Starting phenix.real_space_refine on Sat Dec 9 02:02:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1v_0606/12_2023/6o1v_0606_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6347 2.51 5 N 1598 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1239": "NH1" <-> "NH2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1386": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9450 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 32, 'TRANS': 1146} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 176 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'LJP': 1, 'POV': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 6.09, per 1000 atoms: 0.63 Number of scatterers: 9711 At special positions: 0 Unit cell: (78.28, 88.58, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1710 8.00 N 1598 7.00 C 6347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.96 Conformation dependent library (CDL) restraints added in 1.7 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 5 sheets defined 62.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.791A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.920A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.511A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 165 removed outlier: 4.984A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.604A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.515A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.691A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.744A pdb=" N GLY A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 215 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 removed outlier: 4.062A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 4.135A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 279 through 308 removed outlier: 4.210A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 328 removed outlier: 3.737A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.649A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.578A pdb=" N THR A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 375 removed outlier: 3.753A pdb=" N GLN A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.553A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.702A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 857 through 885 Processing helix chain 'A' and resid 908 through 921 removed outlier: 4.008A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 934 through 957 Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 969 through 984 removed outlier: 3.620A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1011 removed outlier: 3.665A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1060 removed outlier: 3.670A pdb=" N VAL A1020 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.996A pdb=" N VAL A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A1027 " --> pdb=" O VAL A1024 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A1028 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1031 " --> pdb=" O MET A1028 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A1034 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A1035 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A1041 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A1042 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A1044 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A1045 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A1046 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.895A pdb=" N THR A1053 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS A1054 " --> pdb=" O ILE A1051 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1056 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A1057 " --> pdb=" O HIS A1054 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A1058 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1120 removed outlier: 3.981A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1167 removed outlier: 4.003A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.629A pdb=" N PHE A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1283 Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 3.565A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.500A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1325 through 1329' Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.575A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1390 removed outlier: 3.637A pdb=" N LYS A1389 " --> pdb=" O ARG A1386 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A1390 " --> pdb=" O THR A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.527A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1433 Processing helix chain 'A' and resid 1436 through 1439 No H-bonds generated for 'chain 'A' and resid 1436 through 1439' Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 4.131A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.765A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.520A pdb=" N GLU A 395 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 393 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 454 through 457 removed outlier: 7.187A pdb=" N LYS A 615 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA A 457 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 617 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.535A pdb=" N LEU A 568 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N CYS A 491 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 570 " --> pdb=" O CYS A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1232 through 1234 Processing sheet with id= E, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 3.695A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1242 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: 3.09 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1813 1.33 - 1.46: 2365 1.46 - 1.58: 5644 1.58 - 1.70: 12 1.70 - 1.82: 79 Bond restraints: 9913 Sorted by residual: bond pdb=" C11 LJP A2001 " pdb=" C5 LJP A2001 " ideal model delta sigma weight residual 1.608 1.390 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV A2010 " pdb="C210 POV A2010 " ideal model delta sigma weight residual 1.333 1.533 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C13 LJP A2001 " pdb=" C14 LJP A2001 " ideal model delta sigma weight residual 1.529 1.349 0.180 2.00e-02 2.50e+03 8.07e+01 bond pdb=" C11 LJP A2001 " pdb=" C12 LJP A2001 " ideal model delta sigma weight residual 1.526 1.377 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" N3 LJP A2001 " pdb=" N4 LJP A2001 " ideal model delta sigma weight residual 1.388 1.273 0.115 2.00e-02 2.50e+03 3.33e+01 ... (remaining 9908 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.48: 230 106.48 - 113.50: 5370 113.50 - 120.52: 4352 120.52 - 127.54: 3381 127.54 - 134.56: 76 Bond angle restraints: 13409 Sorted by residual: angle pdb=" PB ATP A2005 " pdb=" O3B ATP A2005 " pdb=" PG ATP A2005 " ideal model delta sigma weight residual 139.87 125.69 14.18 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A2005 " pdb=" O3A ATP A2005 " pdb=" PB ATP A2005 " ideal model delta sigma weight residual 136.83 123.32 13.51 1.00e+00 1.00e+00 1.83e+02 angle pdb=" PB ATP A2004 " pdb=" O3B ATP A2004 " pdb=" PG ATP A2004 " ideal model delta sigma weight residual 139.87 126.62 13.25 1.00e+00 1.00e+00 1.76e+02 angle pdb=" PA ATP A2004 " pdb=" O3A ATP A2004 " pdb=" PB ATP A2004 " ideal model delta sigma weight residual 136.83 125.53 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" C28 POV A2010 " pdb=" C29 POV A2010 " pdb="C210 POV A2010 " ideal model delta sigma weight residual 127.79 108.76 19.03 3.00e+00 1.11e-01 4.02e+01 ... (remaining 13404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5427 17.11 - 34.22: 397 34.22 - 51.33: 123 51.33 - 68.43: 19 68.43 - 85.54: 7 Dihedral angle restraints: 5973 sinusoidal: 2497 harmonic: 3476 Sorted by residual: dihedral pdb=" CA ARG A 29 " pdb=" C ARG A 29 " pdb=" N GLN A 30 " pdb=" CA GLN A 30 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LEU A 138 " pdb=" C LEU A 138 " pdb=" N HIS A 139 " pdb=" CA HIS A 139 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 621 0.050 - 0.099: 552 0.099 - 0.148: 287 0.148 - 0.198: 74 0.198 - 0.247: 7 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CA ARG A 600 " pdb=" N ARG A 600 " pdb=" C ARG A 600 " pdb=" CB ARG A 600 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A1234 " pdb=" N ILE A1234 " pdb=" C ILE A1234 " pdb=" CB ILE A1234 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1538 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 LJP A2001 " -0.045 2.00e-02 2.50e+03 1.26e-01 4.37e+02 pdb=" C11 LJP A2001 " -0.004 2.00e-02 2.50e+03 pdb=" C12 LJP A2001 " 0.028 2.00e-02 2.50e+03 pdb=" C4 LJP A2001 " 0.109 2.00e-02 2.50e+03 pdb=" C5 LJP A2001 " 0.034 2.00e-02 2.50e+03 pdb=" C6 LJP A2001 " -0.009 2.00e-02 2.50e+03 pdb=" C7 LJP A2001 " 0.020 2.00e-02 2.50e+03 pdb=" N1 LJP A2001 " -0.280 2.00e-02 2.50e+03 pdb=" N2 LJP A2001 " -0.063 2.00e-02 2.50e+03 pdb=" O2 LJP A2001 " 0.269 2.00e-02 2.50e+03 pdb=" S1 LJP A2001 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A2010 " -0.125 2.00e-02 2.50e+03 1.27e-01 1.61e+02 pdb=" C29 POV A2010 " 0.119 2.00e-02 2.50e+03 pdb="C210 POV A2010 " 0.135 2.00e-02 2.50e+03 pdb="C211 POV A2010 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 348 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C MET A 348 " -0.049 2.00e-02 2.50e+03 pdb=" O MET A 348 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 349 " 0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 28 2.53 - 3.12: 6412 3.12 - 3.71: 14535 3.71 - 4.31: 20123 4.31 - 4.90: 34544 Nonbonded interactions: 75642 Sorted by model distance: nonbonded pdb="MG MG A2003 " pdb=" O2B ATP A2005 " model vdw 1.933 2.170 nonbonded pdb="MG MG A2002 " pdb=" O2B ATP A2004 " model vdw 1.959 2.170 nonbonded pdb="MG MG A2002 " pdb=" O3G ATP A2004 " model vdw 1.997 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A2002 " model vdw 2.102 2.170 nonbonded pdb="MG MG A2003 " pdb=" O3G ATP A2005 " model vdw 2.147 2.170 ... (remaining 75637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 6.010 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 29.780 Find NCS groups from input model: 0.270 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.218 9913 Z= 0.917 Angle : 1.791 19.025 13409 Z= 1.343 Chirality : 0.081 0.247 1541 Planarity : 0.006 0.127 1630 Dihedral : 13.834 85.542 3725 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.48 % Allowed : 5.22 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.21), residues: 1169 helix: -1.36 (0.16), residues: 723 sheet: -2.15 (0.60), residues: 69 loop : -2.29 (0.26), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A1098 HIS 0.009 0.002 HIS A1054 PHE 0.019 0.003 PHE A 354 TYR 0.031 0.003 TYR A 161 ARG 0.010 0.001 ARG A1097 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 255 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.2707 time to fit residues: 93.1459 Evaluate side-chains 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 39 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 525 GLN A 552 GLN A1042 GLN A1088 ASN A1100 GLN A1330 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9913 Z= 0.209 Angle : 0.593 9.019 13409 Z= 0.307 Chirality : 0.040 0.203 1541 Planarity : 0.004 0.036 1630 Dihedral : 8.790 85.572 1469 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.42 % Allowed : 11.98 % Favored : 85.60 % 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: -0.51 (0.23), residues: 1169 helix: 0.46 (0.18), residues: 736 sheet: -1.53 (0.62), residues: 69 loop : -1.62 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 865 HIS 0.007 0.001 HIS A 199 PHE 0.023 0.002 PHE A 342 TYR 0.018 0.002 TYR A 304 ARG 0.006 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 182 average time/residue: 0.2459 time to fit residues: 62.3616 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1187 time to fit residues: 3.6144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 39 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9913 Z= 0.191 Angle : 0.546 8.165 13409 Z= 0.276 Chirality : 0.038 0.175 1541 Planarity : 0.003 0.035 1630 Dihedral : 8.163 86.541 1469 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.22 % Allowed : 13.91 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1169 helix: 0.94 (0.19), residues: 740 sheet: -1.12 (0.59), residues: 81 loop : -1.24 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.026 0.001 PHE A 319 TYR 0.014 0.001 TYR A 517 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.300 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 170 average time/residue: 0.2392 time to fit residues: 57.4942 Evaluate side-chains 140 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1007 time to fit residues: 3.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 199 HIS ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9913 Z= 0.183 Angle : 0.526 7.005 13409 Z= 0.265 Chirality : 0.038 0.165 1541 Planarity : 0.003 0.033 1630 Dihedral : 7.426 80.502 1469 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.13 % Allowed : 16.23 % Favored : 81.64 % 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: 0.44 (0.25), residues: 1169 helix: 1.08 (0.19), residues: 739 sheet: -0.99 (0.57), residues: 87 loop : -0.99 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.005 0.001 HIS A1054 PHE 0.025 0.001 PHE A 319 TYR 0.012 0.001 TYR A 517 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 159 average time/residue: 0.2162 time to fit residues: 49.3116 Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1024 time to fit residues: 3.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.0030 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 1.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 207 GLN A 369 ASN A1330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9913 Z= 0.223 Angle : 0.541 7.540 13409 Z= 0.273 Chirality : 0.038 0.160 1541 Planarity : 0.003 0.031 1630 Dihedral : 7.104 77.151 1469 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.22 % Allowed : 16.81 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.25), residues: 1169 helix: 1.06 (0.19), residues: 745 sheet: -0.79 (0.57), residues: 89 loop : -0.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 HIS 0.006 0.001 HIS A1054 PHE 0.024 0.001 PHE A 319 TYR 0.019 0.001 TYR A 385 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 0.1972 time to fit residues: 43.2892 Evaluate side-chains 132 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0952 time to fit residues: 3.0237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 66 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.3266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 949 HIS A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9913 Z= 0.139 Angle : 0.501 7.118 13409 Z= 0.252 Chirality : 0.037 0.175 1541 Planarity : 0.003 0.030 1630 Dihedral : 6.875 81.883 1469 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.55 % Allowed : 18.07 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1169 helix: 1.25 (0.19), residues: 746 sheet: -0.70 (0.58), residues: 84 loop : -0.83 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.004 0.001 HIS A1054 PHE 0.021 0.001 PHE A 319 TYR 0.009 0.001 TYR A 517 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 148 average time/residue: 0.2127 time to fit residues: 46.1115 Evaluate side-chains 134 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0940 time to fit residues: 3.2052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9913 Z= 0.173 Angle : 0.522 8.112 13409 Z= 0.261 Chirality : 0.038 0.215 1541 Planarity : 0.003 0.030 1630 Dihedral : 6.708 86.910 1469 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.16 % Allowed : 17.97 % Favored : 80.87 % 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: 0.77 (0.25), residues: 1169 helix: 1.26 (0.19), residues: 746 sheet: -0.55 (0.59), residues: 84 loop : -0.76 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.004 0.001 HIS A1054 PHE 0.020 0.001 PHE A 319 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.2129 time to fit residues: 42.6089 Evaluate side-chains 135 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1026 time to fit residues: 3.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.0040 chunk 77 optimal weight: 0.2980 chunk 56 optimal weight: 0.0070 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A1038 GLN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9913 Z= 0.141 Angle : 0.502 7.209 13409 Z= 0.253 Chirality : 0.037 0.167 1541 Planarity : 0.003 0.029 1630 Dihedral : 6.551 89.178 1469 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.48 % Allowed : 18.84 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1169 helix: 1.42 (0.19), residues: 743 sheet: -0.48 (0.58), residues: 84 loop : -0.69 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.003 0.001 HIS A1054 PHE 0.018 0.001 PHE A 319 TYR 0.009 0.001 TYR A 304 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 0.2125 time to fit residues: 40.5523 Evaluate side-chains 123 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0916 time to fit residues: 1.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.0670 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A1038 GLN A1330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9913 Z= 0.149 Angle : 0.510 7.475 13409 Z= 0.254 Chirality : 0.037 0.180 1541 Planarity : 0.003 0.029 1630 Dihedral : 6.415 85.077 1469 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.68 % Allowed : 19.23 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1169 helix: 1.42 (0.19), residues: 745 sheet: -0.41 (0.58), residues: 84 loop : -0.69 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 216 HIS 0.004 0.001 HIS A1054 PHE 0.018 0.001 PHE A 78 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 128 average time/residue: 0.2108 time to fit residues: 39.3852 Evaluate side-chains 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1058 time to fit residues: 2.5854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A1330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9913 Z= 0.146 Angle : 0.509 7.734 13409 Z= 0.254 Chirality : 0.037 0.167 1541 Planarity : 0.003 0.029 1630 Dihedral : 6.280 81.570 1469 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.39 % Allowed : 19.52 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1169 helix: 1.45 (0.19), residues: 747 sheet: -0.37 (0.59), residues: 82 loop : -0.64 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 216 HIS 0.004 0.001 HIS A1054 PHE 0.018 0.001 PHE A 319 TYR 0.017 0.001 TYR A 517 ARG 0.004 0.000 ARG A 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 130 average time/residue: 0.2183 time to fit residues: 41.8945 Evaluate side-chains 120 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1762 time to fit residues: 2.1289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 372 GLN A1038 GLN A1330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103579 restraints weight = 14536.451| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.42 r_work: 0.3106 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9913 Z= 0.184 Angle : 0.534 7.965 13409 Z= 0.265 Chirality : 0.038 0.177 1541 Planarity : 0.003 0.029 1630 Dihedral : 6.314 79.612 1469 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.68 % Allowed : 19.61 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1169 helix: 1.38 (0.19), residues: 744 sheet: -0.42 (0.58), residues: 83 loop : -0.60 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 216 HIS 0.004 0.001 HIS A1054 PHE 0.021 0.001 PHE A 78 TYR 0.018 0.001 TYR A 517 ARG 0.004 0.000 ARG A 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.31 seconds wall clock time: 40 minutes 41.81 seconds (2441.81 seconds total)