Starting phenix.real_space_refine on Mon Jul 28 13:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.map" model { file = "/net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6msm_9230/07_2025/6msm_9230.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6343 2.51 5 N 1596 2.21 5 O 1709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9703 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9466 Classifications: {'peptide': 1181} Link IDs: {'PTRANS': 32, 'TRANS': 1148} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 6.89, per 1000 atoms: 0.71 Number of scatterers: 9703 At special positions: 0 Unit cell: (81.37, 88.58, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1709 8.00 N 1596 7.00 C 6343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.4 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 69.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 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: 4.03 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1310 1.46 - 1.58: 5629 1.58 - 1.70: 10 1.70 - 1.82: 79 Bond restraints: 9903 Sorted by residual: bond pdb=" N LEU A 935 " pdb=" CA LEU A 935 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.22e+01 bond pdb=" N ILE A1277 " pdb=" CA ILE A1277 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.09e-02 8.42e+03 1.13e+01 bond pdb=" N VAL A1318 " pdb=" CA VAL A1318 " ideal model delta sigma weight residual 1.460 1.500 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" C5 ATP A1504 " pdb=" C6 ATP A1504 " ideal model delta sigma weight residual 1.409 1.442 -0.033 1.00e-02 1.00e+04 1.11e+01 ... (remaining 9898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 12991 3.38 - 6.76: 389 6.76 - 10.14: 5 10.14 - 13.52: 1 13.52 - 16.90: 4 Bond angle restraints: 13390 Sorted by residual: angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 121.68 15.15 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 125.08 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 123.00 13.83 1.00e+00 1.00e+00 1.91e+02 angle pdb=" C THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta sigma weight residual 111.86 123.12 -11.26 1.34e+00 5.57e-01 7.06e+01 ... (remaining 13385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 5521 19.02 - 38.03: 348 38.03 - 57.05: 95 57.05 - 76.06: 11 76.06 - 95.08: 4 Dihedral angle restraints: 5979 sinusoidal: 2497 harmonic: 3482 Sorted by residual: dihedral pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N LEU A 188 " pdb=" CA LEU A 188 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C THR A 390 " pdb=" N THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta harmonic sigma weight residual -122.00 -132.90 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 583 0.042 - 0.084: 464 0.084 - 0.127: 346 0.127 - 0.169: 132 0.169 - 0.211: 20 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL A 855 " pdb=" N VAL A 855 " pdb=" C VAL A 855 " pdb=" CB VAL A 855 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR A 351 " pdb=" N THR A 351 " pdb=" C THR A 351 " pdb=" CB THR A 351 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1542 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1126 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLU A1126 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A1126 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A1127 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 390 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C THR A 390 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 391 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 348 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C MET A 348 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 348 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 349 " 0.013 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 26 2.54 - 3.13: 6907 3.13 - 3.72: 14356 3.72 - 4.31: 20158 4.31 - 4.90: 34225 Nonbonded interactions: 75672 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.955 2.170 nonbonded pdb=" O ASP A 112 " pdb=" OD1 ASP A 112 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.053 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.142 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.187 2.170 ... (remaining 75667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.044 9903 Z= 0.886 Angle : 1.511 16.903 13390 Z= 1.118 Chirality : 0.078 0.211 1545 Planarity : 0.005 0.058 1628 Dihedral : 13.911 95.076 3727 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.39 % Allowed : 5.11 % Favored : 94.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.20), residues: 1171 helix: -1.39 (0.16), residues: 732 sheet: -1.94 (0.61), residues: 69 loop : -2.39 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1274 HIS 0.008 0.002 HIS A 146 PHE 0.014 0.003 PHE A 337 TYR 0.031 0.003 TYR A 161 ARG 0.011 0.001 ARG A 55 Details of bonding type rmsd hydrogen bonds : bond 0.25738 ( 530) hydrogen bonds : angle 7.94548 ( 1569) covalent geometry : bond 0.01172 ( 9903) covalent geometry : angle 1.51149 (13390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8416 (mptt) cc_final: 0.7940 (tppt) REVERT: A 15 LEU cc_start: 0.8680 (tp) cc_final: 0.8404 (tt) REVERT: A 26 LYS cc_start: 0.8242 (tptp) cc_final: 0.7999 (tttp) REVERT: A 31 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7446 (ttt90) REVERT: A 51 GLU cc_start: 0.8301 (tp30) cc_final: 0.8092 (tp30) REVERT: A 68 LYS cc_start: 0.8211 (mttt) cc_final: 0.7939 (mtpp) REVERT: A 129 LEU cc_start: 0.8313 (tt) cc_final: 0.8099 (mm) REVERT: A 224 PHE cc_start: 0.7534 (m-80) cc_final: 0.6940 (t80) REVERT: A 235 LEU cc_start: 0.8815 (mt) cc_final: 0.8537 (mm) REVERT: A 246 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7745 (tmtt) REVERT: A 315 PHE cc_start: 0.8192 (t80) cc_final: 0.7713 (t80) REVERT: A 351 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 362 TYR cc_start: 0.8183 (m-80) cc_final: 0.7983 (m-80) REVERT: A 373 ASP cc_start: 0.8027 (t70) cc_final: 0.7817 (t0) REVERT: A 383 LEU cc_start: 0.7771 (tt) cc_final: 0.7087 (tt) REVERT: A 448 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 476 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8998 (pm20) REVERT: A 504 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 532 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8448 (ttmt) REVERT: A 905 VAL cc_start: 0.8528 (t) cc_final: 0.8238 (p) REVERT: A 958 GLN cc_start: 0.7794 (pt0) cc_final: 0.7581 (pt0) REVERT: A 985 ASP cc_start: 0.8299 (m-30) cc_final: 0.8063 (m-30) REVERT: A 1046 GLU cc_start: 0.7994 (tt0) cc_final: 0.7502 (tp30) REVERT: A 1060 LYS cc_start: 0.8190 (tttt) cc_final: 0.7850 (ttpt) REVERT: A 1137 MET cc_start: 0.8567 (mmm) cc_final: 0.8280 (mmp) REVERT: A 1224 ASN cc_start: 0.7629 (m110) cc_final: 0.7201 (t0) REVERT: A 1330 GLN cc_start: 0.8461 (tt0) cc_final: 0.8138 (mt0) REVERT: A 1341 ASP cc_start: 0.8253 (t0) cc_final: 0.7949 (t0) REVERT: A 1416 ILE cc_start: 0.8511 (mt) cc_final: 0.8161 (tt) REVERT: A 1444 SER cc_start: 0.7816 (m) cc_final: 0.7304 (t) outliers start: 4 outliers final: 0 residues processed: 270 average time/residue: 0.2974 time to fit residues: 106.1285 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A 949 HIS A1088 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099371 restraints weight = 16741.177| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.84 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: 0.7824 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.145 Angle : 0.596 6.769 13390 Z= 0.312 Chirality : 0.041 0.171 1545 Planarity : 0.004 0.036 1628 Dihedral : 9.153 77.672 1470 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.83 % Allowed : 11.28 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1171 helix: 0.59 (0.18), residues: 752 sheet: -1.49 (0.60), residues: 67 loop : -1.72 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 882 HIS 0.005 0.001 HIS A 199 PHE 0.027 0.001 PHE A 236 TYR 0.016 0.001 TYR A 304 ARG 0.006 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.05394 ( 530) hydrogen bonds : angle 4.31767 ( 1569) covalent geometry : bond 0.00327 ( 9903) covalent geometry : angle 0.59636 (13390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8490 (mptt) cc_final: 0.8061 (tppt) REVERT: A 31 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7406 (ttm170) REVERT: A 51 GLU cc_start: 0.8674 (tp30) cc_final: 0.8402 (tp30) REVERT: A 68 LYS cc_start: 0.8675 (mttt) cc_final: 0.8410 (mtpp) REVERT: A 286 GLU cc_start: 0.8214 (tt0) cc_final: 0.7946 (mt-10) REVERT: A 362 TYR cc_start: 0.8342 (m-80) cc_final: 0.8075 (m-80) REVERT: A 469 MET cc_start: 0.8137 (mmm) cc_final: 0.7888 (mmp) REVERT: A 504 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 532 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8405 (tppt) REVERT: A 636 LEU cc_start: 0.9104 (tt) cc_final: 0.8738 (mt) REVERT: A 1046 GLU cc_start: 0.8241 (tt0) cc_final: 0.7870 (tp30) REVERT: A 1060 LYS cc_start: 0.8559 (tttt) cc_final: 0.8317 (ttpt) REVERT: A 1065 LEU cc_start: 0.8636 (mp) cc_final: 0.8408 (mt) REVERT: A 1224 ASN cc_start: 0.7931 (m110) cc_final: 0.7421 (t0) REVERT: A 1280 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 1341 ASP cc_start: 0.8447 (t0) cc_final: 0.8155 (t0) outliers start: 19 outliers final: 12 residues processed: 200 average time/residue: 0.2508 time to fit residues: 71.0284 Evaluate side-chains 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1404 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 GLN A1238 GLN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096585 restraints weight = 17206.393| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.79 r_work: 0.3066 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9903 Z= 0.148 Angle : 0.560 6.961 13390 Z= 0.288 Chirality : 0.040 0.157 1545 Planarity : 0.003 0.034 1628 Dihedral : 8.137 84.534 1467 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.99 % Allowed : 13.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1171 helix: 1.12 (0.19), residues: 747 sheet: -1.66 (0.58), residues: 69 loop : -1.41 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 882 HIS 0.005 0.001 HIS A1085 PHE 0.022 0.001 PHE A 236 TYR 0.015 0.001 TYR A 919 ARG 0.006 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 530) hydrogen bonds : angle 4.08674 ( 1569) covalent geometry : bond 0.00350 ( 9903) covalent geometry : angle 0.56022 (13390) *********************** 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 173 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8496 (mptt) cc_final: 0.8066 (tppt) REVERT: A 15 LEU cc_start: 0.8928 (tp) cc_final: 0.8510 (tt) REVERT: A 31 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7384 (ttm170) REVERT: A 51 GLU cc_start: 0.8713 (tp30) cc_final: 0.8450 (tp30) REVERT: A 68 LYS cc_start: 0.8726 (mttt) cc_final: 0.8490 (mtpp) REVERT: A 78 PHE cc_start: 0.8490 (t80) cc_final: 0.7940 (t80) REVERT: A 217 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 224 PHE cc_start: 0.8171 (m-80) cc_final: 0.7948 (m-80) REVERT: A 279 GLU cc_start: 0.8123 (mp0) cc_final: 0.7883 (mp0) REVERT: A 362 TYR cc_start: 0.8408 (m-80) cc_final: 0.8162 (m-80) REVERT: A 476 GLU cc_start: 0.8692 (mp0) cc_final: 0.8434 (pm20) REVERT: A 504 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 532 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8363 (tppt) REVERT: A 636 LEU cc_start: 0.9081 (tt) cc_final: 0.8781 (mt) REVERT: A 873 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: A 1059 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 1060 LYS cc_start: 0.8633 (tttt) cc_final: 0.8303 (ttpt) REVERT: A 1101 MET cc_start: 0.8504 (ttt) cc_final: 0.8291 (ttt) REVERT: A 1224 ASN cc_start: 0.7890 (m110) cc_final: 0.7352 (t0) REVERT: A 1280 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 1341 ASP cc_start: 0.8444 (t0) cc_final: 0.8174 (t0) outliers start: 31 outliers final: 20 residues processed: 166 average time/residue: 0.2413 time to fit residues: 58.7212 Evaluate side-chains 150 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 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 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1404 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100010 restraints weight = 16865.710| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.78 r_work: 0.3115 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9903 Z= 0.109 Angle : 0.501 6.747 13390 Z= 0.257 Chirality : 0.038 0.158 1545 Planarity : 0.003 0.033 1628 Dihedral : 6.834 70.858 1467 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.51 % Allowed : 14.27 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1171 helix: 1.39 (0.19), residues: 762 sheet: -1.46 (0.56), residues: 71 loop : -1.25 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.003 0.001 HIS A 199 PHE 0.018 0.001 PHE A 931 TYR 0.011 0.001 TYR A 517 ARG 0.005 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 530) hydrogen bonds : angle 3.85032 ( 1569) covalent geometry : bond 0.00237 ( 9903) covalent geometry : angle 0.50083 (13390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8530 (mptt) cc_final: 0.8099 (tppt) REVERT: A 15 LEU cc_start: 0.8888 (tp) cc_final: 0.8518 (tt) REVERT: A 31 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7383 (ttm170) REVERT: A 51 GLU cc_start: 0.8677 (tp30) cc_final: 0.8412 (tp30) REVERT: A 68 LYS cc_start: 0.8733 (mttt) cc_final: 0.8526 (mtpp) REVERT: A 78 PHE cc_start: 0.8348 (t80) cc_final: 0.7791 (t80) REVERT: A 217 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 249 ASP cc_start: 0.8581 (m-30) cc_final: 0.8370 (p0) REVERT: A 362 TYR cc_start: 0.8225 (m-80) cc_final: 0.7972 (m-80) REVERT: A 504 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 532 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8289 (tppt) REVERT: A 926 LEU cc_start: 0.8894 (mt) cc_final: 0.8465 (mt) REVERT: A 1101 MET cc_start: 0.8407 (ttt) cc_final: 0.8158 (ttt) REVERT: A 1224 ASN cc_start: 0.7829 (m110) cc_final: 0.7252 (t0) REVERT: A 1280 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 1341 ASP cc_start: 0.8232 (t0) cc_final: 0.7952 (t0) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 0.2034 time to fit residues: 49.4447 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.109206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.090756 restraints weight = 17659.999| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.83 r_work: 0.2960 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 9903 Z= 0.325 Angle : 0.688 8.185 13390 Z= 0.352 Chirality : 0.045 0.187 1545 Planarity : 0.004 0.034 1628 Dihedral : 7.311 66.251 1467 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.57 % Allowed : 14.95 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1171 helix: 0.94 (0.18), residues: 753 sheet: -1.46 (0.56), residues: 72 loop : -0.98 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1089 HIS 0.008 0.002 HIS A1054 PHE 0.021 0.002 PHE A 626 TYR 0.018 0.002 TYR A 919 ARG 0.005 0.001 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.06087 ( 530) hydrogen bonds : angle 4.34858 ( 1569) covalent geometry : bond 0.00796 ( 9903) covalent geometry : angle 0.68794 (13390) *********************** 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 162 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8746 (mptt) cc_final: 0.8301 (tppt) REVERT: A 31 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7696 (ttm170) REVERT: A 68 LYS cc_start: 0.8810 (mttt) cc_final: 0.8578 (mtpp) REVERT: A 217 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 279 GLU cc_start: 0.8309 (mp0) cc_final: 0.8044 (mp0) REVERT: A 362 TYR cc_start: 0.8552 (m-80) cc_final: 0.8334 (m-80) REVERT: A 476 GLU cc_start: 0.8793 (mp0) cc_final: 0.8465 (mp0) REVERT: A 504 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 532 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8326 (ttmm) REVERT: A 1224 ASN cc_start: 0.7822 (m110) cc_final: 0.7218 (t0) REVERT: A 1280 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 1330 GLN cc_start: 0.8738 (mt0) cc_final: 0.8375 (mt0) outliers start: 37 outliers final: 29 residues processed: 156 average time/residue: 0.2372 time to fit residues: 53.9161 Evaluate side-chains 145 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 106 optimal weight: 0.0030 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096227 restraints weight = 17286.431| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.81 r_work: 0.3057 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9903 Z= 0.117 Angle : 0.522 7.650 13390 Z= 0.265 Chirality : 0.038 0.152 1545 Planarity : 0.003 0.033 1628 Dihedral : 6.553 56.946 1467 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.70 % Allowed : 16.20 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1171 helix: 1.32 (0.19), residues: 761 sheet: -1.43 (0.53), residues: 76 loop : -1.08 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 882 HIS 0.005 0.001 HIS A 199 PHE 0.037 0.001 PHE A 626 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 530) hydrogen bonds : angle 3.93995 ( 1569) covalent geometry : bond 0.00259 ( 9903) covalent geometry : angle 0.52164 (13390) *********************** 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: 28 poor density : 131 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8621 (mptt) cc_final: 0.8261 (tppt) REVERT: A 31 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7623 (ttm170) REVERT: A 68 LYS cc_start: 0.8800 (mttt) cc_final: 0.8569 (mtpp) REVERT: A 78 PHE cc_start: 0.8459 (t80) cc_final: 0.7818 (t80) REVERT: A 217 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 249 ASP cc_start: 0.8667 (m-30) cc_final: 0.8340 (p0) REVERT: A 279 GLU cc_start: 0.8185 (mp0) cc_final: 0.7978 (mp0) REVERT: A 362 TYR cc_start: 0.8432 (m-80) cc_final: 0.8230 (m-80) REVERT: A 469 MET cc_start: 0.8172 (mmp) cc_final: 0.7827 (mmp) REVERT: A 476 GLU cc_start: 0.8792 (mp0) cc_final: 0.8475 (mp0) REVERT: A 504 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 532 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8347 (ttmm) REVERT: A 1224 ASN cc_start: 0.7863 (m110) cc_final: 0.7275 (t0) REVERT: A 1280 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 1330 GLN cc_start: 0.8588 (mt0) cc_final: 0.8181 (mt0) REVERT: A 1341 ASP cc_start: 0.8325 (t0) cc_final: 0.8049 (t0) outliers start: 28 outliers final: 19 residues processed: 154 average time/residue: 0.3150 time to fit residues: 71.9711 Evaluate side-chains 140 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER 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 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 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096222 restraints weight = 17204.943| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.80 r_work: 0.3065 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4318 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= 0.121 Angle : 0.513 6.974 13390 Z= 0.260 Chirality : 0.038 0.157 1545 Planarity : 0.003 0.033 1628 Dihedral : 6.332 54.694 1467 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.51 % Allowed : 16.97 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1171 helix: 1.44 (0.19), residues: 762 sheet: -1.35 (0.52), residues: 77 loop : -0.96 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.024 0.001 PHE A 626 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 530) hydrogen bonds : angle 3.86215 ( 1569) covalent geometry : bond 0.00277 ( 9903) covalent geometry : angle 0.51349 (13390) *********************** 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 154 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8575 (mptt) cc_final: 0.8221 (tppt) REVERT: A 31 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7480 (ttm170) REVERT: A 68 LYS cc_start: 0.8794 (mttt) cc_final: 0.8584 (mttm) REVERT: A 217 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8003 (tm-30) REVERT: A 279 GLU cc_start: 0.8181 (mp0) cc_final: 0.7974 (mp0) REVERT: A 362 TYR cc_start: 0.8384 (m-80) cc_final: 0.8181 (m-80) REVERT: A 469 MET cc_start: 0.8168 (mmp) cc_final: 0.7784 (mmp) REVERT: A 476 GLU cc_start: 0.8861 (mp0) cc_final: 0.8513 (pm20) REVERT: A 504 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 532 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8306 (ttmm) REVERT: A 1224 ASN cc_start: 0.7879 (m110) cc_final: 0.7304 (t0) REVERT: A 1280 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 1330 GLN cc_start: 0.8618 (mt0) cc_final: 0.8190 (mt0) outliers start: 26 outliers final: 20 residues processed: 146 average time/residue: 0.2500 time to fit residues: 54.7641 Evaluate side-chains 147 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 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 = 0.3452 r_free = 0.3452 target = 0.114707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.096543 restraints weight = 17350.987| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.84 r_work: 0.3071 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4415 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= 0.123 Angle : 0.534 9.586 13390 Z= 0.265 Chirality : 0.038 0.157 1545 Planarity : 0.003 0.033 1628 Dihedral : 6.179 57.151 1467 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.60 % Allowed : 17.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1171 helix: 1.51 (0.19), residues: 761 sheet: -1.21 (0.53), residues: 75 loop : -0.89 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.021 0.001 PHE A 626 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 530) hydrogen bonds : angle 3.88070 ( 1569) covalent geometry : bond 0.00284 ( 9903) covalent geometry : angle 0.53352 (13390) *********************** 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: 27 poor density : 131 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8601 (mptt) cc_final: 0.8287 (tppt) REVERT: A 31 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7569 (ttm170) REVERT: A 68 LYS cc_start: 0.8821 (mttt) cc_final: 0.8579 (mttm) REVERT: A 78 PHE cc_start: 0.8462 (t80) cc_final: 0.7895 (t80) REVERT: A 217 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 279 GLU cc_start: 0.8162 (mp0) cc_final: 0.7953 (mp0) REVERT: A 362 TYR cc_start: 0.8392 (m-80) cc_final: 0.8188 (m-80) REVERT: A 469 MET cc_start: 0.8156 (mmp) cc_final: 0.7771 (mmp) REVERT: A 476 GLU cc_start: 0.8814 (mp0) cc_final: 0.8506 (mp0) REVERT: A 504 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 532 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8537 (ttmt) REVERT: A 1224 ASN cc_start: 0.8003 (m110) cc_final: 0.7528 (t0) REVERT: A 1280 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 1341 ASP cc_start: 0.8283 (t0) cc_final: 0.8016 (t0) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.2152 time to fit residues: 48.4153 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 : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 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 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096322 restraints weight = 17321.851| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.80 r_work: 0.3060 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4482 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= 0.131 Angle : 0.541 9.046 13390 Z= 0.269 Chirality : 0.039 0.156 1545 Planarity : 0.003 0.032 1628 Dihedral : 6.031 55.169 1467 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.31 % Allowed : 18.32 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1171 helix: 1.52 (0.19), residues: 761 sheet: -1.21 (0.52), residues: 75 loop : -0.89 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.019 0.001 PHE A 236 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 530) hydrogen bonds : angle 3.90354 ( 1569) covalent geometry : bond 0.00308 ( 9903) covalent geometry : angle 0.54112 (13390) *********************** 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 153 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8603 (mptt) cc_final: 0.8317 (tppt) REVERT: A 31 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7642 (ttm170) REVERT: A 68 LYS cc_start: 0.8860 (mttt) cc_final: 0.8631 (mttm) REVERT: A 78 PHE cc_start: 0.8517 (t80) cc_final: 0.7971 (t80) REVERT: A 217 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 279 GLU cc_start: 0.8175 (mp0) cc_final: 0.7972 (mp0) REVERT: A 362 TYR cc_start: 0.8465 (m-80) cc_final: 0.8246 (m-80) REVERT: A 476 GLU cc_start: 0.8796 (mp0) cc_final: 0.8504 (mp0) REVERT: A 532 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8505 (ttmt) REVERT: A 1224 ASN cc_start: 0.8044 (m110) cc_final: 0.7578 (t0) REVERT: A 1280 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 1330 GLN cc_start: 0.8639 (mt0) cc_final: 0.8362 (mt0) REVERT: A 1341 ASP cc_start: 0.8319 (t0) cc_final: 0.8071 (t0) outliers start: 24 outliers final: 24 residues processed: 145 average time/residue: 0.1951 time to fit residues: 41.6317 Evaluate side-chains 149 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 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 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097447 restraints weight = 17331.335| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.83 r_work: 0.3088 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4557 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= 0.115 Angle : 0.535 9.068 13390 Z= 0.263 Chirality : 0.038 0.156 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.775 58.247 1467 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.93 % Allowed : 18.51 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1171 helix: 1.61 (0.19), residues: 755 sheet: -1.15 (0.53), residues: 75 loop : -0.79 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.019 0.001 PHE A 236 TYR 0.010 0.001 TYR A1381 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 530) hydrogen bonds : angle 3.85168 ( 1569) covalent geometry : bond 0.00261 ( 9903) covalent geometry : angle 0.53514 (13390) ********************** 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 153 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8553 (mptt) cc_final: 0.8281 (tppt) REVERT: A 31 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7547 (ttm170) REVERT: A 68 LYS cc_start: 0.8820 (mttt) cc_final: 0.8593 (mttm) REVERT: A 78 PHE cc_start: 0.8470 (t80) cc_final: 0.7944 (t80) REVERT: A 212 MET cc_start: 0.7727 (tpp) cc_final: 0.7413 (mmt) REVERT: A 217 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 279 GLU cc_start: 0.8138 (mp0) cc_final: 0.7931 (mp0) REVERT: A 362 TYR cc_start: 0.8384 (m-80) cc_final: 0.8183 (m-80) REVERT: A 476 GLU cc_start: 0.8848 (mp0) cc_final: 0.8539 (mp0) REVERT: A 532 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8493 (ttmt) REVERT: A 1166 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 1224 ASN cc_start: 0.7999 (m110) cc_final: 0.7505 (t0) REVERT: A 1277 ILE cc_start: 0.8709 (tp) cc_final: 0.8221 (tt) REVERT: A 1280 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 1341 ASP cc_start: 0.8249 (t0) cc_final: 0.7977 (t0) outliers start: 20 outliers final: 19 residues processed: 147 average time/residue: 0.2030 time to fit residues: 43.8922 Evaluate side-chains 148 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1273 SER Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094923 restraints weight = 17444.898| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.82 r_work: 0.3042 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9903 Z= 0.147 Angle : 0.556 8.907 13390 Z= 0.275 Chirality : 0.039 0.156 1545 Planarity : 0.003 0.032 1628 Dihedral : 5.818 55.194 1467 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.12 % Allowed : 18.61 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1171 helix: 1.52 (0.19), residues: 757 sheet: -1.21 (0.52), residues: 75 loop : -0.75 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1089 HIS 0.005 0.001 HIS A1054 PHE 0.019 0.001 PHE A 236 TYR 0.012 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 530) hydrogen bonds : angle 3.93618 ( 1569) covalent geometry : bond 0.00352 ( 9903) covalent geometry : angle 0.55556 (13390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.13 seconds wall clock time: 77 minutes 51.18 seconds (4671.18 seconds total)