Starting phenix.real_space_refine on Mon Jun 9 05:50:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.map" model { file = "/net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sv7_25445/06_2025/7sv7_25445.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6345 2.51 5 N 1585 2.21 5 O 1685 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9334 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 32, 'TRANS': 1140} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 48 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: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 254 Unusual residues: {' MG': 2, 'ATP': 2, 'C14': 1, 'CLR': 2, 'CV6': 1, 'D12': 4, 'DD9': 2, 'PJ8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 6.85, per 1000 atoms: 0.71 Number of scatterers: 9673 At special positions: 0 Unit cell: (81.37, 83.43, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1685 8.00 N 1585 7.00 C 6345 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 70.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.582A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.662A pdb=" N ILE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 64 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.644A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.960A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.189A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.532A pdb=" N SER A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.688A pdb=" N ILE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.649A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.745A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.748A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.762A 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 217 Proline residue: A 205 - end of helix removed outlier: 3.689A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.901A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 309 removed outlier: 4.089A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 313 through 329 Proline residue: A 324 - end of helix removed outlier: 3.826A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.462A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.579A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.850A pdb=" N LEU A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.368A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 927 removed outlier: 3.818A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 958 removed outlier: 3.525A pdb=" N ILE A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 943 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.701A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 986 removed outlier: 4.143A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 removed outlier: 3.565A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1047 Proline residue: A1021 - end of helix removed outlier: 3.618A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.509A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.524A pdb=" N ALA A1067 " --> pdb=" O TRP A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1122 removed outlier: 3.512A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1168 removed outlier: 3.783A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 4.039A 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: 3.648A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1331 removed outlier: 4.106A pdb=" N PHE A1331 " --> pdb=" O VAL A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.549A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 3.616A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1409 " --> pdb=" O ALA A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 3.563A pdb=" N ARG A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1440 removed outlier: 3.632A pdb=" N ALA A1440 " --> pdb=" O LEU A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 3.558A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 6.292A pdb=" N ILE A 331 " --> pdb=" O ILE A 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.847A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 397 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A 479 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.548A pdb=" N LEU A 454 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 5.554A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE A1232 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS A1213 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE A1234 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N THR A1211 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL A1212 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN A1268 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.261A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP A1370 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 3.08 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: 2955 1.34 - 1.46: 1602 1.46 - 1.58: 5226 1.58 - 1.69: 10 1.69 - 1.81: 79 Bond restraints: 9872 Sorted by residual: bond pdb=" O5' ATP A1503 " pdb=" PA ATP A1503 " ideal model delta sigma weight residual 1.579 1.641 -0.062 1.10e-02 8.26e+03 3.17e+01 bond pdb=" O5' ATP A1504 " pdb=" PA ATP A1504 " ideal model delta sigma weight residual 1.579 1.638 -0.059 1.10e-02 8.26e+03 2.84e+01 bond pdb=" O2A ATP A1503 " pdb=" PA ATP A1503 " ideal model delta sigma weight residual 1.529 1.567 -0.038 2.20e-02 2.07e+03 2.99e+00 bond pdb=" C25 CV6 A1515 " pdb=" F1 CV6 A1515 " ideal model delta sigma weight residual 1.348 1.317 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C16 CV6 A1515 " pdb=" C19 CV6 A1515 " ideal model delta sigma weight residual 1.498 1.528 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.40: 13337 8.40 - 16.79: 5 16.79 - 25.19: 2 25.19 - 33.58: 0 33.58 - 41.98: 4 Bond angle restraints: 13348 Sorted by residual: angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 72.44 41.98 3.53e+00 8.04e-02 1.42e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 69.89 40.76 3.49e+00 8.21e-02 1.36e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.33 40.09 3.53e+00 8.04e-02 1.29e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 71.66 38.99 3.49e+00 8.21e-02 1.25e+02 angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 130.34 9.53 1.00e+00 1.00e+00 9.09e+01 ... (remaining 13343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5588 18.00 - 36.00: 334 36.00 - 53.99: 89 53.99 - 71.99: 14 71.99 - 89.99: 6 Dihedral angle restraints: 6031 sinusoidal: 2575 harmonic: 3456 Sorted by residual: dihedral pdb=" CA LYS A 536 " pdb=" C LYS A 536 " pdb=" N ASP A 537 " pdb=" CA ASP A 537 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASN A1432 " pdb=" CB ASN A1432 " pdb=" CG ASN A1432 " pdb=" OD1 ASN A1432 " ideal model delta sinusoidal sigma weight residual 120.00 -173.28 -66.72 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA GLU A 267 " pdb=" CB GLU A 267 " pdb=" CG GLU A 267 " pdb=" CD GLU A 267 " ideal model delta sinusoidal sigma weight residual 60.00 117.04 -57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 6028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 992 0.033 - 0.066: 431 0.066 - 0.099: 75 0.099 - 0.133: 37 0.133 - 0.166: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C16 CV6 A1515 " pdb=" C15 CV6 A1515 " pdb=" C17 CV6 A1515 " pdb=" C19 CV6 A1515 " both_signs ideal model delta sigma weight residual True 1.48 1.64 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE A 448 " pdb=" N ILE A 448 " pdb=" C ILE A 448 " pdb=" CB ILE A 448 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A1366 " pdb=" N ILE A1366 " pdb=" C ILE A1366 " pdb=" CB ILE A1366 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1533 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 CV6 A1515 " 0.072 2.00e-02 2.50e+03 1.16e-01 3.05e+02 pdb=" C19 CV6 A1515 " 0.028 2.00e-02 2.50e+03 pdb=" C20 CV6 A1515 " -0.094 2.00e-02 2.50e+03 pdb=" C21 CV6 A1515 " -0.187 2.00e-02 2.50e+03 pdb=" C22 CV6 A1515 " -0.156 2.00e-02 2.50e+03 pdb=" C23 CV6 A1515 " -0.022 2.00e-02 2.50e+03 pdb=" C24 CV6 A1515 " 0.069 2.00e-02 2.50e+03 pdb=" O4 CV6 A1515 " 0.126 2.00e-02 2.50e+03 pdb=" O5 CV6 A1515 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N CV6 A1515 " -0.026 2.00e-02 2.50e+03 6.31e-02 1.29e+02 pdb=" C1 CV6 A1515 " 0.155 2.00e-02 2.50e+03 pdb=" C10 CV6 A1515 " 0.015 2.00e-02 2.50e+03 pdb=" C11 CV6 A1515 " -0.026 2.00e-02 2.50e+03 pdb=" C12 CV6 A1515 " -0.108 2.00e-02 2.50e+03 pdb=" C4 CV6 A1515 " 0.001 2.00e-02 2.50e+03 pdb=" C5 CV6 A1515 " -0.033 2.00e-02 2.50e+03 pdb=" C6 CV6 A1515 " -0.042 2.00e-02 2.50e+03 pdb=" C7 CV6 A1515 " -0.041 2.00e-02 2.50e+03 pdb=" C8 CV6 A1515 " -0.005 2.00e-02 2.50e+03 pdb=" C9 CV6 A1515 " 0.032 2.00e-02 2.50e+03 pdb=" F CV6 A1515 " 0.093 2.00e-02 2.50e+03 pdb=" N1 CV6 A1515 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 CV6 A1515 " -0.003 2.00e-02 2.50e+03 1.35e-02 2.29e+00 pdb=" C16 CV6 A1515 " 0.011 2.00e-02 2.50e+03 pdb=" C8 CV6 A1515 " 0.016 2.00e-02 2.50e+03 pdb=" N1 CV6 A1515 " -0.023 2.00e-02 2.50e+03 pdb=" O3 CV6 A1515 " -0.002 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 18 2.58 - 3.16: 7888 3.16 - 3.74: 14182 3.74 - 4.32: 19601 4.32 - 4.90: 32726 Nonbonded interactions: 74415 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.003 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 2.026 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.133 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.261 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.277 2.170 ... (remaining 74410 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 group one per residue 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: 2.690 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.090 Find NCS groups from input model: 0.100 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.003 0.062 9872 Z= 0.154 Angle : 0.939 41.979 13348 Z= 0.386 Chirality : 0.038 0.166 1536 Planarity : 0.004 0.116 1608 Dihedral : 12.830 89.990 3795 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.69 % Allowed : 3.56 % Favored : 95.74 % 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: -0.82 (0.23), residues: 1163 helix: -0.21 (0.18), residues: 746 sheet: -1.41 (0.51), residues: 79 loop : -0.73 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1274 HIS 0.002 0.001 HIS A1085 PHE 0.010 0.001 PHE A 931 TYR 0.011 0.001 TYR A 517 ARG 0.003 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.21443 ( 554) hydrogen bonds : angle 6.55825 ( 1641) covalent geometry : bond 0.00297 ( 9872) covalent geometry : angle 0.93933 (13348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 1.080 Fit side-chains REVERT: A 3 ARG cc_start: 0.7250 (ptt90) cc_final: 0.7008 (ptt180) REVERT: A 190 LYS cc_start: 0.9011 (ttpt) cc_final: 0.7949 (mttt) REVERT: A 216 TRP cc_start: 0.8646 (t60) cc_final: 0.8441 (t60) REVERT: A 503 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8023 (ttmm) REVERT: A 525 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: A 529 ASP cc_start: 0.8635 (m-30) cc_final: 0.8352 (m-30) REVERT: A 606 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8604 (mmmm) REVERT: A 611 LYS cc_start: 0.7869 (mmtp) cc_final: 0.7517 (tttm) REVERT: A 629 THR cc_start: 0.7366 (m) cc_final: 0.6883 (p) REVERT: A 1045 SER cc_start: 0.8904 (t) cc_final: 0.8611 (p) REVERT: A 1063 TRP cc_start: 0.8681 (m-10) cc_final: 0.8476 (m-90) REVERT: A 1103 ILE cc_start: 0.9417 (tp) cc_final: 0.9043 (tp) REVERT: A 1145 TRP cc_start: 0.8412 (t60) cc_final: 0.8202 (t60) REVERT: A 1213 LYS cc_start: 0.8124 (mttt) cc_final: 0.7380 (tptt) REVERT: A 1219 TYR cc_start: 0.8314 (m-80) cc_final: 0.7914 (m-80) REVERT: A 1243 LEU cc_start: 0.8166 (pp) cc_final: 0.7444 (mp) REVERT: A 1273 SER cc_start: 0.8870 (t) cc_final: 0.8411 (m) REVERT: A 1317 LYS cc_start: 0.8546 (tptt) cc_final: 0.8021 (tptt) REVERT: A 1401 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 1407 MET cc_start: 0.8162 (mmp) cc_final: 0.7713 (mtp) REVERT: A 1423 GLN cc_start: 0.7654 (pt0) cc_final: 0.7428 (pp30) REVERT: A 1439 GLN cc_start: 0.7022 (mm110) cc_final: 0.6214 (pp30) outliers start: 7 outliers final: 1 residues processed: 223 average time/residue: 0.2480 time to fit residues: 76.8568 Evaluate side-chains 139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 GLN Chi-restraints excluded: chain A residue 1114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 268 ASN A 287 ASN A 290 GLN A 372 GLN A 378 GLN A 525 GLN A 609 HIS A1035 GLN A1039 GLN A1054 HIS A1100 GLN A1148 ASN A1281 GLN A1412 GLN A1419 ASN A1423 GLN A1432 ASN A1439 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118249 restraints weight = 14234.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121761 restraints weight = 7283.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123327 restraints weight = 4254.085| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9872 Z= 0.138 Angle : 0.555 7.431 13348 Z= 0.285 Chirality : 0.041 0.190 1536 Planarity : 0.004 0.033 1608 Dihedral : 7.803 75.343 1593 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.78 % Allowed : 11.09 % Favored : 87.13 % 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: 0.02 (0.24), residues: 1163 helix: 0.60 (0.19), residues: 757 sheet: -1.36 (0.51), residues: 79 loop : -0.77 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1274 HIS 0.003 0.001 HIS A 954 PHE 0.024 0.002 PHE A 236 TYR 0.019 0.001 TYR A 380 ARG 0.005 0.000 ARG A1259 Details of bonding type rmsd hydrogen bonds : bond 0.05248 ( 554) hydrogen bonds : angle 4.27646 ( 1641) covalent geometry : bond 0.00299 ( 9872) covalent geometry : angle 0.55500 (13348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.104 Fit side-chains REVERT: A 125 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 129 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7740 (mp) REVERT: A 145 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 190 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8038 (mttt) REVERT: A 265 MET cc_start: 0.8332 (tmm) cc_final: 0.8067 (tmm) REVERT: A 503 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7922 (ttmm) REVERT: A 525 GLN cc_start: 0.7897 (mp10) cc_final: 0.7605 (mp10) REVERT: A 629 THR cc_start: 0.7731 (m) cc_final: 0.7369 (p) REVERT: A 1213 LYS cc_start: 0.8044 (mttt) cc_final: 0.7349 (tptt) REVERT: A 1219 TYR cc_start: 0.8341 (m-80) cc_final: 0.8133 (m-80) REVERT: A 1273 SER cc_start: 0.8700 (t) cc_final: 0.8394 (m) REVERT: A 1377 ASP cc_start: 0.7321 (p0) cc_final: 0.6970 (p0) REVERT: A 1401 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7669 (tp30) REVERT: A 1439 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6265 (pp30) outliers start: 18 outliers final: 7 residues processed: 161 average time/residue: 0.2042 time to fit residues: 47.7280 Evaluate side-chains 134 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 207 GLN A 268 ASN A1054 HIS A1411 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.137332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120594 restraints weight = 14464.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123903 restraints weight = 7632.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126207 restraints weight = 4394.729| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9872 Z= 0.119 Angle : 0.512 8.083 13348 Z= 0.262 Chirality : 0.040 0.170 1536 Planarity : 0.003 0.031 1608 Dihedral : 7.504 76.763 1590 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.77 % Allowed : 11.98 % Favored : 85.25 % 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: 0.54 (0.25), residues: 1163 helix: 1.02 (0.19), residues: 756 sheet: -0.85 (0.56), residues: 68 loop : -0.73 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1145 HIS 0.002 0.001 HIS A 199 PHE 0.021 0.001 PHE A 236 TYR 0.017 0.001 TYR A 380 ARG 0.002 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 554) hydrogen bonds : angle 3.97014 ( 1641) covalent geometry : bond 0.00258 ( 9872) covalent geometry : angle 0.51236 (13348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.027 Fit side-chains REVERT: A 125 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 190 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8006 (mttt) REVERT: A 265 MET cc_start: 0.8436 (tmm) cc_final: 0.8206 (tmm) REVERT: A 381 LYS cc_start: 0.8077 (pttt) cc_final: 0.7874 (pttt) REVERT: A 476 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 503 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7912 (ttmm) REVERT: A 525 GLN cc_start: 0.7897 (mp10) cc_final: 0.7559 (mp10) REVERT: A 629 THR cc_start: 0.7783 (m) cc_final: 0.7394 (p) REVERT: A 1213 LYS cc_start: 0.8057 (mttt) cc_final: 0.7304 (tptt) REVERT: A 1273 SER cc_start: 0.8816 (t) cc_final: 0.8543 (m) REVERT: A 1377 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6988 (p0) REVERT: A 1401 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7335 (mm-30) REVERT: A 1407 MET cc_start: 0.7881 (mmm) cc_final: 0.7414 (mtt) REVERT: A 1439 GLN cc_start: 0.6918 (mm-40) cc_final: 0.6313 (pp30) outliers start: 28 outliers final: 16 residues processed: 154 average time/residue: 0.1892 time to fit residues: 43.0528 Evaluate side-chains 144 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.0770 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120377 restraints weight = 14170.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123708 restraints weight = 7512.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125948 restraints weight = 4311.137| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9872 Z= 0.102 Angle : 0.484 7.107 13348 Z= 0.247 Chirality : 0.039 0.173 1536 Planarity : 0.003 0.031 1608 Dihedral : 7.103 77.131 1590 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 14.46 % Favored : 83.56 % 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: 0.88 (0.25), residues: 1163 helix: 1.31 (0.19), residues: 758 sheet: -0.79 (0.54), residues: 78 loop : -0.65 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.002 0.000 HIS A 199 PHE 0.019 0.001 PHE A 236 TYR 0.015 0.001 TYR A1219 ARG 0.002 0.000 ARG A1259 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 554) hydrogen bonds : angle 3.80524 ( 1641) covalent geometry : bond 0.00207 ( 9872) covalent geometry : angle 0.48357 (13348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.113 Fit side-chains REVERT: A 190 LYS cc_start: 0.8934 (ttpt) cc_final: 0.7969 (mttt) REVERT: A 381 LYS cc_start: 0.8079 (pttt) cc_final: 0.7835 (pttt) REVERT: A 476 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 503 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7895 (ttmm) REVERT: A 525 GLN cc_start: 0.7846 (mp10) cc_final: 0.7456 (mp10) REVERT: A 629 THR cc_start: 0.7753 (m) cc_final: 0.7356 (p) REVERT: A 1042 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: A 1103 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9182 (tp) REVERT: A 1213 LYS cc_start: 0.7968 (mttt) cc_final: 0.7212 (tptt) REVERT: A 1273 SER cc_start: 0.8833 (t) cc_final: 0.8543 (m) REVERT: A 1377 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6904 (p0) REVERT: A 1401 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7350 (mm-30) REVERT: A 1407 MET cc_start: 0.7856 (mmm) cc_final: 0.7420 (mtt) REVERT: A 1439 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6285 (pp30) outliers start: 20 outliers final: 13 residues processed: 154 average time/residue: 0.2016 time to fit residues: 45.3656 Evaluate side-chains 142 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1377 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.0270 chunk 94 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 220 GLN A 376 GLN A1054 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118263 restraints weight = 14488.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121473 restraints weight = 7798.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123813 restraints weight = 4587.742| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9872 Z= 0.149 Angle : 0.532 6.478 13348 Z= 0.270 Chirality : 0.041 0.204 1536 Planarity : 0.003 0.033 1608 Dihedral : 7.136 74.838 1590 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.17 % Allowed : 14.75 % Favored : 82.08 % 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: 0.79 (0.25), residues: 1163 helix: 1.24 (0.19), residues: 762 sheet: -1.10 (0.51), residues: 78 loop : -0.64 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.002 0.001 HIS A 146 PHE 0.019 0.002 PHE A1107 TYR 0.014 0.001 TYR A 380 ARG 0.006 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 554) hydrogen bonds : angle 3.85822 ( 1641) covalent geometry : bond 0.00347 ( 9872) covalent geometry : angle 0.53160 (13348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.091 Fit side-chains REVERT: A 165 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 190 LYS cc_start: 0.8890 (ttpt) cc_final: 0.7921 (mttt) REVERT: A 244 MET cc_start: 0.8277 (tmm) cc_final: 0.8077 (tmm) REVERT: A 381 LYS cc_start: 0.7994 (pttt) cc_final: 0.7784 (pttt) REVERT: A 476 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 503 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7910 (ttmm) REVERT: A 525 GLN cc_start: 0.7937 (mp10) cc_final: 0.7528 (mp10) REVERT: A 629 THR cc_start: 0.7812 (m) cc_final: 0.7417 (p) REVERT: A 1042 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7959 (tp40) REVERT: A 1213 LYS cc_start: 0.8044 (mttt) cc_final: 0.7184 (tptt) REVERT: A 1377 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7093 (p0) REVERT: A 1401 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7483 (mm-30) REVERT: A 1407 MET cc_start: 0.7676 (mmm) cc_final: 0.7424 (mtt) REVERT: A 1421 VAL cc_start: 0.8810 (m) cc_final: 0.8566 (t) REVERT: A 1439 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6387 (pp30) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.1936 time to fit residues: 44.8781 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1268 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118610 restraints weight = 14235.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121899 restraints weight = 7416.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124075 restraints weight = 4270.877| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9872 Z= 0.111 Angle : 0.496 7.411 13348 Z= 0.252 Chirality : 0.040 0.180 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.879 74.001 1590 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.17 % Allowed : 15.35 % 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: 0.97 (0.25), residues: 1163 helix: 1.42 (0.19), residues: 760 sheet: -0.97 (0.51), residues: 78 loop : -0.69 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1145 HIS 0.003 0.001 HIS A 199 PHE 0.022 0.001 PHE A 931 TYR 0.013 0.001 TYR A 380 ARG 0.004 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 554) hydrogen bonds : angle 3.72194 ( 1641) covalent geometry : bond 0.00247 ( 9872) covalent geometry : angle 0.49623 (13348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.029 Fit side-chains REVERT: A 165 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 190 LYS cc_start: 0.8882 (ttpt) cc_final: 0.7957 (mttt) REVERT: A 212 MET cc_start: 0.7883 (mmm) cc_final: 0.7476 (mmm) REVERT: A 244 MET cc_start: 0.8324 (tmm) cc_final: 0.8102 (tmm) REVERT: A 381 LYS cc_start: 0.8039 (pttt) cc_final: 0.7832 (pttt) REVERT: A 476 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 503 LYS cc_start: 0.8243 (ttpt) cc_final: 0.7942 (ttmm) REVERT: A 629 THR cc_start: 0.7831 (m) cc_final: 0.7460 (p) REVERT: A 1042 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8034 (tp40) REVERT: A 1103 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9161 (tp) REVERT: A 1213 LYS cc_start: 0.8008 (mttt) cc_final: 0.7213 (tptt) REVERT: A 1377 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7081 (p0) REVERT: A 1401 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 1439 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6403 (pp30) outliers start: 32 outliers final: 21 residues processed: 154 average time/residue: 0.1998 time to fit residues: 45.6248 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1435 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118877 restraints weight = 14514.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122212 restraints weight = 7567.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124402 restraints weight = 4362.603| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9872 Z= 0.109 Angle : 0.490 7.562 13348 Z= 0.248 Chirality : 0.039 0.173 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.692 73.425 1590 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.17 % Allowed : 16.14 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1163 helix: 1.47 (0.19), residues: 765 sheet: -0.86 (0.50), residues: 84 loop : -0.58 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1145 HIS 0.002 0.000 HIS A 199 PHE 0.021 0.001 PHE A 931 TYR 0.012 0.001 TYR A 380 ARG 0.003 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 554) hydrogen bonds : angle 3.69041 ( 1641) covalent geometry : bond 0.00241 ( 9872) covalent geometry : angle 0.48966 (13348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.131 Fit side-chains REVERT: A 165 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 190 LYS cc_start: 0.8876 (ttpt) cc_final: 0.7982 (mttt) REVERT: A 212 MET cc_start: 0.7852 (mmm) cc_final: 0.7495 (mmm) REVERT: A 281 MET cc_start: 0.8373 (mmp) cc_final: 0.8167 (mmm) REVERT: A 381 LYS cc_start: 0.8026 (pttt) cc_final: 0.7731 (pttt) REVERT: A 503 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7974 (ttmm) REVERT: A 525 GLN cc_start: 0.7996 (mp10) cc_final: 0.7620 (mp10) REVERT: A 629 THR cc_start: 0.7931 (m) cc_final: 0.7509 (p) REVERT: A 1042 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8035 (tp40) REVERT: A 1103 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9196 (tp) REVERT: A 1213 LYS cc_start: 0.7981 (mttt) cc_final: 0.7221 (tptt) REVERT: A 1377 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7078 (p0) REVERT: A 1401 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7400 (mm-30) REVERT: A 1439 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6474 (pp30) outliers start: 32 outliers final: 26 residues processed: 150 average time/residue: 0.2107 time to fit residues: 48.1802 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1268 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 220 GLN A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119659 restraints weight = 14418.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.123052 restraints weight = 7492.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125241 restraints weight = 4320.390| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9872 Z= 0.107 Angle : 0.493 6.758 13348 Z= 0.250 Chirality : 0.040 0.171 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.552 72.751 1590 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.37 % Allowed : 16.44 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1163 helix: 1.48 (0.19), residues: 771 sheet: -0.78 (0.54), residues: 75 loop : -0.48 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 865 HIS 0.002 0.001 HIS A 199 PHE 0.021 0.001 PHE A 931 TYR 0.012 0.001 TYR A 380 ARG 0.004 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 554) hydrogen bonds : angle 3.65041 ( 1641) covalent geometry : bond 0.00238 ( 9872) covalent geometry : angle 0.49277 (13348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.034 Fit side-chains REVERT: A 165 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8412 (tp) REVERT: A 190 LYS cc_start: 0.8826 (ttpt) cc_final: 0.7969 (mttt) REVERT: A 503 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7908 (ttmm) REVERT: A 629 THR cc_start: 0.7928 (m) cc_final: 0.7500 (p) REVERT: A 1042 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8010 (tp40) REVERT: A 1103 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9166 (tp) REVERT: A 1213 LYS cc_start: 0.7995 (mttt) cc_final: 0.7222 (tptt) REVERT: A 1377 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7103 (p0) REVERT: A 1401 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 1439 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6458 (pp30) outliers start: 34 outliers final: 26 residues processed: 150 average time/residue: 0.1991 time to fit residues: 43.8307 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1435 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118605 restraints weight = 14452.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.121977 restraints weight = 7489.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124494 restraints weight = 4334.036| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9872 Z= 0.123 Angle : 0.516 7.644 13348 Z= 0.258 Chirality : 0.040 0.179 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.594 71.766 1590 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.27 % Allowed : 16.14 % Favored : 80.59 % 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: 1.16 (0.25), residues: 1163 helix: 1.48 (0.19), residues: 770 sheet: -0.84 (0.53), residues: 75 loop : -0.45 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1145 HIS 0.002 0.001 HIS A 199 PHE 0.022 0.001 PHE A 931 TYR 0.013 0.001 TYR A1381 ARG 0.003 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 554) hydrogen bonds : angle 3.68331 ( 1641) covalent geometry : bond 0.00285 ( 9872) covalent geometry : angle 0.51645 (13348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.200 Fit side-chains REVERT: A 165 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 190 LYS cc_start: 0.8773 (ttpt) cc_final: 0.7906 (mttt) REVERT: A 503 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7922 (ttmm) REVERT: A 629 THR cc_start: 0.7941 (m) cc_final: 0.7512 (p) REVERT: A 1042 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8003 (tp40) REVERT: A 1103 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9133 (tp) REVERT: A 1166 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 1213 LYS cc_start: 0.8010 (mttt) cc_final: 0.7197 (tptt) REVERT: A 1377 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7142 (p0) REVERT: A 1401 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 1413 PHE cc_start: 0.8927 (m-80) cc_final: 0.8702 (m-10) REVERT: A 1439 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6530 (pp30) outliers start: 33 outliers final: 26 residues processed: 146 average time/residue: 0.2191 time to fit residues: 48.6191 Evaluate side-chains 149 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1261 LEU Chi-restraints excluded: chain A residue 1268 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 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 220 GLN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120282 restraints weight = 14510.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.123647 restraints weight = 7620.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125998 restraints weight = 4451.164| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9872 Z= 0.106 Angle : 0.491 7.010 13348 Z= 0.247 Chirality : 0.040 0.267 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.451 71.066 1590 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.97 % Allowed : 16.93 % Favored : 80.10 % 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: 1.28 (0.25), residues: 1163 helix: 1.59 (0.19), residues: 770 sheet: -0.67 (0.58), residues: 65 loop : -0.52 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1145 HIS 0.003 0.001 HIS A 199 PHE 0.022 0.001 PHE A 931 TYR 0.014 0.001 TYR A1381 ARG 0.003 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 554) hydrogen bonds : angle 3.62576 ( 1641) covalent geometry : bond 0.00235 ( 9872) covalent geometry : angle 0.49135 (13348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.176 Fit side-chains REVERT: A 165 LEU cc_start: 0.8660 (mm) cc_final: 0.8329 (tp) REVERT: A 190 LYS cc_start: 0.8766 (ttpt) cc_final: 0.7909 (mttt) REVERT: A 503 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7981 (ttmm) REVERT: A 629 THR cc_start: 0.7900 (m) cc_final: 0.7476 (p) REVERT: A 1042 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7961 (tp40) REVERT: A 1103 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9148 (tp) REVERT: A 1166 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6517 (t80) REVERT: A 1213 LYS cc_start: 0.8010 (mttt) cc_final: 0.7230 (tptt) REVERT: A 1377 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7090 (p0) REVERT: A 1439 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6557 (pp30) outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 0.2346 time to fit residues: 49.9483 Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1261 LEU Chi-restraints excluded: chain A residue 1268 GLN Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 220 GLN A1371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120248 restraints weight = 14452.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123737 restraints weight = 7467.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125580 restraints weight = 4461.472| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9872 Z= 0.106 Angle : 0.491 7.918 13348 Z= 0.247 Chirality : 0.039 0.177 1536 Planarity : 0.003 0.032 1608 Dihedral : 6.395 70.407 1590 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 16.93 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1163 helix: 1.62 (0.19), residues: 776 sheet: -0.60 (0.58), residues: 65 loop : -0.57 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 865 HIS 0.002 0.001 HIS A 199 PHE 0.022 0.001 PHE A 931 TYR 0.014 0.001 TYR A1381 ARG 0.003 0.000 ARG A1066 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 554) hydrogen bonds : angle 3.61597 ( 1641) covalent geometry : bond 0.00235 ( 9872) covalent geometry : angle 0.49126 (13348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.27 seconds wall clock time: 51 minutes 43.12 seconds (3103.12 seconds total)