Starting phenix.real_space_refine on Fri Feb 14 16:17:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.map" model { file = "/net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1v_0606/02_2025/6o1v_0606.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6347 2.51 5 N 1598 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9450 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 32, 'TRANS': 1146} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 176 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'LJP': 1, 'POV': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 6.75, per 1000 atoms: 0.70 Number of scatterers: 9711 At special positions: 0 Unit cell: (78.28, 88.58, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1710 8.00 N 1598 7.00 C 6347 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: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 69.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 20 through 30 removed outlier: 4.068A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.697A pdb=" N LEU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.700A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.760A pdb=" N LEU A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 166 removed outlier: 3.524A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.604A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.906A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 199 through 219 Proline residue: A 205 - end of helix removed outlier: 3.606A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 245 removed outlier: 3.724A pdb=" N CYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.728A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.719A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 307 removed outlier: 4.210A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 4.201A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.649A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.578A pdb=" N THR A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.753A pdb=" N GLN A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.963A pdb=" N GLY A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 532 removed outlier: 3.553A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.702A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.167A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 4.008A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 922 removed outlier: 3.564A pdb=" N TYR A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.643A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 927' Processing helix chain 'A' and resid 933 through 958 removed outlier: 3.808A pdb=" N LEU A 937 " --> pdb=" O ARG A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.582A pdb=" N LEU A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.587A pdb=" N ILE A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.451A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1047 removed outlier: 3.963A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.563A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.624A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 removed outlier: 3.676A pdb=" N LEU A1065 " --> pdb=" O GLY A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1121 removed outlier: 3.522A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1168 removed outlier: 4.003A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.629A pdb=" N PHE A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 removed outlier: 3.568A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1322 removed outlier: 3.565A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.500A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.575A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1391 removed outlier: 3.999A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 3.621A pdb=" N ALA A1406 " --> pdb=" O ARG A1403 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 4.138A pdb=" N LEU A1430 " --> pdb=" O SER A1426 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1441 removed outlier: 3.689A pdb=" N ILE A1441 " --> pdb=" O PHE A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 4.131A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.765A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.446A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 479 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.376A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 5.838A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A1232 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS A1213 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A1234 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR A1211 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 6.565A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1551 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: 3.52 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1813 1.33 - 1.46: 2365 1.46 - 1.58: 5644 1.58 - 1.70: 12 1.70 - 1.82: 79 Bond restraints: 9913 Sorted by residual: bond pdb=" C29 POV A2010 " pdb="C210 POV A2010 " ideal model delta sigma weight residual 1.333 1.533 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C6 LJP A2001 " pdb=" S1 LJP A2001 " ideal model delta sigma weight residual 1.737 1.612 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C13 LJP A2001 " pdb=" C14 LJP A2001 " ideal model delta sigma weight residual 1.474 1.349 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C10 LJP A2001 " pdb=" S1 LJP A2001 " ideal model delta sigma weight residual 1.730 1.621 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C11 LJP A2001 " pdb=" C12 LJP A2001 " ideal model delta sigma weight residual 1.477 1.377 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 9908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 12902 3.81 - 7.61: 500 7.61 - 11.42: 2 11.42 - 15.22: 3 15.22 - 19.03: 2 Bond angle restraints: 13409 Sorted by residual: angle pdb=" PB ATP A2005 " pdb=" O3B ATP A2005 " pdb=" PG ATP A2005 " ideal model delta sigma weight residual 139.87 125.69 14.18 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A2005 " pdb=" O3A ATP A2005 " pdb=" PB ATP A2005 " ideal model delta sigma weight residual 136.83 123.32 13.51 1.00e+00 1.00e+00 1.83e+02 angle pdb=" PB ATP A2004 " pdb=" O3B ATP A2004 " pdb=" PG ATP A2004 " ideal model delta sigma weight residual 139.87 126.62 13.25 1.00e+00 1.00e+00 1.76e+02 angle pdb=" PA ATP A2004 " pdb=" O3A ATP A2004 " pdb=" PB ATP A2004 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" C28 POV A2010 " pdb=" C29 POV A2010 " pdb="C210 POV A2010 " ideal model delta sigma weight residual 127.79 108.76 19.03 3.00e+00 1.11e-01 4.02e+01 ... (remaining 13404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5446 17.11 - 34.22: 395 34.22 - 51.33: 123 51.33 - 68.43: 18 68.43 - 85.54: 7 Dihedral angle restraints: 5989 sinusoidal: 2513 harmonic: 3476 Sorted by residual: dihedral pdb=" CA ARG A 29 " pdb=" C ARG A 29 " pdb=" N GLN A 30 " pdb=" CA GLN A 30 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU A 138 " pdb=" C LEU A 138 " pdb=" N HIS A 139 " pdb=" CA HIS A 139 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 621 0.050 - 0.099: 552 0.099 - 0.148: 287 0.148 - 0.198: 74 0.198 - 0.247: 7 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CA ARG A 600 " pdb=" N ARG A 600 " pdb=" C ARG A 600 " pdb=" CB ARG A 600 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A1234 " pdb=" N ILE A1234 " pdb=" C ILE A1234 " pdb=" CB ILE A1234 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1538 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 LJP A2001 " -0.045 2.00e-02 2.50e+03 1.26e-01 4.37e+02 pdb=" C11 LJP A2001 " -0.004 2.00e-02 2.50e+03 pdb=" C12 LJP A2001 " 0.028 2.00e-02 2.50e+03 pdb=" C4 LJP A2001 " 0.109 2.00e-02 2.50e+03 pdb=" C5 LJP A2001 " 0.034 2.00e-02 2.50e+03 pdb=" C6 LJP A2001 " -0.009 2.00e-02 2.50e+03 pdb=" C7 LJP A2001 " 0.020 2.00e-02 2.50e+03 pdb=" N1 LJP A2001 " -0.280 2.00e-02 2.50e+03 pdb=" N2 LJP A2001 " -0.063 2.00e-02 2.50e+03 pdb=" O2 LJP A2001 " 0.269 2.00e-02 2.50e+03 pdb=" S1 LJP A2001 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A2010 " -0.125 2.00e-02 2.50e+03 1.27e-01 1.61e+02 pdb=" C29 POV A2010 " 0.119 2.00e-02 2.50e+03 pdb="C210 POV A2010 " 0.135 2.00e-02 2.50e+03 pdb="C211 POV A2010 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 348 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C MET A 348 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 348 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 349 " 0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 28 2.53 - 3.12: 6353 3.12 - 3.71: 14482 3.71 - 4.31: 19997 4.31 - 4.90: 34518 Nonbonded interactions: 75378 Sorted by model distance: nonbonded pdb="MG MG A2003 " pdb=" O2B ATP A2005 " model vdw 1.933 2.170 nonbonded pdb="MG MG A2002 " pdb=" O2B ATP A2004 " model vdw 1.959 2.170 nonbonded pdb="MG MG A2002 " pdb=" O3G ATP A2004 " model vdw 1.997 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A2002 " model vdw 2.102 2.170 nonbonded pdb="MG MG A2003 " pdb=" O3G ATP A2005 " model vdw 2.147 2.170 ... (remaining 75373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.014 0.200 9913 Z= 0.887 Angle : 1.789 19.025 13409 Z= 1.342 Chirality : 0.081 0.247 1541 Planarity : 0.006 0.127 1630 Dihedral : 13.774 85.542 3741 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.48 % Allowed : 5.22 % Favored : 94.30 % 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: -2.71 (0.21), residues: 1169 helix: -1.36 (0.16), residues: 723 sheet: -2.15 (0.60), residues: 69 loop : -2.29 (0.26), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A1098 HIS 0.009 0.002 HIS A1054 PHE 0.019 0.003 PHE A 354 TYR 0.031 0.003 TYR A 161 ARG 0.010 0.001 ARG A1097 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 255 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7541 (mttm) REVERT: A 31 ARG cc_start: 0.7422 (ttm170) cc_final: 0.6629 (tpt90) REVERT: A 36 ASP cc_start: 0.7590 (m-30) cc_final: 0.7382 (m-30) REVERT: A 51 GLU cc_start: 0.7777 (tp30) cc_final: 0.7486 (tp30) REVERT: A 68 LYS cc_start: 0.6816 (mttt) cc_final: 0.6531 (mtpt) REVERT: A 78 PHE cc_start: 0.7824 (t80) cc_final: 0.7557 (t80) REVERT: A 115 GLU cc_start: 0.7824 (pt0) cc_final: 0.7425 (mm-30) REVERT: A 166 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7579 (mtpp) REVERT: A 192 ASP cc_start: 0.8425 (m-30) cc_final: 0.8203 (m-30) REVERT: A 217 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8315 (tt0) REVERT: A 242 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6354 (tmt170) REVERT: A 267 GLU cc_start: 0.7556 (tt0) cc_final: 0.7183 (tp30) REVERT: A 312 PHE cc_start: 0.7728 (m-80) cc_final: 0.7387 (m-80) REVERT: A 379 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8539 (mm-30) REVERT: A 396 ASN cc_start: 0.7628 (t0) cc_final: 0.6793 (t0) REVERT: A 409 PHE cc_start: 0.4923 (t80) cc_final: 0.4683 (t80) REVERT: A 442 LYS cc_start: 0.8146 (pttt) cc_final: 0.7887 (ptpp) REVERT: A 450 ARG cc_start: 0.8538 (ptt90) cc_final: 0.7901 (ttp-110) REVERT: A 487 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6293 (mmm-85) REVERT: A 569 TYR cc_start: 0.8339 (m-80) cc_final: 0.7875 (m-10) REVERT: A 585 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7279 (mm-30) REVERT: A 608 GLU cc_start: 0.7435 (tt0) cc_final: 0.7044 (tp30) REVERT: A 1110 PHE cc_start: 0.7175 (m-80) cc_final: 0.6947 (m-80) REVERT: A 1126 GLU cc_start: 0.7538 (tt0) cc_final: 0.7070 (tp30) REVERT: A 1128 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7355 (mtt180) REVERT: A 1165 LYS cc_start: 0.7237 (mttt) cc_final: 0.6940 (tptp) REVERT: A 1292 LYS cc_start: 0.7700 (ttpt) cc_final: 0.7382 (ptmm) REVERT: A 1320 ASP cc_start: 0.7911 (p0) cc_final: 0.7662 (p0) REVERT: A 1329 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 1330 GLN cc_start: 0.7994 (tt0) cc_final: 0.7664 (mt0) REVERT: A 1365 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6628 (mmmt) REVERT: A 1390 GLN cc_start: 0.7852 (mt0) cc_final: 0.7550 (mt0) REVERT: A 1394 ASP cc_start: 0.8316 (m-30) cc_final: 0.7983 (m-30) outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.2730 time to fit residues: 94.1457 Evaluate side-chains 159 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 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 30 GLN A 39 GLN A 207 GLN A 270 GLN A 525 GLN A 609 HIS A1042 GLN A1100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106022 restraints weight = 14067.777| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.55 r_work: 0.3124 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9913 Z= 0.205 Angle : 0.592 8.651 13409 Z= 0.310 Chirality : 0.040 0.147 1541 Planarity : 0.004 0.041 1630 Dihedral : 8.585 89.073 1485 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.22 % Allowed : 10.72 % Favored : 87.05 % 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: -0.41 (0.23), residues: 1169 helix: 0.55 (0.18), residues: 754 sheet: -1.57 (0.59), residues: 77 loop : -1.70 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 865 HIS 0.006 0.001 HIS A 199 PHE 0.026 0.001 PHE A 342 TYR 0.017 0.001 TYR A 517 ARG 0.007 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8204 (mttm) REVERT: A 31 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7398 (tpt90) REVERT: A 51 GLU cc_start: 0.8105 (tp30) cc_final: 0.7675 (mm-30) REVERT: A 68 LYS cc_start: 0.8013 (mttt) cc_final: 0.7504 (mtpt) REVERT: A 78 PHE cc_start: 0.8586 (t80) cc_final: 0.8287 (t80) REVERT: A 125 ILE cc_start: 0.7403 (mm) cc_final: 0.7019 (mm) REVERT: A 242 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7250 (tmt170) REVERT: A 334 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7157 (ttt-90) REVERT: A 409 PHE cc_start: 0.5786 (t80) cc_final: 0.5470 (t80) REVERT: A 487 ARG cc_start: 0.7721 (mtt180) cc_final: 0.7130 (mmm-85) REVERT: A 1046 GLU cc_start: 0.7854 (tt0) cc_final: 0.7275 (tp30) REVERT: A 1243 LEU cc_start: 0.8006 (pt) cc_final: 0.7790 (mp) REVERT: A 1280 GLN cc_start: 0.8338 (tt0) cc_final: 0.7879 (tm-30) REVERT: A 1329 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 1341 ASP cc_start: 0.8058 (t70) cc_final: 0.7593 (t0) REVERT: A 1365 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7461 (mmmt) REVERT: A 1419 ASN cc_start: 0.8418 (m110) cc_final: 0.7690 (t0) outliers start: 23 outliers final: 12 residues processed: 188 average time/residue: 0.2607 time to fit residues: 67.7098 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 199 HIS A 207 GLN A 250 GLN A 372 GLN A 552 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097965 restraints weight = 14641.371| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.56 r_work: 0.3005 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9913 Z= 0.346 Angle : 0.631 8.660 13409 Z= 0.324 Chirality : 0.042 0.146 1541 Planarity : 0.004 0.039 1630 Dihedral : 7.904 83.640 1485 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.06 % Allowed : 12.08 % Favored : 83.86 % 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: 0.14 (0.24), residues: 1169 helix: 0.88 (0.19), residues: 750 sheet: -1.44 (0.57), residues: 76 loop : -1.18 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 401 HIS 0.007 0.001 HIS A1085 PHE 0.029 0.002 PHE A 319 TYR 0.014 0.002 TYR A 304 ARG 0.005 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8338 (mttm) REVERT: A 16 PHE cc_start: 0.8210 (m-80) cc_final: 0.7944 (m-80) REVERT: A 29 ARG cc_start: 0.7237 (ptp-170) cc_final: 0.6221 (mmp-170) REVERT: A 30 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6927 (pt0) REVERT: A 31 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7274 (tpt90) REVERT: A 51 GLU cc_start: 0.8197 (tp30) cc_final: 0.7739 (mm-30) REVERT: A 68 LYS cc_start: 0.8189 (mttt) cc_final: 0.7683 (mtpt) REVERT: A 78 PHE cc_start: 0.8673 (t80) cc_final: 0.8382 (t80) REVERT: A 125 ILE cc_start: 0.7430 (mm) cc_final: 0.6886 (mm) REVERT: A 128 CYS cc_start: 0.8318 (m) cc_final: 0.7989 (m) REVERT: A 242 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7399 (tmt170) REVERT: A 334 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7242 (ttt-90) REVERT: A 390 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7704 (p) REVERT: A 442 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8352 (ptpp) REVERT: A 487 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7201 (mmm-85) REVERT: A 607 MET cc_start: 0.8305 (mmm) cc_final: 0.8011 (mmt) REVERT: A 1012 GLN cc_start: 0.7596 (mt0) cc_final: 0.7153 (mt0) REVERT: A 1046 GLU cc_start: 0.7971 (tt0) cc_final: 0.7630 (tp30) REVERT: A 1165 LYS cc_start: 0.7791 (tptt) cc_final: 0.7140 (tptt) REVERT: A 1280 GLN cc_start: 0.8223 (tt0) cc_final: 0.7865 (tm-30) REVERT: A 1310 TRP cc_start: 0.8510 (m100) cc_final: 0.8253 (m100) REVERT: A 1330 GLN cc_start: 0.8006 (mt0) cc_final: 0.7695 (mt0) REVERT: A 1341 ASP cc_start: 0.8119 (t70) cc_final: 0.7594 (t0) REVERT: A 1365 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7433 (mmmt) outliers start: 42 outliers final: 21 residues processed: 176 average time/residue: 0.2441 time to fit residues: 59.5345 Evaluate side-chains 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101331 restraints weight = 14364.799| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.46 r_work: 0.2947 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9913 Z= 0.207 Angle : 0.549 8.138 13409 Z= 0.278 Chirality : 0.039 0.146 1541 Planarity : 0.003 0.037 1630 Dihedral : 7.430 89.895 1485 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.90 % Allowed : 15.07 % Favored : 82.03 % 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: 0.65 (0.24), residues: 1169 helix: 1.24 (0.19), residues: 752 sheet: -1.11 (0.59), residues: 71 loop : -0.92 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.026 0.001 PHE A 319 TYR 0.011 0.001 TYR A 304 ARG 0.008 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8483 (t80) cc_final: 0.8260 (t80) REVERT: A 29 ARG cc_start: 0.6836 (ptp-170) cc_final: 0.5827 (mmp-170) REVERT: A 30 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: A 31 ARG cc_start: 0.7838 (ttm170) cc_final: 0.6928 (tpt90) REVERT: A 51 GLU cc_start: 0.8096 (tp30) cc_final: 0.7667 (mm-30) REVERT: A 68 LYS cc_start: 0.7955 (mttt) cc_final: 0.7451 (mtpt) REVERT: A 78 PHE cc_start: 0.8415 (t80) cc_final: 0.8073 (t80) REVERT: A 125 ILE cc_start: 0.7020 (mm) cc_final: 0.6511 (mm) REVERT: A 128 CYS cc_start: 0.7983 (m) cc_final: 0.7753 (m) REVERT: A 242 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7093 (tmt170) REVERT: A 244 MET cc_start: 0.8437 (tmm) cc_final: 0.8110 (tmm) REVERT: A 327 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 339 THR cc_start: 0.8500 (m) cc_final: 0.8286 (p) REVERT: A 442 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8211 (ptpp) REVERT: A 487 ARG cc_start: 0.7713 (mtt180) cc_final: 0.6933 (mmm-85) REVERT: A 504 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8028 (mt-10) REVERT: A 1012 GLN cc_start: 0.7252 (mt0) cc_final: 0.6868 (mt0) REVERT: A 1046 GLU cc_start: 0.7648 (tt0) cc_final: 0.7308 (tp30) REVERT: A 1165 LYS cc_start: 0.7372 (tptt) cc_final: 0.6671 (tptt) REVERT: A 1280 GLN cc_start: 0.8052 (tt0) cc_final: 0.7563 (tm-30) REVERT: A 1292 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7359 (ptmm) REVERT: A 1310 TRP cc_start: 0.8424 (m100) cc_final: 0.8111 (m100) REVERT: A 1320 ASP cc_start: 0.8432 (m-30) cc_final: 0.7891 (t0) REVERT: A 1330 GLN cc_start: 0.7902 (mt0) cc_final: 0.7573 (mt0) REVERT: A 1365 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7039 (mmmt) outliers start: 30 outliers final: 19 residues processed: 177 average time/residue: 0.2133 time to fit residues: 53.2805 Evaluate side-chains 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1292 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099573 restraints weight = 14439.989| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.51 r_work: 0.3019 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9913 Z= 0.258 Angle : 0.560 6.922 13409 Z= 0.284 Chirality : 0.040 0.143 1541 Planarity : 0.003 0.035 1630 Dihedral : 7.060 83.459 1485 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.96 % Allowed : 15.65 % Favored : 80.39 % 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: 0.76 (0.25), residues: 1169 helix: 1.28 (0.19), residues: 753 sheet: -1.03 (0.62), residues: 70 loop : -0.80 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 882 HIS 0.005 0.001 HIS A 199 PHE 0.026 0.002 PHE A 319 TYR 0.013 0.001 TYR A 304 ARG 0.003 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8858 (mttt) cc_final: 0.8413 (mttm) REVERT: A 28 TYR cc_start: 0.8737 (t80) cc_final: 0.8533 (t80) REVERT: A 29 ARG cc_start: 0.7007 (ptp-170) cc_final: 0.6087 (mmp80) REVERT: A 30 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6696 (pt0) REVERT: A 31 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7088 (tpt90) REVERT: A 51 GLU cc_start: 0.8116 (tp30) cc_final: 0.7742 (mm-30) REVERT: A 68 LYS cc_start: 0.8074 (mttt) cc_final: 0.7629 (mtpt) REVERT: A 78 PHE cc_start: 0.8542 (t80) cc_final: 0.8221 (t80) REVERT: A 125 ILE cc_start: 0.7225 (mm) cc_final: 0.6696 (mm) REVERT: A 128 CYS cc_start: 0.8186 (m) cc_final: 0.7892 (m) REVERT: A 242 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7293 (tmt170) REVERT: A 327 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 339 THR cc_start: 0.8623 (m) cc_final: 0.8388 (p) REVERT: A 394 MET cc_start: 0.8211 (ttt) cc_final: 0.7857 (ttm) REVERT: A 442 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8351 (ptmm) REVERT: A 487 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7043 (mmm-85) REVERT: A 504 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 539 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 882 TRP cc_start: 0.6480 (t-100) cc_final: 0.6049 (t60) REVERT: A 1012 GLN cc_start: 0.7446 (mt0) cc_final: 0.7096 (mt0) REVERT: A 1046 GLU cc_start: 0.7878 (tt0) cc_final: 0.7580 (tp30) REVERT: A 1165 LYS cc_start: 0.7682 (tptt) cc_final: 0.7061 (tptt) REVERT: A 1280 GLN cc_start: 0.8191 (tt0) cc_final: 0.7760 (tm-30) REVERT: A 1310 TRP cc_start: 0.8493 (m100) cc_final: 0.8172 (m100) REVERT: A 1317 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8299 (tptp) REVERT: A 1320 ASP cc_start: 0.8340 (m-30) cc_final: 0.7850 (t0) REVERT: A 1330 GLN cc_start: 0.7874 (mt0) cc_final: 0.7575 (mt0) REVERT: A 1365 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7165 (mmmt) outliers start: 41 outliers final: 26 residues processed: 167 average time/residue: 0.2277 time to fit residues: 53.8813 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102483 restraints weight = 14425.543| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.39 r_work: 0.3083 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9913 Z= 0.193 Angle : 0.520 6.704 13409 Z= 0.264 Chirality : 0.038 0.160 1541 Planarity : 0.003 0.033 1630 Dihedral : 6.796 81.077 1485 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.00 % Allowed : 17.10 % 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: 1.02 (0.25), residues: 1169 helix: 1.50 (0.19), residues: 753 sheet: -0.85 (0.61), residues: 72 loop : -0.74 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.023 0.001 PHE A 319 TYR 0.011 0.001 TYR A 304 ARG 0.003 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8807 (t80) cc_final: 0.8587 (t80) REVERT: A 29 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6110 (mmp80) REVERT: A 30 GLN cc_start: 0.7287 (mt0) cc_final: 0.6949 (pt0) REVERT: A 31 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7317 (ttt90) REVERT: A 51 GLU cc_start: 0.8017 (tp30) cc_final: 0.7807 (mm-30) REVERT: A 68 LYS cc_start: 0.8217 (mttt) cc_final: 0.7782 (mtpt) REVERT: A 78 PHE cc_start: 0.8519 (t80) cc_final: 0.8251 (t80) REVERT: A 128 CYS cc_start: 0.8318 (m) cc_final: 0.8009 (m) REVERT: A 242 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7504 (tmt170) REVERT: A 244 MET cc_start: 0.8859 (tmm) cc_final: 0.8556 (tmm) REVERT: A 267 GLU cc_start: 0.8337 (tp30) cc_final: 0.7551 (tp30) REVERT: A 327 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (mm) REVERT: A 339 THR cc_start: 0.8637 (m) cc_final: 0.8389 (p) REVERT: A 394 MET cc_start: 0.8315 (ttt) cc_final: 0.7939 (ttm) REVERT: A 442 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8196 (ptmm) REVERT: A 487 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7210 (mmm-85) REVERT: A 504 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 882 TRP cc_start: 0.6610 (t-100) cc_final: 0.6164 (t60) REVERT: A 1028 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8082 (mtt) REVERT: A 1046 GLU cc_start: 0.8075 (tt0) cc_final: 0.7855 (tp30) REVERT: A 1118 SER cc_start: 0.8272 (t) cc_final: 0.7735 (p) REVERT: A 1165 LYS cc_start: 0.8006 (tptt) cc_final: 0.7411 (tptt) REVERT: A 1280 GLN cc_start: 0.8248 (tt0) cc_final: 0.7896 (tm-30) REVERT: A 1310 TRP cc_start: 0.8539 (m100) cc_final: 0.8248 (m100) REVERT: A 1320 ASP cc_start: 0.8290 (m-30) cc_final: 0.7817 (t0) REVERT: A 1330 GLN cc_start: 0.7867 (mt0) cc_final: 0.7572 (mt0) REVERT: A 1365 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7319 (mmmt) REVERT: A 1417 GLU cc_start: 0.7070 (pt0) cc_final: 0.6658 (pm20) outliers start: 31 outliers final: 21 residues processed: 164 average time/residue: 0.2242 time to fit residues: 52.3306 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101383 restraints weight = 14662.696| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.38 r_work: 0.3068 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9913 Z= 0.234 Angle : 0.535 6.797 13409 Z= 0.272 Chirality : 0.039 0.170 1541 Planarity : 0.003 0.033 1630 Dihedral : 6.660 79.097 1485 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.67 % Allowed : 16.23 % 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: 1.06 (0.25), residues: 1169 helix: 1.53 (0.19), residues: 753 sheet: -0.75 (0.62), residues: 72 loop : -0.74 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.023 0.001 PHE A 319 TYR 0.012 0.001 TYR A 304 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8899 (t80) cc_final: 0.8681 (t80) REVERT: A 29 ARG cc_start: 0.7297 (ptp-170) cc_final: 0.6144 (mmp80) REVERT: A 30 GLN cc_start: 0.7404 (mt0) cc_final: 0.7033 (pt0) REVERT: A 31 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7155 (ttt90) REVERT: A 51 GLU cc_start: 0.8258 (tp30) cc_final: 0.7842 (mm-30) REVERT: A 68 LYS cc_start: 0.8244 (mttt) cc_final: 0.7800 (mtpt) REVERT: A 78 PHE cc_start: 0.8588 (t80) cc_final: 0.8285 (t80) REVERT: A 128 CYS cc_start: 0.8367 (m) cc_final: 0.8084 (m) REVERT: A 242 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7467 (tmt170) REVERT: A 267 GLU cc_start: 0.8452 (tp30) cc_final: 0.7665 (tp30) REVERT: A 327 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 339 THR cc_start: 0.8734 (m) cc_final: 0.8431 (p) REVERT: A 394 MET cc_start: 0.8387 (ttt) cc_final: 0.7958 (ttm) REVERT: A 442 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8212 (ptmm) REVERT: A 487 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7277 (mmm-85) REVERT: A 504 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 882 TRP cc_start: 0.6597 (t-100) cc_final: 0.6216 (t60) REVERT: A 1028 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8167 (mtt) REVERT: A 1046 GLU cc_start: 0.8098 (tt0) cc_final: 0.7867 (tp30) REVERT: A 1165 LYS cc_start: 0.8025 (tptt) cc_final: 0.7454 (tptt) REVERT: A 1280 GLN cc_start: 0.8366 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 1310 TRP cc_start: 0.8610 (m100) cc_final: 0.8312 (m100) REVERT: A 1317 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8373 (tptp) REVERT: A 1320 ASP cc_start: 0.8435 (m-30) cc_final: 0.7945 (t0) REVERT: A 1330 GLN cc_start: 0.7968 (mt0) cc_final: 0.7673 (mt0) REVERT: A 1365 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7302 (mmmt) REVERT: A 1404 ILE cc_start: 0.9105 (mm) cc_final: 0.8871 (mm) outliers start: 38 outliers final: 32 residues processed: 162 average time/residue: 0.2155 time to fit residues: 50.0953 Evaluate side-chains 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1317 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102604 restraints weight = 14578.492| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.39 r_work: 0.3084 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9913 Z= 0.195 Angle : 0.514 6.729 13409 Z= 0.260 Chirality : 0.038 0.180 1541 Planarity : 0.003 0.032 1630 Dihedral : 6.504 78.962 1485 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.38 % Allowed : 17.00 % Favored : 79.61 % 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: 1.24 (0.25), residues: 1169 helix: 1.67 (0.19), residues: 752 sheet: -0.69 (0.62), residues: 72 loop : -0.68 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.021 0.001 PHE A 319 TYR 0.014 0.001 TYR A 517 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8281 (m-80) cc_final: 0.8033 (m-80) REVERT: A 29 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.6197 (mmp80) REVERT: A 30 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: A 31 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7023 (ttt90) REVERT: A 51 GLU cc_start: 0.7969 (tp30) cc_final: 0.7767 (mm-30) REVERT: A 68 LYS cc_start: 0.8184 (mttt) cc_final: 0.7730 (mtpt) REVERT: A 78 PHE cc_start: 0.8503 (t80) cc_final: 0.8252 (t80) REVERT: A 128 CYS cc_start: 0.8363 (m) cc_final: 0.8067 (m) REVERT: A 185 SER cc_start: 0.8924 (t) cc_final: 0.8694 (p) REVERT: A 217 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8469 (tt0) REVERT: A 242 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7505 (tmt170) REVERT: A 244 MET cc_start: 0.8849 (tmm) cc_final: 0.8523 (tmm) REVERT: A 267 GLU cc_start: 0.8208 (tp30) cc_final: 0.7460 (tp30) REVERT: A 327 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 339 THR cc_start: 0.8622 (m) cc_final: 0.8340 (p) REVERT: A 394 MET cc_start: 0.8282 (ttt) cc_final: 0.7884 (ttm) REVERT: A 442 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8277 (ptmm) REVERT: A 487 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7262 (mmm-85) REVERT: A 504 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8227 (mt-10) REVERT: A 873 GLU cc_start: 0.8018 (tp30) cc_final: 0.7687 (tp30) REVERT: A 882 TRP cc_start: 0.6701 (t-100) cc_final: 0.6240 (t60) REVERT: A 1028 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: A 1046 GLU cc_start: 0.8012 (tt0) cc_final: 0.7764 (tp30) REVERT: A 1157 MET cc_start: 0.8679 (tpp) cc_final: 0.8411 (tpp) REVERT: A 1165 LYS cc_start: 0.7942 (tptt) cc_final: 0.7396 (tptt) REVERT: A 1280 GLN cc_start: 0.8244 (tt0) cc_final: 0.7868 (tm-30) REVERT: A 1310 TRP cc_start: 0.8522 (m100) cc_final: 0.8241 (m100) REVERT: A 1320 ASP cc_start: 0.8324 (m-30) cc_final: 0.7889 (t0) REVERT: A 1330 GLN cc_start: 0.7862 (mt0) cc_final: 0.7554 (mt0) REVERT: A 1365 LYS cc_start: 0.7830 (mmtm) cc_final: 0.7316 (mmmt) REVERT: A 1417 GLU cc_start: 0.7098 (pt0) cc_final: 0.6466 (pm20) outliers start: 35 outliers final: 26 residues processed: 164 average time/residue: 0.2212 time to fit residues: 52.1987 Evaluate side-chains 166 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101820 restraints weight = 14719.660| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.47 r_work: 0.3079 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9913 Z= 0.195 Angle : 0.523 7.387 13409 Z= 0.262 Chirality : 0.038 0.195 1541 Planarity : 0.003 0.032 1630 Dihedral : 6.442 78.828 1485 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.38 % Allowed : 17.10 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1169 helix: 1.70 (0.19), residues: 753 sheet: -0.74 (0.61), residues: 74 loop : -0.66 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.020 0.001 PHE A 319 TYR 0.015 0.001 TYR A 517 ARG 0.002 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.6153 (mmp80) REVERT: A 30 GLN cc_start: 0.7184 (mt0) cc_final: 0.6891 (pt0) REVERT: A 31 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7046 (ttt90) REVERT: A 68 LYS cc_start: 0.8177 (mttt) cc_final: 0.7726 (mtpt) REVERT: A 78 PHE cc_start: 0.8517 (t80) cc_final: 0.8260 (t80) REVERT: A 128 CYS cc_start: 0.8375 (m) cc_final: 0.8071 (m) REVERT: A 217 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8479 (tt0) REVERT: A 242 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7492 (tmt170) REVERT: A 244 MET cc_start: 0.8805 (tmm) cc_final: 0.8493 (tmm) REVERT: A 267 GLU cc_start: 0.8213 (tp30) cc_final: 0.7469 (tp30) REVERT: A 327 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 339 THR cc_start: 0.8624 (m) cc_final: 0.8343 (p) REVERT: A 391 GLU cc_start: 0.7870 (tt0) cc_final: 0.7485 (tm-30) REVERT: A 394 MET cc_start: 0.8214 (ttt) cc_final: 0.7814 (ttm) REVERT: A 442 LYS cc_start: 0.8811 (ptpp) cc_final: 0.8271 (ptmm) REVERT: A 448 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7417 (mt) REVERT: A 487 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7277 (mmm-85) REVERT: A 504 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 614 ASP cc_start: 0.7715 (t0) cc_final: 0.7503 (m-30) REVERT: A 873 GLU cc_start: 0.8019 (tp30) cc_final: 0.7682 (tp30) REVERT: A 882 TRP cc_start: 0.6746 (t-100) cc_final: 0.6308 (t60) REVERT: A 1028 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: A 1046 GLU cc_start: 0.8032 (tt0) cc_final: 0.7786 (tp30) REVERT: A 1165 LYS cc_start: 0.7944 (tptt) cc_final: 0.7395 (tptt) REVERT: A 1280 GLN cc_start: 0.8265 (tt0) cc_final: 0.7880 (tm-30) REVERT: A 1310 TRP cc_start: 0.8532 (m100) cc_final: 0.8254 (m100) REVERT: A 1320 ASP cc_start: 0.8343 (m-30) cc_final: 0.7882 (t0) REVERT: A 1325 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7631 (tpt170) REVERT: A 1330 GLN cc_start: 0.7795 (mt0) cc_final: 0.7500 (mt0) REVERT: A 1365 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7330 (mmmt) REVERT: A 1417 GLU cc_start: 0.7131 (pt0) cc_final: 0.6488 (pm20) outliers start: 35 outliers final: 28 residues processed: 157 average time/residue: 0.2427 time to fit residues: 55.1168 Evaluate side-chains 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1233 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 105 optimal weight: 0.0670 chunk 36 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A1088 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104899 restraints weight = 14711.976| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9913 Z= 0.145 Angle : 0.497 6.620 13409 Z= 0.249 Chirality : 0.037 0.210 1541 Planarity : 0.003 0.031 1630 Dihedral : 6.271 81.894 1485 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.51 % Allowed : 17.78 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.25), residues: 1169 helix: 1.80 (0.19), residues: 760 sheet: -0.66 (0.61), residues: 74 loop : -0.60 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.020 0.001 PHE A 319 TYR 0.014 0.001 TYR A 517 ARG 0.002 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7389 (ptp-170) cc_final: 0.6091 (mmp-170) REVERT: A 30 GLN cc_start: 0.7192 (mt0) cc_final: 0.6908 (pt0) REVERT: A 31 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7020 (ttt90) REVERT: A 68 LYS cc_start: 0.8164 (mttt) cc_final: 0.7669 (mtpt) REVERT: A 78 PHE cc_start: 0.8412 (t80) cc_final: 0.8146 (t80) REVERT: A 128 CYS cc_start: 0.8333 (m) cc_final: 0.8032 (m) REVERT: A 217 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8536 (tt0) REVERT: A 242 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7452 (tmt170) REVERT: A 244 MET cc_start: 0.8790 (tmm) cc_final: 0.8570 (tmm) REVERT: A 267 GLU cc_start: 0.8168 (tp30) cc_final: 0.7429 (tp30) REVERT: A 327 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8179 (mm) REVERT: A 339 THR cc_start: 0.8597 (m) cc_final: 0.8314 (p) REVERT: A 391 GLU cc_start: 0.7905 (tt0) cc_final: 0.7392 (tm-30) REVERT: A 442 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8228 (ptmm) REVERT: A 448 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7500 (mt) REVERT: A 487 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7260 (mmm-85) REVERT: A 504 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 873 GLU cc_start: 0.7918 (tp30) cc_final: 0.7572 (tp30) REVERT: A 882 TRP cc_start: 0.6698 (t-100) cc_final: 0.6299 (t60) REVERT: A 883 LEU cc_start: 0.8233 (tt) cc_final: 0.7879 (mm) REVERT: A 1028 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8088 (mtt) REVERT: A 1046 GLU cc_start: 0.7951 (tt0) cc_final: 0.7659 (tp30) REVERT: A 1111 PHE cc_start: 0.8588 (t80) cc_final: 0.8382 (t80) REVERT: A 1165 LYS cc_start: 0.7823 (tptt) cc_final: 0.7248 (tptt) REVERT: A 1280 GLN cc_start: 0.8233 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 1310 TRP cc_start: 0.8494 (m100) cc_final: 0.8226 (m100) REVERT: A 1320 ASP cc_start: 0.8318 (m-30) cc_final: 0.7899 (t0) REVERT: A 1325 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7133 (tpt170) REVERT: A 1330 GLN cc_start: 0.7737 (mt0) cc_final: 0.7410 (mt0) REVERT: A 1341 ASP cc_start: 0.8272 (t70) cc_final: 0.8032 (m-30) REVERT: A 1365 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7387 (mmmt) REVERT: A 1417 GLU cc_start: 0.7133 (pt0) cc_final: 0.6498 (pm20) REVERT: A 1419 ASN cc_start: 0.8654 (m-40) cc_final: 0.8143 (t0) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.2126 time to fit residues: 49.2268 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1023 ILE Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 147 HIS A 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103547 restraints weight = 14482.173| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.42 r_work: 0.3113 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9913 Z= 0.175 Angle : 0.515 9.360 13409 Z= 0.256 Chirality : 0.038 0.201 1541 Planarity : 0.003 0.032 1630 Dihedral : 6.289 82.243 1485 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.00 % Allowed : 18.07 % Favored : 78.94 % 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: 1.45 (0.25), residues: 1169 helix: 1.81 (0.19), residues: 760 sheet: -0.63 (0.60), residues: 74 loop : -0.57 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.019 0.001 PHE A 319 TYR 0.014 0.001 TYR A 517 ARG 0.002 0.000 ARG A 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.47 seconds wall clock time: 71 minutes 15.21 seconds (4275.21 seconds total)