Starting phenix.real_space_refine on Mon Dec 30 06:06:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dw9_47239/12_2024/9dw9_47239.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dw9_47239/12_2024/9dw9_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_47239/12_2024/9dw9_47239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dw9_47239/12_2024/9dw9_47239.map" model { file = "/net/cci-nas-00/data/ceres_data/9dw9_47239/12_2024/9dw9_47239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dw9_47239/12_2024/9dw9_47239.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'TYR:plan': 1, 'GLU: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, 'TPO:plan-1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 169 Unusual residues: {' CL': 4, ' MG': 2, 'ATP': 2, 'CLR': 1, 'D10': 4, 'UND': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} 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: 9.92, per 1000 atoms: 0.80 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.42 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: 4.42 Time building geometry restraints manager: 3.57 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: 5.130 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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= 0.243 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (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 TRP 0.020 0.002 TRP A1145 HIS 0.006 0.001 HIS A 146 PHE 0.023 0.002 PHE A 81 TYR 0.017 0.002 TYR A 304 ARG 0.008 0.001 ARG A 3 *********************** 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 : 1.584 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: 1.5602 time to fit residues: 257.1551 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 : 1.334 ------------------------------------------------------------------------------- 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 126 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 GLN A1439 GLN G 63 HIS G 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12587 Z= 0.321 Angle : 0.608 6.497 17009 Z= 0.323 Chirality : 0.045 0.179 1924 Planarity : 0.004 0.054 2076 Dihedral : 8.936 67.249 1891 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.84 % Allowed : 10.74 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1488 helix: 1.18 (0.18), residues: 872 sheet: -0.18 (0.45), residues: 120 loop : -1.00 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1145 HIS 0.004 0.001 HIS A 139 PHE 0.024 0.002 PHE A 81 TYR 0.019 0.002 TYR A 304 ARG 0.006 0.001 ARG A 170 *********************** 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 160 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.330 Fit side-chains REVERT: A 47 ASP cc_start: 0.7951 (t70) cc_final: 0.7687 (t70) REVERT: A 174 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7506 (mmtt) REVERT: A 469 MET cc_start: 0.8834 (mmp) cc_final: 0.8562 (mmt) REVERT: A 528 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 1166 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7887 (t80) REVERT: G 59 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7240 (ppp) REVERT: G 63 HIS cc_start: 0.6815 (OUTLIER) cc_final: 0.6012 (t-90) REVERT: G 108 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: G 112 LYS cc_start: 0.7285 (tptt) cc_final: 0.6249 (pmtt) REVERT: G 195 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7734 (ttt-90) REVERT: G 214 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7456 (tppp) outliers start: 37 outliers final: 14 residues processed: 148 average time/residue: 1.6654 time to fit residues: 264.7517 Evaluate side-chains 132 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 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 1220 THR Chi-restraints excluded: chain G residue 16 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.0270 chunk 147 optimal weight: 0.5980 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 GLN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12587 Z= 0.162 Angle : 0.468 5.278 17009 Z= 0.252 Chirality : 0.039 0.149 1924 Planarity : 0.003 0.035 2076 Dihedral : 7.979 64.557 1870 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.15 % Allowed : 12.27 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1488 helix: 1.64 (0.18), residues: 873 sheet: -0.00 (0.46), residues: 120 loop : -0.97 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 865 HIS 0.003 0.001 HIS A 856 PHE 0.015 0.001 PHE A 81 TYR 0.013 0.001 TYR A 304 ARG 0.004 0.000 ARG A1446 *********************** 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 155 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.448 Fit side-chains REVERT: A 51 GLU cc_start: 0.7920 (tp30) cc_final: 0.7452 (tp30) REVERT: A 174 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7445 (mmmt) REVERT: A 528 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 1166 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7846 (t80) REVERT: G 59 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7207 (ppp) REVERT: G 63 HIS cc_start: 0.6660 (OUTLIER) cc_final: 0.5910 (t-90) REVERT: G 112 LYS cc_start: 0.7265 (tptt) cc_final: 0.6244 (pmtt) REVERT: G 195 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7863 (mtt-85) REVERT: G 214 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7351 (tppp) outliers start: 28 outliers final: 12 residues processed: 148 average time/residue: 1.5258 time to fit residues: 243.5328 Evaluate side-chains 139 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 907 ILE Chi-restraints excluded: chain A residue 1166 PHE 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 214 LYS Chi-restraints excluded: chain G residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.5327 > 50: distance: 41 - 46: 26.794 distance: 46 - 47: 43.950 distance: 47 - 48: 45.699 distance: 47 - 50: 20.796 distance: 48 - 49: 41.269 distance: 48 - 53: 40.451 distance: 50 - 51: 27.556 distance: 50 - 52: 31.121 distance: 53 - 54: 36.422 distance: 54 - 55: 23.793 distance: 54 - 57: 13.135 distance: 55 - 56: 19.307 distance: 55 - 62: 24.796 distance: 57 - 58: 15.639 distance: 58 - 59: 9.683 distance: 62 - 63: 27.921 distance: 63 - 64: 22.891 distance: 64 - 65: 30.303 distance: 64 - 66: 40.077 distance: 66 - 67: 20.325 distance: 67 - 68: 39.234 distance: 67 - 70: 38.095 distance: 68 - 69: 16.117 distance: 68 - 77: 36.371 distance: 70 - 71: 13.321 distance: 71 - 72: 28.550 distance: 72 - 73: 6.762 distance: 73 - 74: 3.078 distance: 74 - 76: 3.565 distance: 77 - 78: 3.554 distance: 78 - 79: 13.161 distance: 79 - 80: 20.340 distance: 79 - 84: 16.579 distance: 81 - 82: 3.103 distance: 81 - 83: 10.571 distance: 84 - 85: 3.786 distance: 85 - 88: 4.121 distance: 86 - 98: 3.849 distance: 98 - 99: 6.197 distance: 99 - 100: 3.341 distance: 99 - 102: 6.243 distance: 100 - 101: 3.774 distance: 100 - 109: 4.457 distance: 102 - 103: 3.250 distance: 109 - 110: 12.644 distance: 110 - 111: 20.818 distance: 110 - 113: 5.954 distance: 111 - 112: 38.789 distance: 111 - 117: 22.114 distance: 113 - 114: 12.126 distance: 114 - 115: 6.903 distance: 114 - 116: 10.271 distance: 117 - 118: 36.860 distance: 118 - 119: 16.581 distance: 118 - 121: 34.064 distance: 119 - 120: 24.751 distance: 119 - 123: 23.857 distance: 121 - 122: 7.554 distance: 123 - 124: 20.521 distance: 124 - 125: 30.283 distance: 125 - 126: 11.992 distance: 125 - 127: 28.367