Starting phenix.real_space_refine on Fri Jul 3 05:40:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.map" model { file = "/net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw9_47239/07_2026/9dw9_47239.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 11 5.49 5 Mg 4 5.21 5 S 56 5.16 5 Cl 4 4.86 5 C 8041 2.51 5 N 2038 2.21 5 O 2178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12332 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9495 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 1151} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2632 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 14, 'TRANS': 313} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 165 Ad-hoc single atom residues: {' CL': 4} Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'D10': 4, 'UND': 3} Classifications: {'undetermined': 12} Link IDs: {None: 10} Chain breaks: 4 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 2.72, per 1000 atoms: 0.22 Number of scatterers: 12332 At special positions: 0 Unit cell: (73.684, 129.116, 138.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 56 16.00 P 11 15.00 Mg 4 11.99 O 2178 8.00 N 2038 7.00 C 8041 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: 1.12 Conformation dependent library (CDL) restraints added in 603.8 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2844 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 63.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.935A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.500A pdb=" N ILE A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.714A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 108 removed outlier: 3.526A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Proline residue: A 99 - end of helix removed outlier: 4.113A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.590A pdb=" N SER A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.631A pdb=" N LEU A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.564A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 4.209A pdb=" N ASP A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.504A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 217 Proline residue: A 205 - end of helix removed outlier: 3.533A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 4.161A pdb=" N GLY A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.605A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 removed outlier: 3.561A pdb=" N PHE A 312 " --> pdb=" O ALA A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 313 through 329 removed outlier: 4.330A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 4.190A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 4.007A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 375 removed outlier: 3.791A pdb=" N TRP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.695A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.504A pdb=" N SER A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.649A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.756A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 634 removed outlier: 3.580A pdb=" N GLN A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 848 through 854 Processing helix chain 'A' and resid 856 through 884 removed outlier: 3.939A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.892A pdb=" N SER A 912 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 927 removed outlier: 3.977A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 958 removed outlier: 3.791A pdb=" N LEU A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) Proline residue: A 936 - end of helix removed outlier: 3.549A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 4.093A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1012 removed outlier: 4.057A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.622A pdb=" N ASP A 993 " --> pdb=" O LEU A 989 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1047 removed outlier: 3.846A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.908A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.777A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1122 removed outlier: 3.515A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1168 removed outlier: 4.007A pdb=" N ILE A1131 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A1132 " --> pdb=" O ARG A1128 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 removed outlier: 3.580A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1324 through 1329 Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.568A pdb=" N LYS A1351 " --> pdb=" O SER A1347 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.777A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1410 removed outlier: 3.664A pdb=" N GLU A1409 " --> pdb=" O ALA A1406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A1410 " --> pdb=" O MET A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 3.942A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1440 removed outlier: 3.729A pdb=" N ALA A1440 " --> pdb=" O LEU A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 3.902A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 33 removed outlier: 3.883A pdb=" N ALA G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 86 through 97 removed outlier: 3.591A pdb=" N LEU G 90 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 137 removed outlier: 3.891A pdb=" N HIS G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 161 removed outlier: 3.686A pdb=" N TYR G 147 " --> pdb=" O HIS G 143 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN G 150 " --> pdb=" O PHE G 146 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU G 161 " --> pdb=" O TYR G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 202 through 206 Processing helix chain 'G' and resid 207 through 212 Processing helix chain 'G' and resid 219 through 235 removed outlier: 3.707A pdb=" N TRP G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 254 removed outlier: 3.796A pdb=" N GLU G 249 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 274 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 302 through 309 removed outlier: 3.563A pdb=" N TYR G 307 " --> pdb=" O TRP G 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 6.512A pdb=" N ILE A 331 " --> pdb=" O ILE A 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 449 removed outlier: 6.558A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 397 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU A 479 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.621A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA5, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 6.909A pdb=" N GLU A1228 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A1216 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A1212 " --> pdb=" O GLN A1268 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN A1268 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASP A1214 " --> pdb=" O GLU A1266 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A1266 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.544A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP A1370 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1298 through 1299 Processing sheet with id=AA8, first strand: chain 'G' and resid 58 through 62 removed outlier: 7.039A pdb=" N TYR G 118 " --> pdb=" O SER G 110 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER G 110 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL G 120 " --> pdb=" O GLU G 108 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'G' and resid 173 through 175 643 hydrogen bonds defined for protein. 1875 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: 3.07 Time building geometry restraints manager: 1.50 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: 2322 1.33 - 1.45: 3037 1.45 - 1.57: 7113 1.57 - 1.69: 19 1.69 - 1.81: 96 Bond restraints: 12587 Sorted by residual: bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.70e+01 bond pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.374 1.322 0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.439 -0.051 1.00e-02 1.00e+04 2.55e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.453 -0.044 1.00e-02 1.00e+04 1.98e+01 bond pdb=" C8 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 1.370 1.331 0.039 1.20e-02 6.94e+03 1.06e+01 ... (remaining 12582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 16942 3.69 - 7.38: 61 7.38 - 11.07: 4 11.07 - 14.77: 1 14.77 - 18.46: 1 Bond angle restraints: 17009 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 122.83 14.00 1.00e+00 1.00e+00 1.96e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.72 8.08 1.00e+00 1.00e+00 6.53e+01 angle pdb=" N LEU G 50 " pdb=" CA LEU G 50 " pdb=" C LEU G 50 " ideal model delta sigma weight residual 111.07 118.26 -7.19 1.07e+00 8.73e-01 4.52e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 122.12 6.57 1.00e+00 1.00e+00 4.32e+01 ... (remaining 17004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6831 17.71 - 35.43: 546 35.43 - 53.14: 154 53.14 - 70.85: 43 70.85 - 88.56: 17 Dihedral angle restraints: 7591 sinusoidal: 3193 harmonic: 4398 Sorted by residual: dihedral pdb=" C VAL G 16 " pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" CB VAL G 16 " ideal model delta harmonic sigma weight residual -122.00 -131.67 9.67 0 2.50e+00 1.60e-01 1.50e+01 dihedral pdb=" CA TYR G 165 " pdb=" C TYR G 165 " pdb=" N ARG G 166 " pdb=" CA ARG G 166 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" N VAL G 16 " pdb=" C VAL G 16 " pdb=" CA VAL G 16 " pdb=" CB VAL G 16 " ideal model delta harmonic sigma weight residual 123.40 132.21 -8.81 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 7588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1659 0.061 - 0.123: 253 0.123 - 0.184: 8 0.184 - 0.245: 1 0.245 - 0.306: 3 Chirality restraints: 1924 Sorted by residual: chirality pdb=" CA LYS G 17 " pdb=" N LYS G 17 " pdb=" C LYS G 17 " pdb=" CB LYS G 17 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA PHE G 19 " pdb=" N PHE G 19 " pdb=" C PHE G 19 " pdb=" CB PHE G 19 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA VAL G 16 " pdb=" N VAL G 16 " pdb=" C VAL G 16 " pdb=" CB VAL G 16 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1921 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 13 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C GLN G 13 " 0.030 2.00e-02 2.50e+03 pdb=" O GLN G 13 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU G 14 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 84 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C LYS G 84 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS G 84 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN G 85 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 204 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 205 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " 0.020 5.00e-02 4.00e+02 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 21 2.52 - 3.12: 8702 3.12 - 3.71: 17790 3.71 - 4.31: 26141 4.31 - 4.90: 44121 Nonbonded interactions: 96775 Sorted by model distance: nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 1.931 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1503 " model vdw 2.017 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1602 " model vdw 2.021 2.170 nonbonded pdb=" OD2 ASP G 185 " pdb="MG MG G 403 " model vdw 2.169 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1504 " model vdw 2.193 2.170 ... (remaining 96770 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: 8.330 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 0.004 0.061 12587 Z= 0.217 Angle : 0.668 18.457 17009 Z= 0.410 Chirality : 0.044 0.306 1924 Planarity : 0.003 0.035 2076 Dihedral : 15.318 88.563 4747 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.69 % Allowed : 10.43 % Favored : 87.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1488 helix: 1.01 (0.18), residues: 855 sheet: 0.03 (0.47), residues: 120 loop : -0.65 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 3 TYR 0.017 0.002 TYR A 304 PHE 0.023 0.002 PHE A 81 TRP 0.020 0.002 TRP A1145 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.22 (12587) covalent geometry : angle 0.66815 / 0.41 (17009) hydrogen bonds : bond 0.17769 / 11.54 ( 643) hydrogen bonds : angle 5.53096 / 4.05 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.492 Fit side-chains REVERT: A 54 GLU cc_start: 0.8373 (tt0) cc_final: 0.8119 (mt-10) REVERT: A 174 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7501 (mmtt) REVERT: A 469 MET cc_start: 0.8785 (mmp) cc_final: 0.8570 (mmt) REVERT: A 481 LYS cc_start: 0.8321 (mttm) cc_final: 0.7775 (tptt) REVERT: A 825 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 830 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7532 (ttmt) REVERT: A 1166 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7715 (t80) REVERT: G 17 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7572 (mtpt) REVERT: G 26 ASP cc_start: 0.8095 (t0) cc_final: 0.7802 (t0) REVERT: G 57 ARG cc_start: 0.6365 (OUTLIER) cc_final: 0.5874 (tmt90) REVERT: G 63 HIS cc_start: 0.6594 (OUTLIER) cc_final: 0.6108 (t70) REVERT: G 79 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.7090 (ttpt) REVERT: G 112 LYS cc_start: 0.7126 (tptt) cc_final: 0.6260 (pmtt) REVERT: G 195 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7715 (ttt-90) outliers start: 22 outliers final: 10 residues processed: 153 average time/residue: 0.6867 time to fit residues: 113.1510 Evaluate side-chains 131 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 825 ASN Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 79 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1280 GLN A1419 ASN A1439 GLN G 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107382 restraints weight = 15423.356| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.51 r_work: 0.3132 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12587 Z= 0.148 Angle : 0.523 6.405 17009 Z= 0.280 Chirality : 0.041 0.167 1924 Planarity : 0.004 0.034 2076 Dihedral : 8.466 67.541 1891 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.45 % Allowed : 10.74 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1488 helix: 1.42 (0.18), residues: 876 sheet: 0.00 (0.46), residues: 120 loop : -0.88 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1446 TYR 0.016 0.001 TYR A 304 PHE 0.022 0.002 PHE A 81 TRP 0.013 0.001 TRP A 865 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (12587) covalent geometry : angle 0.52306 / 0.28 (17009) hydrogen bonds : bond 0.07069 / 4.65 ( 643) hydrogen bonds : angle 4.12608 / 3.06 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.552 Fit side-chains REVERT: A 47 ASP cc_start: 0.7665 (t70) cc_final: 0.7453 (t70) REVERT: A 54 GLU cc_start: 0.8407 (tt0) cc_final: 0.8077 (mt-10) REVERT: A 174 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7511 (mmtt) REVERT: A 469 MET cc_start: 0.8819 (mmp) cc_final: 0.8514 (mmt) REVERT: A 528 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 830 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7355 (ttmt) REVERT: A 1166 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 1438 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: G 63 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5981 (t-90) REVERT: G 108 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: G 112 LYS cc_start: 0.7173 (tptt) cc_final: 0.6213 (pmtt) REVERT: G 195 ARG cc_start: 0.8119 (tpp80) cc_final: 0.7700 (ttt-90) REVERT: G 214 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7219 (tppp) outliers start: 32 outliers final: 11 residues processed: 152 average time/residue: 0.7004 time to fit residues: 114.4932 Evaluate side-chains 137 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1438 ARG Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1439 GLN G 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105637 restraints weight = 15505.410| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.49 r_work: 0.3094 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12587 Z= 0.159 Angle : 0.527 6.453 17009 Z= 0.281 Chirality : 0.042 0.180 1924 Planarity : 0.004 0.034 2076 Dihedral : 8.246 65.756 1870 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.76 % Allowed : 12.04 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.22), residues: 1488 helix: 1.56 (0.18), residues: 873 sheet: -0.01 (0.47), residues: 120 loop : -0.98 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 170 TYR 0.017 0.002 TYR A 304 PHE 0.020 0.002 PHE A 81 TRP 0.013 0.001 TRP A 865 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (12587) covalent geometry : angle 0.52667 / 0.28 (17009) hydrogen bonds : bond 0.07379 / 4.87 ( 643) hydrogen bonds : angle 3.97840 / 2.95 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.476 Fit side-chains REVERT: A 47 ASP cc_start: 0.7785 (t70) cc_final: 0.7562 (t70) REVERT: A 51 GLU cc_start: 0.8048 (tp30) cc_final: 0.7599 (tp30) REVERT: A 174 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7463 (mmmt) REVERT: A 469 MET cc_start: 0.8858 (mmp) cc_final: 0.8577 (mmt) REVERT: A 528 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: A 1166 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 1280 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: G 59 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7272 (ppp) REVERT: G 63 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.5753 (t-90) REVERT: G 108 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: G 112 LYS cc_start: 0.7277 (tptt) cc_final: 0.6256 (pmtt) REVERT: G 195 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7877 (mtt-85) REVERT: G 214 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7411 (tppp) outliers start: 36 outliers final: 15 residues processed: 147 average time/residue: 0.6761 time to fit residues: 106.9064 Evaluate side-chains 138 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 39 optimal weight: 0.0670 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110249 restraints weight = 15459.531| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.48 r_work: 0.3155 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12587 Z= 0.108 Angle : 0.442 6.809 17009 Z= 0.237 Chirality : 0.039 0.184 1924 Planarity : 0.003 0.031 2076 Dihedral : 7.654 63.188 1870 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.38 % Allowed : 13.27 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1488 helix: 1.84 (0.18), residues: 886 sheet: 0.17 (0.48), residues: 118 loop : -0.95 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1446 TYR 0.011 0.001 TYR A 304 PHE 0.012 0.001 PHE A 81 TRP 0.014 0.001 TRP A 865 HIS 0.002 0.000 HIS A 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (12587) covalent geometry : angle 0.44155 / 0.24 (17009) hydrogen bonds : bond 0.05464 / 3.61 ( 643) hydrogen bonds : angle 3.68153 / 2.71 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.418 Fit side-chains REVERT: A 51 GLU cc_start: 0.7955 (tp30) cc_final: 0.7553 (tp30) REVERT: A 174 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7467 (mmmt) REVERT: A 528 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 1166 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7719 (t80) REVERT: A 1280 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: G 63 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5677 (t-90) REVERT: G 112 LYS cc_start: 0.7239 (tptt) cc_final: 0.6255 (pmtt) REVERT: G 195 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7859 (mtt-85) REVERT: G 214 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7293 (tppp) outliers start: 31 outliers final: 10 residues processed: 151 average time/residue: 0.6420 time to fit residues: 104.2256 Evaluate side-chains 139 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A1439 GLN G 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105286 restraints weight = 15531.412| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.48 r_work: 0.3090 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12587 Z= 0.169 Angle : 0.523 6.267 17009 Z= 0.278 Chirality : 0.041 0.220 1924 Planarity : 0.004 0.037 2076 Dihedral : 8.094 66.888 1866 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 13.57 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.22), residues: 1488 helix: 1.72 (0.18), residues: 872 sheet: 0.12 (0.48), residues: 118 loop : -1.04 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1446 TYR 0.017 0.002 TYR A 304 PHE 0.018 0.002 PHE A 81 TRP 0.012 0.001 TRP G 31 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (12587) covalent geometry : angle 0.52308 / 0.28 (17009) hydrogen bonds : bond 0.07287 / 4.81 ( 643) hydrogen bonds : angle 3.86685 / 2.87 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.518 Fit side-chains REVERT: A 51 GLU cc_start: 0.7994 (tp30) cc_final: 0.7593 (tp30) REVERT: A 174 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7512 (mmtt) REVERT: A 516 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: A 528 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: A 1126 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: A 1166 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7857 (t80) REVERT: A 1280 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: G 25 GLU cc_start: 0.8267 (tt0) cc_final: 0.8063 (tp30) REVERT: G 63 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.5690 (t-90) REVERT: G 112 LYS cc_start: 0.7283 (tptt) cc_final: 0.6301 (pmtt) REVERT: G 195 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7888 (mtt-85) REVERT: G 214 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7397 (tppp) outliers start: 32 outliers final: 15 residues processed: 147 average time/residue: 0.6530 time to fit residues: 102.9897 Evaluate side-chains 144 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 57 optimal weight: 0.0050 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111226 restraints weight = 15439.170| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.49 r_work: 0.3184 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12587 Z= 0.103 Angle : 0.437 7.638 17009 Z= 0.235 Chirality : 0.038 0.187 1924 Planarity : 0.003 0.058 2076 Dihedral : 7.401 63.278 1866 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.22 % Allowed : 14.26 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1488 helix: 2.03 (0.18), residues: 881 sheet: 0.30 (0.49), residues: 118 loop : -0.98 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.011 0.001 TYR G 165 PHE 0.011 0.001 PHE A 446 TRP 0.014 0.001 TRP A 865 HIS 0.002 0.000 HIS A 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.10 (12587) covalent geometry : angle 0.43735 / 0.23 (17009) hydrogen bonds : bond 0.05083 / 3.37 ( 643) hydrogen bonds : angle 3.57727 / 2.63 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.483 Fit side-chains REVERT: A 51 GLU cc_start: 0.7946 (tp30) cc_final: 0.7567 (tp30) REVERT: A 174 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7457 (mmtt) REVERT: A 830 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7255 (ttmt) REVERT: A 1166 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7717 (t80) REVERT: A 1280 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: G 63 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5562 (t-90) REVERT: G 112 LYS cc_start: 0.7271 (tptt) cc_final: 0.6311 (pmtt) REVERT: G 214 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7258 (tppp) outliers start: 29 outliers final: 12 residues processed: 158 average time/residue: 0.6103 time to fit residues: 103.9888 Evaluate side-chains 144 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1389 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 103 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 137 optimal weight: 0.0870 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1423 GLN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107429 restraints weight = 15485.795| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.49 r_work: 0.3106 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12587 Z= 0.135 Angle : 0.481 7.041 17009 Z= 0.255 Chirality : 0.040 0.168 1924 Planarity : 0.004 0.069 2076 Dihedral : 7.608 65.668 1862 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.30 % Allowed : 14.95 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1488 helix: 2.03 (0.18), residues: 870 sheet: 0.30 (0.49), residues: 118 loop : -1.04 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.015 0.001 TYR A 304 PHE 0.016 0.001 PHE A 81 TRP 0.011 0.001 TRP A 865 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12587) covalent geometry : angle 0.48093 / 0.26 (17009) hydrogen bonds : bond 0.06331 / 4.19 ( 643) hydrogen bonds : angle 3.69379 / 2.73 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.404 Fit side-chains REVERT: A 51 GLU cc_start: 0.7976 (tp30) cc_final: 0.7595 (tp30) REVERT: A 59 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: A 174 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7446 (mmtt) REVERT: A 329 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7041 (pttp) REVERT: A 528 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: A 1166 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7826 (t80) REVERT: A 1280 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: G 63 HIS cc_start: 0.6209 (OUTLIER) cc_final: 0.5544 (t-90) REVERT: G 112 LYS cc_start: 0.7281 (tptt) cc_final: 0.6330 (pmtt) REVERT: G 119 MET cc_start: 0.7903 (mtp) cc_final: 0.7703 (ttm) REVERT: G 214 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7313 (tppp) outliers start: 30 outliers final: 13 residues processed: 152 average time/residue: 0.6400 time to fit residues: 104.5854 Evaluate side-chains 148 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 51 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 104 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106394 restraints weight = 15466.552| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.48 r_work: 0.3107 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12587 Z= 0.144 Angle : 0.495 8.425 17009 Z= 0.262 Chirality : 0.040 0.164 1924 Planarity : 0.004 0.072 2076 Dihedral : 7.823 67.919 1861 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.07 % Allowed : 15.41 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1488 helix: 1.92 (0.18), residues: 873 sheet: 0.28 (0.49), residues: 118 loop : -1.04 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 170 TYR 0.015 0.001 TYR A 304 PHE 0.015 0.001 PHE A 81 TRP 0.012 0.001 TRP A 865 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12587) covalent geometry : angle 0.49496 / 0.26 (17009) hydrogen bonds : bond 0.06663 / 4.41 ( 643) hydrogen bonds : angle 3.75315 / 2.77 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.456 Fit side-chains REVERT: A 51 GLU cc_start: 0.8007 (tp30) cc_final: 0.7641 (tp30) REVERT: A 59 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7968 (ttm170) REVERT: A 174 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7503 (mmtt) REVERT: A 528 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: A 1126 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: A 1166 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 1280 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: G 63 HIS cc_start: 0.6333 (OUTLIER) cc_final: 0.5699 (t-90) REVERT: G 112 LYS cc_start: 0.7284 (tptt) cc_final: 0.6330 (pmtt) REVERT: G 214 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7389 (tppp) outliers start: 27 outliers final: 14 residues processed: 147 average time/residue: 0.6776 time to fit residues: 106.9943 Evaluate side-chains 145 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 133 optimal weight: 0.0270 chunk 112 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 overall best weight: 1.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107691 restraints weight = 15383.215| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.48 r_work: 0.3140 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12587 Z= 0.125 Angle : 0.469 7.884 17009 Z= 0.249 Chirality : 0.039 0.153 1924 Planarity : 0.004 0.071 2076 Dihedral : 7.680 67.626 1861 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.92 % Allowed : 16.10 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1488 helix: 2.05 (0.18), residues: 861 sheet: 0.30 (0.49), residues: 118 loop : -0.95 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.013 0.001 TYR A 304 PHE 0.014 0.001 PHE A 81 TRP 0.013 0.001 TRP A 865 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12587) covalent geometry : angle 0.46868 / 0.25 (17009) hydrogen bonds : bond 0.06132 / 4.06 ( 643) hydrogen bonds : angle 3.69445 / 2.73 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.447 Fit side-chains REVERT: A 51 GLU cc_start: 0.8007 (tp30) cc_final: 0.7635 (tp30) REVERT: A 59 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7934 (ttm170) REVERT: A 174 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7502 (mmtt) REVERT: A 528 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 1126 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: A 1166 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7858 (t80) REVERT: A 1280 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: G 63 HIS cc_start: 0.6291 (OUTLIER) cc_final: 0.5719 (t-90) REVERT: G 112 LYS cc_start: 0.7280 (tptt) cc_final: 0.6334 (pmtt) outliers start: 25 outliers final: 15 residues processed: 146 average time/residue: 0.6809 time to fit residues: 106.7115 Evaluate side-chains 147 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103119 restraints weight = 15638.322| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.45 r_work: 0.3062 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12587 Z= 0.227 Angle : 0.585 8.282 17009 Z= 0.308 Chirality : 0.044 0.159 1924 Planarity : 0.004 0.090 2076 Dihedral : 8.486 72.140 1861 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.84 % Allowed : 16.41 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1488 helix: 1.63 (0.18), residues: 872 sheet: 0.20 (0.48), residues: 120 loop : -1.13 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 170 TYR 0.020 0.002 TYR A 304 PHE 0.016 0.002 PHE A 446 TRP 0.010 0.002 TRP A 865 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.23 (12587) covalent geometry : angle 0.58459 / 0.31 (17009) hydrogen bonds : bond 0.08257 / 5.45 ( 643) hydrogen bonds : angle 3.97719 / 2.95 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.474 Fit side-chains REVERT: A 51 GLU cc_start: 0.8018 (tp30) cc_final: 0.7636 (tp30) REVERT: A 59 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: A 174 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7549 (mmtt) REVERT: A 469 MET cc_start: 0.8838 (mmp) cc_final: 0.8604 (mmt) REVERT: A 528 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 1280 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: G 63 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.5772 (t-90) REVERT: G 106 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8058 (ptmm) REVERT: G 112 LYS cc_start: 0.7318 (tptt) cc_final: 0.6355 (pmtt) outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 0.7103 time to fit residues: 103.1610 Evaluate side-chains 135 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1261 LEU Chi-restraints excluded: chain A residue 1280 GLN Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 63 HIS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 149 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108890 restraints weight = 15348.779| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.46 r_work: 0.3152 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12587 Z= 0.112 Angle : 0.459 8.324 17009 Z= 0.245 Chirality : 0.038 0.142 1924 Planarity : 0.004 0.087 2076 Dihedral : 7.675 68.483 1861 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.15 % Allowed : 16.95 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1488 helix: 1.98 (0.18), residues: 869 sheet: 0.27 (0.48), residues: 118 loop : -1.00 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 170 TYR 0.010 0.001 TYR G 165 PHE 0.011 0.001 PHE A 83 TRP 0.016 0.001 TRP A 865 HIS 0.002 0.000 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (12587) covalent geometry : angle 0.45936 / 0.24 (17009) hydrogen bonds : bond 0.05659 / 3.75 ( 643) hydrogen bonds : angle 3.69151 / 2.72 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.94 seconds wall clock time: 69 minutes 10.42 seconds (4150.42 seconds total)