Starting phenix.real_space_refine on Fri Sep 11 16:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.map" model { file = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6msm_9230/09_2026/6msm_9230.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 145 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 1.66, per 1000 atoms: 0.17 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: 0.64 Conformation dependent library (CDL) restraints added in 341.2 milliseconds 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: 0.29 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: 1.67 Time building geometry restraints manager: 0.91 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: 5440 19.02 - 38.03: 320 38.03 - 57.05: 89 57.05 - 76.06: 9 76.06 - 95.08: 3 Dihedral angle restraints: 5861 sinusoidal: 2379 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 5858 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: 1.760 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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= 0.886 Angle : 1.511 16.903 13390 Z= 1.118 Chirality : 0.078 0.211 1545 Planarity : 0.005 0.058 1628 Dihedral : 13.611 95.076 3609 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (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 ARG 0.011 0.001 ARG A 55 TYR 0.031 0.003 TYR A 161 PHE 0.014 0.003 PHE A 337 TRP 0.016 0.002 TRP A1274 HIS 0.008 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.89 ( 9903) covalent geometry : angle 1.51149 / 1.12 (13390) hydrogen bonds : bond 0.25738 / 17.13 ( 530) hydrogen bonds : angle 7.94548 / 5.61 ( 1569) *********************** 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 : 0.332 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: 0.8300 (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: 0.8029 (ttpp) cc_final: 0.7744 (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: 0.7630 (m110) cc_final: 0.7202 (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: 0.8510 (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: 0.1107 time to fit residues: 39.8774 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 : 0.363 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3484 r_free = 0.3484 target = 0.117283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098268 restraints weight = 16904.446| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.86 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2762 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= 0.150 Angle : 0.601 6.846 13390 Z= 0.314 Chirality : 0.041 0.172 1545 Planarity : 0.004 0.037 1628 Dihedral : 7.425 87.859 1352 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.03 % Allowed : 11.19 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1171 helix: 0.54 (0.18), residues: 750 sheet: -1.49 (0.60), residues: 67 loop : -1.76 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 347 TYR 0.016 0.001 TYR A 304 PHE 0.026 0.001 PHE A 236 TRP 0.014 0.001 TRP A 882 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9903) covalent geometry : angle 0.60081 / 0.31 (13390) hydrogen bonds : bond 0.05651 / 3.70 ( 530) hydrogen bonds : angle 4.36419 / 3.09 ( 1569) *********************** 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 199 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.369 Fit side-chains REVERT: A 8 LYS cc_start: 0.8510 (mptt) cc_final: 0.8081 (tppt) REVERT: A 31 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7466 (ttm170) REVERT: A 51 GLU cc_start: 0.8664 (tp30) cc_final: 0.8391 (tp30) REVERT: A 68 LYS cc_start: 0.8695 (mttt) cc_final: 0.8429 (mtpp) REVERT: A 303 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8369 (ttp80) REVERT: A 315 PHE cc_start: 0.8207 (t80) cc_final: 0.8002 (t80) REVERT: A 362 TYR cc_start: 0.8372 (m-80) cc_final: 0.8091 (m-80) REVERT: A 469 MET cc_start: 0.8146 (mmm) cc_final: 0.7899 (mmp) REVERT: A 504 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 532 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8399 (tppt) REVERT: A 849 TYR cc_start: 0.8741 (m-80) cc_final: 0.8193 (m-80) REVERT: A 1046 GLU cc_start: 0.8279 (tt0) cc_final: 0.7891 (tp30) REVERT: A 1060 LYS cc_start: 0.8551 (tttt) cc_final: 0.8217 (ttpt) REVERT: A 1224 ASN cc_start: 0.7952 (m110) cc_final: 0.7485 (t0) REVERT: A 1280 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 1341 ASP cc_start: 0.8459 (t0) cc_final: 0.8168 (t0) REVERT: A 1444 SER cc_start: 0.7990 (m) cc_final: 0.7736 (p) outliers start: 21 outliers final: 13 residues processed: 196 average time/residue: 0.0917 time to fit residues: 25.6254 Evaluate side-chains 149 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 599 THR 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 8 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 11 optimal weight: 0.0270 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098428 restraints weight = 17090.809| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.81 r_work: 0.3097 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9903 Z= 0.125 Angle : 0.539 6.863 13390 Z= 0.277 Chirality : 0.039 0.154 1545 Planarity : 0.003 0.034 1628 Dihedral : 6.343 87.003 1349 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.31 % Allowed : 13.69 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1171 helix: 1.19 (0.19), residues: 747 sheet: -1.59 (0.57), residues: 71 loop : -1.38 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.013 0.001 TYR A 919 PHE 0.020 0.001 PHE A 78 TRP 0.010 0.001 TRP A 882 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9903) covalent geometry : angle 0.53915 / 0.28 (13390) hydrogen bonds : bond 0.04769 / 3.13 ( 530) hydrogen bonds : angle 4.00734 / 2.82 ( 1569) *********************** 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 174 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8460 (mptt) cc_final: 0.8030 (tppt) REVERT: A 31 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7387 (ttm170) REVERT: A 51 GLU cc_start: 0.8701 (tp30) cc_final: 0.8497 (tp30) REVERT: A 68 LYS cc_start: 0.8705 (mttt) cc_final: 0.8470 (mtpp) REVERT: A 78 PHE cc_start: 0.8481 (t80) cc_final: 0.7877 (t80) REVERT: A 217 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 303 ARG cc_start: 0.8552 (ttp-170) cc_final: 0.8347 (ttp80) REVERT: A 362 TYR cc_start: 0.8347 (m-80) cc_final: 0.8096 (m-80) REVERT: A 504 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 532 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8279 (tppt) REVERT: A 636 LEU cc_start: 0.9073 (tt) cc_final: 0.8767 (mt) REVERT: A 873 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: A 1059 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 1060 LYS cc_start: 0.8624 (tttt) cc_final: 0.8289 (ttpt) REVERT: A 1224 ASN cc_start: 0.7876 (m110) cc_final: 0.7360 (t0) REVERT: A 1280 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 1341 ASP cc_start: 0.8405 (t0) cc_final: 0.8124 (t0) outliers start: 24 outliers final: 15 residues processed: 170 average time/residue: 0.0766 time to fit residues: 18.8967 Evaluate side-chains 147 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 1045 SER 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 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 38 optimal weight: 0.9990 chunk 116 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3450 r_free = 0.3450 target = 0.114645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096212 restraints weight = 17156.577| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.79 r_work: 0.3062 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3814 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= 0.142 Angle : 0.542 6.972 13390 Z= 0.277 Chirality : 0.039 0.161 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.852 78.668 1349 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.47 % Allowed : 13.69 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1171 helix: 1.30 (0.19), residues: 766 sheet: -1.49 (0.55), residues: 76 loop : -1.34 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.011 0.001 TYR A 304 PHE 0.018 0.001 PHE A 236 TRP 0.009 0.001 TRP A 882 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9903) covalent geometry : angle 0.54190 / 0.28 (13390) hydrogen bonds : bond 0.04752 / 3.12 ( 530) hydrogen bonds : angle 3.95423 / 2.79 ( 1569) *********************** 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 171 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8602 (mptt) cc_final: 0.8130 (tppt) REVERT: A 15 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (tt) REVERT: A 31 ARG cc_start: 0.7741 (ttm170) cc_final: 0.7461 (ttm170) REVERT: A 51 GLU cc_start: 0.8721 (tp30) cc_final: 0.8521 (tp30) REVERT: A 68 LYS cc_start: 0.8754 (mttt) cc_final: 0.8531 (mtpp) REVERT: A 78 PHE cc_start: 0.8461 (t80) cc_final: 0.7846 (t80) REVERT: A 217 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7961 (tm-30) REVERT: A 303 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8238 (ttp80) REVERT: A 362 TYR cc_start: 0.8395 (m-80) cc_final: 0.8145 (m-80) REVERT: A 394 MET cc_start: 0.8572 (ttp) cc_final: 0.8303 (ttp) REVERT: A 504 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8073 (mt-10) REVERT: A 532 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8288 (ttmm) REVERT: A 926 LEU cc_start: 0.8896 (mt) cc_final: 0.8529 (mt) REVERT: A 1060 LYS cc_start: 0.8567 (tttt) cc_final: 0.8226 (ttpt) REVERT: A 1224 ASN cc_start: 0.7837 (m110) cc_final: 0.7286 (t0) REVERT: A 1280 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 1341 ASP cc_start: 0.8281 (t0) cc_final: 0.8009 (t0) outliers start: 36 outliers final: 25 residues processed: 166 average time/residue: 0.0801 time to fit residues: 19.3073 Evaluate side-chains 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU 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 327 LEU 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 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 989 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1045 SER 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 1322 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 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 46 optimal weight: 0.0570 chunk 63 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099031 restraints weight = 17106.528| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.82 r_work: 0.3104 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9903 Z= 0.108 Angle : 0.504 6.748 13390 Z= 0.255 Chirality : 0.038 0.150 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.497 79.633 1349 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.41 % Allowed : 15.53 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1171 helix: 1.46 (0.19), residues: 758 sheet: -1.45 (0.53), residues: 76 loop : -1.18 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.010 0.001 TYR A 517 PHE 0.025 0.001 PHE A 626 TRP 0.009 0.001 TRP A 202 HIS 0.003 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9903) covalent geometry : angle 0.50369 / 0.26 (13390) hydrogen bonds : bond 0.04169 / 2.72 ( 530) hydrogen bonds : angle 3.81054 / 2.69 ( 1569) *********************** 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 164 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8574 (mptt) cc_final: 0.8114 (tppt) REVERT: A 31 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7444 (ttm170) REVERT: A 51 GLU cc_start: 0.8679 (tp30) cc_final: 0.8439 (tp30) REVERT: A 68 LYS cc_start: 0.8780 (mttt) cc_final: 0.8564 (mttm) REVERT: A 78 PHE cc_start: 0.8397 (t80) cc_final: 0.7800 (t80) REVERT: A 217 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 362 TYR cc_start: 0.8335 (m-80) cc_final: 0.8110 (m-80) REVERT: A 469 MET cc_start: 0.8069 (mmp) cc_final: 0.7673 (mmp) REVERT: A 504 GLU cc_start: 0.8285 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 532 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8377 (ttmt) REVERT: A 1224 ASN cc_start: 0.7898 (m110) cc_final: 0.7331 (t0) REVERT: A 1280 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 1330 GLN cc_start: 0.8648 (mt0) cc_final: 0.8359 (mt0) REVERT: A 1341 ASP cc_start: 0.8238 (t0) cc_final: 0.7955 (t0) outliers start: 25 outliers final: 20 residues processed: 159 average time/residue: 0.0830 time to fit residues: 19.3534 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 327 LEU 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 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 1045 SER 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 1410 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095467 restraints weight = 17373.205| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.82 r_work: 0.3054 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9903 Z= 0.147 Angle : 0.532 7.097 13390 Z= 0.270 Chirality : 0.039 0.169 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.544 84.511 1349 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.09 % Allowed : 16.20 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1171 helix: 1.41 (0.19), residues: 762 sheet: -1.39 (0.53), residues: 74 loop : -1.00 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.012 0.001 TYR A 919 PHE 0.022 0.001 PHE A 236 TRP 0.009 0.001 TRP A1145 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9903) covalent geometry : angle 0.53242 / 0.27 (13390) hydrogen bonds : bond 0.04739 / 3.10 ( 530) hydrogen bonds : angle 3.90629 / 2.77 ( 1569) *********************** 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 159 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8663 (mptt) cc_final: 0.8239 (tppt) REVERT: A 31 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7488 (ttm170) REVERT: A 68 LYS cc_start: 0.8758 (mttt) cc_final: 0.8529 (mttm) REVERT: A 78 PHE cc_start: 0.8518 (t80) cc_final: 0.7766 (t80) REVERT: A 217 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 279 GLU cc_start: 0.8073 (mp0) cc_final: 0.7784 (mp0) REVERT: A 362 TYR cc_start: 0.8423 (m-80) cc_final: 0.8196 (m-80) REVERT: A 532 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8364 (ttmm) REVERT: A 929 MET cc_start: 0.8659 (mtm) cc_final: 0.8424 (mtp) REVERT: A 1028 MET cc_start: 0.8380 (mtp) cc_final: 0.8149 (mtm) REVERT: A 1224 ASN cc_start: 0.7931 (m110) cc_final: 0.7427 (t0) REVERT: A 1280 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 1330 GLN cc_start: 0.8659 (mt0) cc_final: 0.8358 (mt0) REVERT: A 1341 ASP cc_start: 0.8304 (t0) cc_final: 0.8031 (t0) outliers start: 32 outliers final: 22 residues processed: 152 average time/residue: 0.0842 time to fit residues: 19.0426 Evaluate side-chains 142 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 327 LEU 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 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 1410 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3462 r_free = 0.3462 target = 0.115328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097117 restraints weight = 17116.599| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.80 r_work: 0.3076 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4286 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= 0.116 Angle : 0.510 7.003 13390 Z= 0.257 Chirality : 0.038 0.154 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.423 87.360 1349 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.41 % Allowed : 17.45 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1171 helix: 1.48 (0.19), residues: 762 sheet: -1.40 (0.52), residues: 77 loop : -0.97 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.011 0.001 TYR A1381 PHE 0.020 0.001 PHE A 236 TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9903) covalent geometry : angle 0.51045 / 0.26 (13390) hydrogen bonds : bond 0.04277 / 2.79 ( 530) hydrogen bonds : angle 3.85544 / 2.73 ( 1569) *********************** 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 159 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8663 (mptt) cc_final: 0.8254 (tppt) REVERT: A 31 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7499 (ttm170) REVERT: A 68 LYS cc_start: 0.8779 (mttt) cc_final: 0.8528 (mttm) REVERT: A 78 PHE cc_start: 0.8367 (t80) cc_final: 0.7690 (t80) REVERT: A 217 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 279 GLU cc_start: 0.8021 (mp0) cc_final: 0.7719 (mp0) REVERT: A 362 TYR cc_start: 0.8380 (m-80) cc_final: 0.8177 (m-80) REVERT: A 476 GLU cc_start: 0.8847 (mp0) cc_final: 0.8622 (pm20) REVERT: A 532 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8361 (ttmm) REVERT: A 929 MET cc_start: 0.8651 (mtm) cc_final: 0.8447 (mtp) REVERT: A 1028 MET cc_start: 0.8351 (mtp) cc_final: 0.8100 (mtm) REVERT: A 1224 ASN cc_start: 0.8034 (m110) cc_final: 0.7568 (t0) REVERT: A 1280 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 1330 GLN cc_start: 0.8667 (mt0) cc_final: 0.8364 (mt0) REVERT: A 1341 ASP cc_start: 0.8240 (t0) cc_final: 0.7957 (t0) outliers start: 25 outliers final: 21 residues processed: 152 average time/residue: 0.0887 time to fit residues: 19.8480 Evaluate side-chains 145 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 327 LEU 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 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 1410 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3477 r_free = 0.3477 target = 0.116392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098120 restraints weight = 17162.253| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.82 r_work: 0.3090 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9903 Z= 0.109 Angle : 0.501 7.482 13390 Z= 0.253 Chirality : 0.038 0.156 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.308 89.678 1349 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.70 % Allowed : 17.65 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1171 helix: 1.57 (0.19), residues: 761 sheet: -1.28 (0.53), residues: 74 loop : -0.95 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.010 0.001 TYR A1381 PHE 0.022 0.001 PHE A 236 TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9903) covalent geometry : angle 0.50134 / 0.25 (13390) hydrogen bonds : bond 0.04105 / 2.68 ( 530) hydrogen bonds : angle 3.81388 / 2.69 ( 1569) *********************** 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 158 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8655 (mptt) cc_final: 0.8255 (tppt) REVERT: A 31 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7504 (ttm170) REVERT: A 68 LYS cc_start: 0.8755 (mttt) cc_final: 0.8513 (mttm) REVERT: A 78 PHE cc_start: 0.8347 (t80) cc_final: 0.7696 (t80) REVERT: A 217 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8123 (tm-30) REVERT: A 532 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8394 (ttmt) REVERT: A 1128 ARG cc_start: 0.6963 (tpt170) cc_final: 0.6320 (mtm180) REVERT: A 1157 MET cc_start: 0.8927 (tpp) cc_final: 0.8660 (tpp) REVERT: A 1224 ASN cc_start: 0.7994 (m110) cc_final: 0.7507 (t0) REVERT: A 1280 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 1330 GLN cc_start: 0.8616 (mt0) cc_final: 0.8299 (mt0) REVERT: A 1341 ASP cc_start: 0.8223 (t0) cc_final: 0.7938 (t0) outliers start: 28 outliers final: 23 residues processed: 150 average time/residue: 0.0855 time to fit residues: 19.1145 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 327 LEU 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 963 THR Chi-restraints excluded: chain A residue 989 LEU 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 1410 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 HIS ** 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 = 0.3475 r_free = 0.3475 target = 0.116259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097944 restraints weight = 17077.556| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.82 r_work: 0.3089 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4458 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= 0.114 Angle : 0.520 9.563 13390 Z= 0.258 Chirality : 0.039 0.174 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.216 87.327 1349 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.41 % Allowed : 18.61 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1171 helix: 1.59 (0.19), residues: 762 sheet: -1.30 (0.52), residues: 77 loop : -0.96 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.010 0.001 TYR A1381 PHE 0.021 0.001 PHE A 236 TRP 0.011 0.001 TRP A1089 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 9903) covalent geometry : angle 0.52035 / 0.26 (13390) hydrogen bonds : bond 0.04136 / 2.70 ( 530) hydrogen bonds : angle 3.81392 / 2.69 ( 1569) *********************** 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 157 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8666 (mptt) cc_final: 0.8307 (tppt) REVERT: A 31 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7531 (ttm170) REVERT: A 68 LYS cc_start: 0.8809 (mttt) cc_final: 0.8584 (mttm) REVERT: A 78 PHE cc_start: 0.8461 (t80) cc_final: 0.7829 (t80) REVERT: A 217 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 450 ARG cc_start: 0.7668 (ptt90) cc_final: 0.7436 (ptm160) REVERT: A 469 MET cc_start: 0.8066 (mmm) cc_final: 0.7740 (mmp) REVERT: A 532 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8416 (ttmt) REVERT: A 1128 ARG cc_start: 0.6932 (tpt170) cc_final: 0.6288 (mtm180) REVERT: A 1224 ASN cc_start: 0.7989 (m110) cc_final: 0.7509 (t0) REVERT: A 1277 ILE cc_start: 0.8731 (tp) cc_final: 0.8241 (tt) REVERT: A 1280 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 1330 GLN cc_start: 0.8509 (mt0) cc_final: 0.8180 (mt0) REVERT: A 1341 ASP cc_start: 0.8230 (t0) cc_final: 0.7943 (t0) outliers start: 25 outliers final: 23 residues processed: 150 average time/residue: 0.0902 time to fit residues: 19.5820 Evaluate side-chains 151 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 327 LEU 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 963 THR Chi-restraints excluded: chain A residue 989 LEU 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 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3471 r_free = 0.3471 target = 0.116234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097557 restraints weight = 17237.993| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.88 r_work: 0.3072 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9903 Z= 0.126 Angle : 0.537 9.335 13390 Z= 0.265 Chirality : 0.039 0.158 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.194 84.151 1349 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 18.90 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1171 helix: 1.63 (0.19), residues: 755 sheet: -1.17 (0.53), residues: 75 loop : -0.79 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.011 0.001 TYR A1381 PHE 0.022 0.001 PHE A 236 TRP 0.009 0.001 TRP A1089 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9903) covalent geometry : angle 0.53658 / 0.26 (13390) hydrogen bonds : bond 0.04313 / 2.81 ( 530) hydrogen bonds : angle 3.84392 / 2.72 ( 1569) ********************** 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 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8716 (mptt) cc_final: 0.8357 (tppt) REVERT: A 31 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7619 (ttm170) REVERT: A 68 LYS cc_start: 0.8812 (mttt) cc_final: 0.8585 (mttm) REVERT: A 78 PHE cc_start: 0.8524 (t80) cc_final: 0.8068 (t80) REVERT: A 217 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 279 GLU cc_start: 0.8040 (mp0) cc_final: 0.7755 (mp0) REVERT: A 450 ARG cc_start: 0.7674 (ptt90) cc_final: 0.7452 (ptm160) REVERT: A 532 LYS cc_start: 0.8887 (ttmt) cc_final: 0.8447 (ttmt) REVERT: A 1128 ARG cc_start: 0.6935 (tpt170) cc_final: 0.6283 (mtm180) REVERT: A 1224 ASN cc_start: 0.7991 (m110) cc_final: 0.7510 (t0) REVERT: A 1280 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 1330 GLN cc_start: 0.8519 (mt0) cc_final: 0.8192 (mt0) REVERT: A 1341 ASP cc_start: 0.8328 (t0) cc_final: 0.8069 (t0) outliers start: 23 outliers final: 23 residues processed: 144 average time/residue: 0.0876 time to fit residues: 18.2953 Evaluate side-chains 149 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 327 LEU 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 963 THR Chi-restraints excluded: chain A residue 989 LEU 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 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3472 r_free = 0.3472 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097880 restraints weight = 17091.204| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.81 r_work: 0.3086 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4530 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= 0.117 Angle : 0.533 9.198 13390 Z= 0.262 Chirality : 0.039 0.151 1545 Planarity : 0.003 0.031 1628 Dihedral : 5.121 82.128 1349 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.22 % Allowed : 19.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1171 helix: 1.65 (0.19), residues: 756 sheet: -1.13 (0.54), residues: 75 loop : -0.77 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.010 0.001 TYR A1381 PHE 0.021 0.001 PHE A 236 TRP 0.010 0.001 TRP A1089 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9903) covalent geometry : angle 0.53332 / 0.26 (13390) hydrogen bonds : bond 0.04218 / 2.74 ( 530) hydrogen bonds : angle 3.82336 / 2.70 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.33 seconds wall clock time: 31 minutes 43.53 seconds (1903.53 seconds total)