A 1341 ASP cc_start: 0.8174 (t0) cc_final: 0.7904 (t0) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.2001 time to fit residues: 46.6968 Evaluate side-chains 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093429 restraints weight = 17556.214| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.84 r_work: 0.3018 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9903 Z= 0.313 Angle : 0.600 9.647 13390 Z= 0.300 Chirality : 0.041 0.179 1545 Planarity : 0.003 0.031 1628 Dihedral : 6.352 55.990 1467 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.70 % Allowed : 18.61 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1171 helix: 1.36 (0.19), residues: 759 sheet: -1.20 (0.52), residues: 75 loop : -0.85 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1089 HIS 0.006 0.001 HIS A1085 PHE 0.021 0.002 PHE A 236 TYR 0.013 0.001 TYR A 919 ARG 0.004 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8679 (mptt) cc_final: 0.8327 (tppt) REVERT: A 31 ARG cc_start: 0.8039 (ttm170) cc_final: 0.7714 (ttm170) REVERT: A 68 LYS cc_start: 0.8839 (mttt) cc_final: 0.8616 (mtpp) REVERT: A 78 PHE cc_start: 0.8587 (t80) cc_final: 0.7957 (t80) REVERT: A 217 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 279 GLU cc_start: 0.8127 (mp0) cc_final: 0.7854 (mp0) REVERT: A 394 MET cc_start: 0.8670 (mtm) cc_final: 0.8433 (ttp) REVERT: A 476 GLU cc_start: 0.8829 (mp0) cc_final: 0.8530 (mp0) REVERT: A 532 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8501 (ttmt) REVERT: A 1224 ASN cc_start: 0.8039 (m110) cc_final: 0.7546 (t0) REVERT: A 1280 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 1310 TRP cc_start: 0.8936 (m100) cc_final: 0.8683 (m100) REVERT: A 1330 GLN cc_start: 0.8731 (mt0) cc_final: 0.8429 (mt0) REVERT: A 1341 ASP cc_start: 0.8398 (t0) cc_final: 0.8157 (t0) outliers start: 28 outliers final: 24 residues processed: 149 average time/residue: 0.2012 time to fit residues: 44.1455 Evaluate side-chains 146 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 62 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS A 151 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096851 restraints weight = 17135.215| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.84 r_work: 0.3085 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9903 Z= 0.167 Angle : 0.533 9.088 13390 Z= 0.265 Chirality : 0.039 0.159 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.974 56.014 1467 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.31 % Allowed : 19.29 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1171 helix: 1.57 (0.19), residues: 751 sheet: -1.21 (0.52), residues: 75 loop : -0.80 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.020 0.001 PHE A 931 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8642 (mptt) cc_final: 0.8295 (tppt) REVERT: A 31 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7576 (ttm170) REVERT: A 68 LYS cc_start: 0.8846 (mttt) cc_final: 0.8609 (mttm) REVERT: A 78 PHE cc_start: 0.8379 (t80) cc_final: 0.7788 (t80) REVERT: A 217 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 249 ASP cc_start: 0.8548 (m-30) cc_final: 0.8215 (p0) REVERT: A 279 GLU cc_start: 0.8012 (mp0) cc_final: 0.7737 (mp0) REVERT: A 476 GLU cc_start: 0.8846 (mp0) cc_final: 0.8598 (mp0) REVERT: A 532 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8387 (ttmt) REVERT: A 1128 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6332 (mtm180) REVERT: A 1224 ASN cc_start: 0.7999 (m110) cc_final: 0.7506 (t0) REVERT: A 1280 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 1330 GLN cc_start: 0.8655 (mt0) cc_final: 0.8358 (mt0) REVERT: A 1341 ASP cc_start: 0.8288 (t0) cc_final: 0.8017 (t0) outliers start: 24 outliers final: 23 residues processed: 142 average time/residue: 0.2037 time to fit residues: 42.2605 Evaluate side-chains 146 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095841 restraints weight = 17427.248| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.83 r_work: 0.3060 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9903 Z= 0.214 Angle : 0.551 8.972 13390 Z= 0.274 Chirality : 0.039 0.165 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.902 59.365 1467 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.41 % Allowed : 19.19 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.25), residues: 1171 helix: 1.56 (0.19), residues: 755 sheet: -1.20 (0.53), residues: 74 loop : -0.83 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1089 HIS 0.005 0.001 HIS A 199 PHE 0.019 0.001 PHE A 931 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8642 (mptt) cc_final: 0.8342 (tppt) REVERT: A 31 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7629 (ttm170) REVERT: A 68 LYS cc_start: 0.8851 (mttt) cc_final: 0.8616 (mttm) REVERT: A 78 PHE cc_start: 0.8425 (t80) cc_final: 0.7855 (t80) REVERT: A 217 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 279 GLU cc_start: 0.8034 (mp0) cc_final: 0.7759 (mp0) REVERT: A 476 GLU cc_start: 0.8848 (mp0) cc_final: 0.8590 (mp0) REVERT: A 532 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8474 (ttmt) REVERT: A 1224 ASN cc_start: 0.8005 (m110) cc_final: 0.7513 (t0) REVERT: A 1280 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 1341 ASP cc_start: 0.8300 (t0) cc_final: 0.8027 (t0) outliers start: 25 outliers final: 24 residues processed: 141 average time/residue: 0.2049 time to fit residues: 42.4592 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 0.0050 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 110 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098734 restraints weight = 17149.713| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.87 r_work: 0.3092 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9903 Z= 0.162 Angle : 0.523 8.892 13390 Z= 0.259 Chirality : 0.038 0.155 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.596 53.338 1467 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.51 % Allowed : 19.09 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.25), residues: 1171 helix: 1.65 (0.19), residues: 753 sheet: -1.05 (0.54), residues: 75 loop : -0.76 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.019 0.001 PHE A 236 TYR 0.010 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3703.70 seconds wall clock time: 67 minutes 2.70 seconds (4022.70 seconds total)