Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:06:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/04_2023/5w81_8782_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/04_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_8782/04_2023/5w81_8782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/04_2023/5w81_8782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/04_2023/5w81_8782_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w81_8782/04_2023/5w81_8782_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.42, per 1000 atoms: 0.58 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: 3.72 Conformation dependent library (CDL) restraints added in 1.6 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: 1.60 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: 2.97 Time building geometry restraints manager: 4.05 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 - 14.79: 5121 14.79 - 29.57: 414 29.57 - 44.36: 137 44.36 - 59.15: 41 59.15 - 73.93: 6 Dihedral angle restraints: 5719 sinusoidal: 2300 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 5716 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: 4.020 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: 12.350 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- 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 : 13.302 73.931 3507 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 % 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 *********************** 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 : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2470 time to fit residues: 99.6944 Evaluate side-chains 170 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5546 ------------------------------------------------------------------------------- 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: 0.6168 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9597 Z= 0.212 Angle : 0.677 9.461 12985 Z= 0.339 Chirality : 0.042 0.263 1490 Planarity : 0.005 0.067 1589 Dihedral : 5.403 68.328 1273 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 3.46 % 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: -0.86 (0.23), residues: 1163 helix: 0.24 (0.18), residues: 715 sheet: -1.97 (0.55), residues: 81 loop : -1.71 (0.30), residues: 367 *********************** 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 229 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 218 average time/residue: 0.2067 time to fit residues: 65.5096 Evaluate side-chains 171 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1079 time to fit residues: 5.1158 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6350 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9597 Z= 0.182 Angle : 0.606 9.976 12985 Z= 0.299 Chirality : 0.039 0.217 1490 Planarity : 0.004 0.065 1589 Dihedral : 4.934 63.264 1273 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.37 % 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: -0.26 (0.24), residues: 1163 helix: 0.69 (0.19), residues: 721 sheet: -1.48 (0.61), residues: 76 loop : -1.52 (0.29), residues: 366 *********************** 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 207 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 196 average time/residue: 0.2032 time to fit residues: 57.0906 Evaluate side-chains 160 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0888 time to fit residues: 2.8878 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6436 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9597 Z= 0.177 Angle : 0.597 8.551 12985 Z= 0.294 Chirality : 0.040 0.237 1490 Planarity : 0.004 0.064 1589 Dihedral : 4.927 62.446 1273 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.47 % 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: -0.00 (0.24), residues: 1163 helix: 0.91 (0.19), residues: 714 sheet: -1.59 (0.57), residues: 76 loop : -1.36 (0.30), residues: 373 *********************** 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 212 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 202 average time/residue: 0.2055 time to fit residues: 59.4009 Evaluate side-chains 175 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0935 time to fit residues: 4.1422 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.8810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9597 Z= 0.282 Angle : 0.680 10.498 12985 Z= 0.337 Chirality : 0.041 0.198 1490 Planarity : 0.004 0.067 1589 Dihedral : 5.291 68.495 1273 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer Outliers : 2.47 % 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: -0.25 (0.24), residues: 1163 helix: 0.66 (0.19), residues: 726 sheet: -1.62 (0.55), residues: 76 loop : -1.43 (0.29), residues: 361 *********************** 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 212 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 203 average time/residue: 0.2197 time to fit residues: 62.6779 Evaluate side-chains 179 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0984 time to fit residues: 4.5933 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 188 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6529 moved from start: 0.9098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9597 Z= 0.170 Angle : 0.596 12.869 12985 Z= 0.289 Chirality : 0.038 0.192 1490 Planarity : 0.004 0.067 1589 Dihedral : 5.018 69.258 1273 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.68 % Rotamer Outliers : 1.09 % 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: -0.05 (0.24), residues: 1163 helix: 0.85 (0.19), residues: 734 sheet: -1.57 (0.54), residues: 76 loop : -1.46 (0.30), residues: 353 *********************** 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 206 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.088 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 200 average time/residue: 0.2084 time to fit residues: 59.6257 Evaluate side-chains 177 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0936 time to fit residues: 2.3338 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.9302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9597 Z= 0.181 Angle : 0.616 10.965 12985 Z= 0.299 Chirality : 0.039 0.195 1490 Planarity : 0.004 0.070 1589 Dihedral : 4.956 68.194 1273 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Rotamer Outliers : 0.99 % 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: -0.00 (0.24), residues: 1163 helix: 0.89 (0.19), residues: 732 sheet: -1.38 (0.54), residues: 76 loop : -1.48 (0.30), residues: 355 *********************** 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 193 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.048 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 188 average time/residue: 0.2126 time to fit residues: 57.3111 Evaluate side-chains 172 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0882 time to fit residues: 2.4057 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 0.0060 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** 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: 0.6521 moved from start: 0.9486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9597 Z= 0.163 Angle : 0.611 12.458 12985 Z= 0.293 Chirality : 0.038 0.199 1490 Planarity : 0.004 0.073 1589 Dihedral : 4.871 68.031 1273 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.25 % Rotamer Outliers : 0.40 % 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: 0.04 (0.24), residues: 1163 helix: 0.89 (0.19), residues: 739 sheet: -1.19 (0.54), residues: 76 loop : -1.47 (0.30), residues: 348 *********************** 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 194 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.096 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 191 average time/residue: 0.1886 time to fit residues: 53.0197 Evaluate side-chains 180 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0875 time to fit residues: 1.9954 ------------------------------------------------------------------------------- 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: 0.0170 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.0222 ------------------------------------------------------------------------------- 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 ** 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: 0.9757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9597 Z= 0.218 Angle : 0.653 13.934 12985 Z= 0.313 Chirality : 0.040 0.199 1490 Planarity : 0.004 0.077 1589 Dihedral : 4.935 67.987 1273 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer Outliers : 0.49 % 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: 0.01 (0.24), residues: 1163 helix: 0.85 (0.19), residues: 738 sheet: -1.23 (0.54), residues: 76 loop : -1.41 (0.30), residues: 349 *********************** 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 176 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.194 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 173 average time/residue: 0.1902 time to fit residues: 48.8873 Evaluate side-chains 168 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1164 time to fit residues: 2.2904 ------------------------------------------------------------------------------- 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: 0.0270 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.9862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9597 Z= 0.166 Angle : 0.646 14.143 12985 Z= 0.307 Chirality : 0.039 0.203 1490 Planarity : 0.004 0.079 1589 Dihedral : 4.815 67.011 1273 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer Outliers : 0.10 % 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: 0.17 (0.24), residues: 1163 helix: 1.03 (0.20), residues: 724 sheet: -1.16 (0.55), residues: 76 loop : -1.41 (0.29), residues: 363 ********************** 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 178 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.149 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1890 time to fit residues: 49.8466 Evaluate side-chains 173 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0843 time to fit residues: 1.6515 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 81 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112646 restraints weight = 18332.282| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.25 r_work: 0.3338 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 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 = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 1.0003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9597 Z= 0.190 Angle : 0.659 14.003 12985 Z= 0.313 Chirality : 0.039 0.200 1490 Planarity : 0.004 0.078 1589 Dihedral : 4.803 66.675 1273 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer Outliers : 0.30 % 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: 0.14 (0.24), residues: 1163 helix: 1.02 (0.20), residues: 724 sheet: -1.09 (0.54), residues: 79 loop : -1.49 (0.29), residues: 360 =============================================================================== Job complete usr+sys time: 2476.71 seconds wall clock time: 45 minutes 19.00 seconds (2719.00 seconds total)