Starting phenix.real_space_refine on Fri Dec 8 23:06:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/12_2023/5w81_8782_updated.pdb" } resolution = 3.37 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= 0.008 sd= 0.209 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 55 5.16 5 C 6091 2.51 5 N 1571 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 1038": "NH1" <-> "NH2" Residue "A ARG 1056": "NH1" <-> "NH2" Residue "A ARG 1078": "NH1" <-> "NH2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A ARG 1170": "NH1" <-> "NH2" Residue "A ARG 1208": "NH1" <-> "NH2" Residue "A ARG 1238": "NH1" <-> "NH2" Residue "A ARG 1318": "NH1" <-> "NH2" Residue "A GLU 1322": "OE1" <-> "OE2" Residue "A ARG 1366": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9393 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9393 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'peptide': 1173, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 41, 'TRANS': 1131, None: 4} Not linked: pdbres="MET A1458 " pdbres="ATP A1501 " Not linked: pdbres="ATP A1501 " pdbres="ATP A1502 " Not linked: pdbres="ATP A1502 " pdbres=" MG A1503 " Not linked: pdbres=" MG A1503 " pdbres=" MG A1504 " Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.10, per 1000 atoms: 0.54 Number of scatterers: 9393 At special positions: 0 Unit cell: (102.5, 119.72, 113.98, 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 55 16.00 P 6 15.00 Mg 2 11.99 O 1668 8.00 N 1571 7.00 C 6091 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 61.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 18 through 29 Proline residue: A 22 - end of helix removed outlier: 3.887A pdb=" N LYS A 26 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 29 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.804A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 108 removed outlier: 3.799A pdb=" N ARG A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N CYS A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.773A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.969A pdb=" N ILE A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 167 removed outlier: 3.561A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.617A pdb=" N ALA A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 178 through 218 removed outlier: 3.614A pdb=" N MET A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLY A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLY A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N MET A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.522A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.612A pdb=" N ALA A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Proline residue: A 247 - end of helix removed outlier: 3.798A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.792A pdb=" N LYS A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 328 removed outlier: 4.058A pdb=" N ILE A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix removed outlier: 3.862A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 376 removed outlier: 4.709A pdb=" N LEU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 3.579A pdb=" N MET A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.678A pdb=" N LEU A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 549 through 562 removed outlier: 3.948A pdb=" N ALA A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 855 through 885 removed outlier: 4.057A pdb=" N PHE A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 934 removed outlier: 3.533A pdb=" N ILE A 926 " --> pdb=" O TYR A 922 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 965 removed outlier: 3.560A pdb=" N LEU A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Proline residue: A 944 - end of helix removed outlier: 4.109A pdb=" N SER A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 974 Processing helix chain 'A' and resid 977 through 985 removed outlier: 4.178A pdb=" N ARG A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 993 Processing helix chain 'A' and resid 995 through 1018 removed outlier: 3.745A pdb=" N VAL A1003 " --> pdb=" O MET A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1055 removed outlier: 3.672A pdb=" N ALA A1026 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR A1028 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 3.570A pdb=" N ILE A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1036 " --> pdb=" O ILE A1033 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A1042 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A1043 " --> pdb=" O TYR A1040 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A1045 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A1046 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN A1047 " --> pdb=" O THR A1044 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A1049 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A1053 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A1054 " --> pdb=" O LEU A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1068 removed outlier: 3.570A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 Processing helix chain 'A' and resid 1079 through 1125 removed outlier: 3.744A pdb=" N HIS A1093 " --> pdb=" O THR A1089 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A1096 " --> pdb=" O THR A1092 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A1112 " --> pdb=" O LEU A1108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A1117 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A1118 " --> pdb=" O LEU A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 3.517A pdb=" N ALA A1144 " --> pdb=" O ILE A1141 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A1146 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A1147 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1175 removed outlier: 4.331A pdb=" N TRP A1153 " --> pdb=" O GLY A1149 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A1167 " --> pdb=" O GLY A1163 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A1169 " --> pdb=" O MET A1165 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1258 removed outlier: 3.892A pdb=" N PHE A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1285 Processing helix chain 'A' and resid 1301 through 1305 Processing helix chain 'A' and resid 1313 through 1323 Processing helix chain 'A' and resid 1326 through 1330 Processing helix chain 'A' and resid 1349 through 1363 removed outlier: 3.770A pdb=" N SER A1360 " --> pdb=" O CYS A1356 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A1362 " --> pdb=" O ALA A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1392 removed outlier: 3.707A pdb=" N LYS A1383 " --> pdb=" O PRO A1379 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN A1391 " --> pdb=" O LYS A1387 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1392 " --> pdb=" O THR A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1428 through 1434 Processing helix chain 'A' and resid 1447 through 1456 Proline residue: A1452 - end of helix removed outlier: 5.663A pdb=" N ASN A1455 " --> pdb=" O PHE A1451 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 480 through 482 removed outlier: 3.762A pdb=" N LYS A 480 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 445 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE A 443 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 622 through 627 removed outlier: 6.927A pdb=" N LEU A 617 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR A 626 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 615 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 614 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG A 599 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 455 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 601 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1211 through 1213 Processing sheet with id= D, first strand: chain 'A' and resid 1422 through 1425 removed outlier: 6.379A pdb=" N ILE A1398 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A1243 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU A1400 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N GLY A1245 " --> pdb=" O LEU A1400 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1254 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: 3.04 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1507 1.33 - 1.45: 2524 1.45 - 1.57: 5462 1.57 - 1.69: 10 1.69 - 1.81: 94 Bond restraints: 9597 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C4 ATP A1502 " pdb=" C5 ATP A1502 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.486 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP A1502 " pdb=" C6 ATP A1502 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C5 ATP A1502 " pdb=" N7 ATP A1502 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 9592 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.75: 253 106.75 - 114.19: 5421 114.19 - 121.62: 4612 121.62 - 129.06: 2623 129.06 - 136.49: 76 Bond angle restraints: 12985 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.59 20.28 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.66 17.17 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PA ATP A1502 " pdb=" O3A ATP A1502 " pdb=" PB ATP A1502 " ideal model delta sigma weight residual 136.83 120.27 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.54 8.26 1.00e+00 1.00e+00 6.82e+01 ... (remaining 12980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 5258 17.38 - 34.75: 379 34.75 - 52.13: 117 52.13 - 69.51: 24 69.51 - 86.88: 3 Dihedral angle restraints: 5781 sinusoidal: 2362 harmonic: 3419 Sorted by residual: dihedral pdb=" CA TRP A1205 " pdb=" C TRP A1205 " pdb=" N PRO A1206 " pdb=" CA PRO A1206 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C ILE A 332 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta harmonic sigma weight residual -122.00 -132.57 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" CA GLU A 218 " pdb=" C GLU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1002 0.053 - 0.106: 347 0.106 - 0.159: 98 0.159 - 0.212: 34 0.212 - 0.265: 9 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA GLU A1406 " pdb=" N GLU A1406 " pdb=" C GLU A1406 " pdb=" CB GLU A1406 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU A 115 " pdb=" N GLU A 115 " pdb=" C GLU A 115 " pdb=" CB GLU A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS A1335 " pdb=" N LYS A1335 " pdb=" C LYS A1335 " pdb=" CB LYS A1335 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1487 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 325 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1448 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C LEU A1448 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A1448 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A1449 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1057 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A1058 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.021 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 14 2.53 - 3.12: 6431 3.12 - 3.72: 13989 3.72 - 4.31: 19133 4.31 - 4.90: 31525 Nonbonded interactions: 71092 Sorted by model distance: nonbonded pdb=" O2B ATP A1502 " pdb="MG MG A1504 " model vdw 1.940 2.170 nonbonded pdb=" O2B ATP A1501 " pdb="MG MG A1503 " model vdw 1.994 2.170 nonbonded pdb=" OE1 GLN A1292 " pdb="MG MG A1504 " model vdw 2.016 2.170 nonbonded pdb=" OG SER A 464 " pdb="MG MG A1503 " model vdw 2.148 2.170 nonbonded pdb=" O ARG A1453 " pdb=" OG SER A1457 " model vdw 2.155 2.440 ... (remaining 71087 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=0.65 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: 2.670 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: 0.000 Extract box with map and model: 12.290 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 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 : 0.008 0.085 9597 Z= 0.523 Angle : 1.261 20.279 12985 Z= 0.900 Chirality : 0.064 0.265 1490 Planarity : 0.004 0.044 1589 Dihedral : 13.886 86.881 3569 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.09 % 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: -3.11 (0.20), residues: 1163 helix: -1.81 (0.15), residues: 693 sheet: -2.73 (0.53), residues: 74 loop : -2.05 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.005 0.001 HIS A1087 PHE 0.017 0.002 PHE A 136 TYR 0.015 0.002 TYR A 922 ARG 0.005 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2401 time to fit residues: 96.0927 Evaluate side-chains 170 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 608 HIS A1062 HIS A1210 GLN A1372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9597 Z= 0.210 Angle : 0.676 9.030 12985 Z= 0.342 Chirality : 0.042 0.269 1490 Planarity : 0.005 0.068 1589 Dihedral : 8.166 80.244 1335 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.75 % Allowed : 13.04 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1163 helix: 0.25 (0.18), residues: 715 sheet: -1.92 (0.55), residues: 81 loop : -1.66 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1275 HIS 0.007 0.001 HIS A 200 PHE 0.023 0.002 PHE A 82 TYR 0.017 0.002 TYR A 921 ARG 0.005 0.001 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 219 average time/residue: 0.1953 time to fit residues: 61.5913 Evaluate side-chains 173 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1079 time to fit residues: 5.2647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9597 Z= 0.332 Angle : 0.758 9.873 12985 Z= 0.387 Chirality : 0.044 0.220 1490 Planarity : 0.005 0.063 1589 Dihedral : 8.316 72.426 1335 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 3.36 % Allowed : 15.42 % Favored : 81.23 % 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: -0.95 (0.23), residues: 1163 helix: 0.04 (0.18), residues: 723 sheet: -1.71 (0.57), residues: 76 loop : -1.57 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 203 HIS 0.007 0.001 HIS A1062 PHE 0.026 0.002 PHE A 624 TYR 0.018 0.002 TYR A1022 ARG 0.006 0.001 ARG A1240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 212 time to evaluate : 1.183 Fit side-chains outliers start: 34 outliers final: 15 residues processed: 235 average time/residue: 0.2091 time to fit residues: 69.3342 Evaluate side-chains 175 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0931 time to fit residues: 4.1735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A1004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9597 Z= 0.280 Angle : 0.660 9.855 12985 Z= 0.328 Chirality : 0.041 0.205 1490 Planarity : 0.004 0.059 1589 Dihedral : 7.994 69.018 1335 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 2.57 % Allowed : 18.97 % Favored : 78.46 % 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: -0.58 (0.24), residues: 1163 helix: 0.40 (0.19), residues: 719 sheet: -1.52 (0.57), residues: 76 loop : -1.58 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 203 HIS 0.006 0.001 HIS A 619 PHE 0.036 0.002 PHE A 625 TYR 0.017 0.002 TYR A 511 ARG 0.004 0.000 ARG A1056 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.087 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 205 average time/residue: 0.2184 time to fit residues: 63.0736 Evaluate side-chains 180 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0912 time to fit residues: 4.3110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.9133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9597 Z= 0.157 Angle : 0.587 9.372 12985 Z= 0.288 Chirality : 0.038 0.189 1490 Planarity : 0.004 0.062 1589 Dihedral : 7.525 66.759 1335 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 1.38 % Allowed : 20.55 % Favored : 78.06 % 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: -0.29 (0.24), residues: 1163 helix: 0.61 (0.19), residues: 730 sheet: -1.43 (0.56), residues: 76 loop : -1.47 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 19 HIS 0.004 0.001 HIS A 619 PHE 0.034 0.001 PHE A 625 TYR 0.014 0.001 TYR A 927 ARG 0.007 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 204 average time/residue: 0.1989 time to fit residues: 58.3833 Evaluate side-chains 177 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1024 time to fit residues: 2.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.9516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9597 Z= 0.253 Angle : 0.657 10.070 12985 Z= 0.323 Chirality : 0.040 0.182 1490 Planarity : 0.004 0.067 1589 Dihedral : 7.642 68.307 1335 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.08 % Allowed : 22.43 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1163 helix: 0.62 (0.19), residues: 733 sheet: -1.36 (0.55), residues: 76 loop : -1.57 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.034 0.001 PHE A 625 TYR 0.014 0.002 TYR A 511 ARG 0.007 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.119 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 190 average time/residue: 0.2024 time to fit residues: 54.9110 Evaluate side-chains 181 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1155 time to fit residues: 3.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.9690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9597 Z= 0.195 Angle : 0.633 9.232 12985 Z= 0.306 Chirality : 0.039 0.192 1490 Planarity : 0.004 0.069 1589 Dihedral : 7.403 65.609 1335 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 0.99 % Allowed : 22.53 % Favored : 76.48 % 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: -0.13 (0.24), residues: 1163 helix: 0.74 (0.19), residues: 733 sheet: -1.19 (0.55), residues: 76 loop : -1.47 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.035 0.001 PHE A 625 TYR 0.012 0.001 TYR A 511 ARG 0.019 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.164 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 194 average time/residue: 0.2225 time to fit residues: 62.8828 Evaluate side-chains 176 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0930 time to fit residues: 2.3371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.9891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9597 Z= 0.188 Angle : 0.649 12.160 12985 Z= 0.311 Chirality : 0.038 0.187 1490 Planarity : 0.004 0.070 1589 Dihedral : 6.987 64.060 1335 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 1.09 % Allowed : 23.02 % Favored : 75.89 % 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: -0.07 (0.24), residues: 1163 helix: 0.80 (0.19), residues: 732 sheet: -1.11 (0.55), residues: 76 loop : -1.50 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.035 0.001 PHE A 625 TYR 0.011 0.001 TYR A 511 ARG 0.007 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.126 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 182 average time/residue: 0.1878 time to fit residues: 50.3824 Evaluate side-chains 178 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1007 time to fit residues: 3.0764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0470 chunk 105 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 1.0020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9597 Z= 0.182 Angle : 0.649 11.363 12985 Z= 0.309 Chirality : 0.039 0.186 1490 Planarity : 0.004 0.074 1589 Dihedral : 6.549 61.298 1335 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 0.40 % Allowed : 23.22 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1163 helix: 0.85 (0.19), residues: 733 sheet: -1.03 (0.54), residues: 79 loop : -1.44 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.036 0.001 PHE A 625 TYR 0.011 0.001 TYR A 511 ARG 0.009 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.191 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 179 average time/residue: 0.1746 time to fit residues: 47.4310 Evaluate side-chains 167 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0908 time to fit residues: 1.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 1.0126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9597 Z= 0.191 Angle : 0.670 15.476 12985 Z= 0.318 Chirality : 0.039 0.185 1490 Planarity : 0.004 0.076 1589 Dihedral : 6.441 64.884 1335 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 0.40 % Allowed : 24.01 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.24), residues: 1163 helix: 0.85 (0.19), residues: 733 sheet: -1.01 (0.55), residues: 79 loop : -1.43 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.036 0.001 PHE A 625 TYR 0.011 0.001 TYR A 511 ARG 0.009 0.000 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 169 average time/residue: 0.1902 time to fit residues: 48.0829 Evaluate side-chains 165 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1282 time to fit residues: 2.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.0670 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112707 restraints weight = 18503.858| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.27 r_work: 0.3350 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 1.0202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9597 Z= 0.176 Angle : 0.663 16.116 12985 Z= 0.311 Chirality : 0.039 0.185 1490 Planarity : 0.004 0.075 1589 Dihedral : 6.323 69.981 1335 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 0.59 % Allowed : 24.01 % Favored : 75.40 % 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: 0.09 (0.24), residues: 1163 helix: 0.91 (0.19), residues: 733 sheet: -0.82 (0.62), residues: 64 loop : -1.45 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 19 HIS 0.004 0.001 HIS A 200 PHE 0.035 0.001 PHE A 625 TYR 0.010 0.001 TYR A 511 ARG 0.012 0.000 ARG A 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.51 seconds wall clock time: 43 minutes 48.70 seconds (2628.70 seconds total)