Starting phenix.real_space_refine on Fri Mar 14 07:19:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_8782.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_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/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_8782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_8782.map" model { file = "/net/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_8782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w81_8782/03_2025/5w81_8782.cif" } 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. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9393 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9329 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 41, 'TRANS': 1131} 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 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.30, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 48 helices and 5 sheets defined 68.2% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 45 through 63 removed outlier: 3.730A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) 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 69 through 98 removed outlier: 3.853A pdb=" N ALA A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.688A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) 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 166 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) Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.702A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.784A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.590A pdb=" N ALA A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 217 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) Processing helix chain 'A' and resid 221 through 269 removed outlier: 4.012A pdb=" N PHE A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) 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 269 through 277 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 279 through 329 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) removed outlier: 3.861A pdb=" N SER A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.719A pdb=" N THR A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 377 removed outlier: 3.805A pdb=" N GLY A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) 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 462 through 472 removed outlier: 3.678A pdb=" N LEU A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.996A pdb=" N LYS A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.571A pdb=" N LEU A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 563 removed outlier: 3.691A pdb=" N LYS A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) 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) removed outlier: 3.785A pdb=" N ARG A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 845 through 854 removed outlier: 4.091A pdb=" N ASN A 854 " --> pdb=" O TYR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 886 removed outlier: 4.044A pdb=" N LEU A 858 " --> pdb=" O ASN A 854 " (cutoff:3.500A) 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 921 through 935 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 938 through 966 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 968 through 975 removed outlier: 3.600A pdb=" N MET A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 994 removed outlier: 3.517A pdb=" N ILE A 980 " --> pdb=" O LYS A 976 " (cutoff:3.500A) 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) removed outlier: 3.651A pdb=" N ASP A 987 " --> pdb=" O ARG A 983 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 988 " --> pdb=" O PHE A 984 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 989 " --> pdb=" O THR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1019 removed outlier: 3.745A pdb=" N VAL A1003 " --> pdb=" O MET A 999 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1056 removed outlier: 3.930A pdb=" N ALA A1026 " --> pdb=" O TYR A1022 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Proline residue: A1029 - end of helix removed outlier: 3.852A pdb=" N ILE A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A1044 " --> pdb=" O TYR A1040 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A1050 " --> pdb=" O GLN A1046 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 4.136A pdb=" N PHE A1060 " --> pdb=" O ARG A1056 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A1069 " --> pdb=" O MET A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1076 removed outlier: 3.615A pdb=" N ILE A1073 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1126 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 1148 Processing helix chain 'A' and resid 1150 through 1166 removed outlier: 3.617A pdb=" N ALA A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1176 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 1250 through 1259 removed outlier: 3.892A pdb=" N PHE A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1286 removed outlier: 3.578A pdb=" N ALA A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1306 Processing helix chain 'A' and resid 1312 through 1323 Processing helix chain 'A' and resid 1325 through 1331 removed outlier: 3.870A pdb=" N ILE A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1364 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) removed outlier: 4.225A pdb=" N GLY A1364 " --> pdb=" O SER A1360 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1393 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 1407 through 1411 removed outlier: 4.016A pdb=" N GLU A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1435 Processing helix chain 'A' and resid 1446 through 1451 removed outlier: 3.907A pdb=" N LEU A1450 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1457 Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 446 removed outlier: 4.947A pdb=" N VAL A 398 " --> pdb=" O ASP A 442 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER A 444 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN A 396 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LYS A 446 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLU A 394 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 480 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A 398 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER A 478 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 490 removed outlier: 6.667A pdb=" N TYR A 568 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL A 602 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 570 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 614 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 615 " --> pdb=" O TYR A 626 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR A 626 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 617 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1228 through 1235 removed outlier: 6.755A pdb=" N LYS A1229 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A1217 " --> pdb=" O LYS A1229 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU A1231 " --> pdb=" O ASN A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1228 through 1235 removed outlier: 6.755A pdb=" N LYS A1229 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR A1217 " --> pdb=" O LYS A1229 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LEU A1231 " --> pdb=" O ASN A1215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1290 removed outlier: 6.203A pdb=" N GLY A1288 " --> pdb=" O LEU A1369 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP A1371 " --> pdb=" O GLY A1288 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A1290 " --> pdb=" O ASP A1371 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A1368 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N SER A1401 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A1370 " --> pdb=" O SER A1401 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG A1240 " --> pdb=" O SER A1413 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LEU A1415 " --> pdb=" O ARG A1240 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A1242 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET A1417 " --> pdb=" O GLY A1242 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A1244 " --> pdb=" O MET A1417 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1497 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: 3.37 Time building geometry restraints manager: 2.98 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: 0.00 - 4.06: 12902 4.06 - 8.11: 73 8.11 - 12.17: 6 12.17 - 16.22: 0 16.22 - 20.28: 4 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: 13 2.53 - 3.12: 6394 3.12 - 3.72: 13963 3.72 - 4.31: 19019 4.31 - 4.90: 31491 Nonbonded interactions: 70880 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 3.040 ... (remaining 70875 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.990 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.040 ------------------------------------------------------------------------------- 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= 0.530 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 to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7173 (t0) cc_final: 0.6927 (t0) REVERT: A 60 GLU cc_start: 0.6832 (tm-30) cc_final: 0.5829 (tm-30) REVERT: A 70 LEU cc_start: 0.7632 (tp) cc_final: 0.7405 (tt) REVERT: A 77 CYS cc_start: 0.6213 (p) cc_final: 0.5951 (p) REVERT: A 100 PRO cc_start: 0.9136 (Cg_exo) cc_final: 0.8888 (Cg_endo) REVERT: A 204 ILE cc_start: 0.4869 (mm) cc_final: 0.4560 (mt) REVERT: A 326 HIS cc_start: 0.8549 (t70) cc_final: 0.8325 (t-90) REVERT: A 384 MET cc_start: 0.6948 (mmp) cc_final: 0.6201 (mmm) REVERT: A 458 SER cc_start: 0.8544 (m) cc_final: 0.7877 (t) REVERT: A 461 SER cc_start: 0.8350 (m) cc_final: 0.7562 (t) REVERT: A 497 MET cc_start: 0.5461 (mtp) cc_final: 0.5168 (ttm) REVERT: A 513 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8321 (tp30) REVERT: A 527 GLU cc_start: 0.7911 (tt0) cc_final: 0.7553 (mp0) REVERT: A 578 ASP cc_start: 0.7289 (m-30) cc_final: 0.6669 (m-30) REVERT: A 625 PHE cc_start: 0.7618 (t80) cc_final: 0.7313 (t80) REVERT: A 854 ASN cc_start: 0.7330 (t0) cc_final: 0.6396 (t0) REVERT: A 1008 VAL cc_start: 0.6781 (t) cc_final: 0.6437 (t) REVERT: A 1231 LEU cc_start: 0.8450 (tt) cc_final: 0.8189 (mm) REVERT: A 1278 MET cc_start: 0.7323 (tpp) cc_final: 0.7099 (tpp) REVERT: A 1285 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8262 (mttt) REVERT: A 1322 GLU cc_start: 0.8346 (tt0) cc_final: 0.7953 (tt0) REVERT: A 1336 LEU cc_start: 0.7841 (mp) cc_final: 0.7244 (tt) REVERT: A 1342 TYR cc_start: 0.4866 (t80) cc_final: 0.4593 (t80) REVERT: A 1374 SER cc_start: 0.8541 (m) cc_final: 0.8262 (p) REVERT: A 1416 MET cc_start: 0.7109 (ttp) cc_final: 0.6838 (tmm) REVERT: A 1428 ILE cc_start: 0.8161 (mm) cc_final: 0.7408 (mp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2552 time to fit residues: 104.2464 Evaluate side-chains 177 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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: 0.4980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 288 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1210 GLN A1372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121506 restraints weight = 17459.578| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.22 r_work: 0.3430 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9597 Z= 0.212 Angle : 0.660 8.442 12985 Z= 0.335 Chirality : 0.043 0.256 1490 Planarity : 0.005 0.066 1589 Dihedral : 8.289 89.912 1335 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.16 % Allowed : 12.85 % Favored : 83.99 % 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: -0.80 (0.23), residues: 1163 helix: 0.26 (0.18), residues: 737 sheet: -2.19 (0.51), residues: 81 loop : -1.65 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1275 HIS 0.008 0.001 HIS A 608 PHE 0.019 0.002 PHE A1115 TYR 0.023 0.002 TYR A 921 ARG 0.008 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 236 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7002 (tp30) cc_final: 0.6392 (mp0) REVERT: A 26 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7274 (ttpp) REVERT: A 36 ASP cc_start: 0.7262 (t0) cc_final: 0.7046 (t0) REVERT: A 317 PHE cc_start: 0.6532 (t80) cc_final: 0.6045 (t80) REVERT: A 513 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8545 (tp30) REVERT: A 527 GLU cc_start: 0.8118 (tt0) cc_final: 0.7850 (mp0) REVERT: A 619 HIS cc_start: 0.7831 (t-170) cc_final: 0.7496 (t-90) REVERT: A 854 ASN cc_start: 0.7729 (t0) cc_final: 0.7356 (t0) REVERT: A 977 THR cc_start: 0.8516 (t) cc_final: 0.8077 (m) REVERT: A 987 ASP cc_start: 0.7349 (m-30) cc_final: 0.7110 (m-30) REVERT: A 1249 SER cc_start: 0.9312 (t) cc_final: 0.9032 (t) REVERT: A 1303 MET cc_start: 0.8285 (mtp) cc_final: 0.8060 (mtp) REVERT: A 1383 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8204 (tptt) REVERT: A 1416 MET cc_start: 0.7331 (ttp) cc_final: 0.6990 (tmm) REVERT: A 1437 HIS cc_start: 0.7741 (m-70) cc_final: 0.7175 (m-70) REVERT: A 1458 MET cc_start: 0.4785 (tpp) cc_final: 0.4480 (tpp) outliers start: 32 outliers final: 16 residues processed: 225 average time/residue: 0.1863 time to fit residues: 61.2592 Evaluate side-chains 172 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 0.0050 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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** A 271 HIS ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118075 restraints weight = 18035.230| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.37 r_work: 0.3399 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.6773 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= 0.217 Angle : 0.658 8.735 12985 Z= 0.334 Chirality : 0.041 0.205 1490 Planarity : 0.004 0.068 1589 Dihedral : 7.730 85.914 1335 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 15.81 % Favored : 80.83 % 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: -0.20 (0.24), residues: 1163 helix: 0.68 (0.18), residues: 749 sheet: -1.65 (0.57), residues: 75 loop : -1.48 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 217 HIS 0.005 0.001 HIS A 608 PHE 0.016 0.002 PHE A 624 TYR 0.020 0.002 TYR A 850 ARG 0.004 0.001 ARG A1447 *********************** 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 242 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7581 (tp30) cc_final: 0.6870 (mp0) REVERT: A 51 GLU cc_start: 0.8916 (pp20) cc_final: 0.8606 (pp20) REVERT: A 123 PHE cc_start: 0.5645 (t80) cc_final: 0.4996 (m-80) REVERT: A 138 LEU cc_start: 0.8817 (tp) cc_final: 0.8585 (tt) REVERT: A 317 PHE cc_start: 0.6738 (t80) cc_final: 0.6472 (t80) REVERT: A 488 SER cc_start: 0.9109 (t) cc_final: 0.8885 (m) REVERT: A 497 MET cc_start: 0.6966 (ttm) cc_final: 0.6649 (mtp) REVERT: A 969 MET cc_start: 0.7642 (mmm) cc_final: 0.7360 (tpp) REVERT: A 986 LYS cc_start: 0.7559 (tppt) cc_final: 0.7198 (ttmm) REVERT: A 999 MET cc_start: 0.7956 (tpt) cc_final: 0.7713 (mmm) REVERT: A 1368 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 1400 LEU cc_start: 0.9033 (mm) cc_final: 0.8735 (mp) REVERT: A 1416 MET cc_start: 0.7551 (ttp) cc_final: 0.7100 (tmm) REVERT: A 1417 MET cc_start: 0.8020 (ttm) cc_final: 0.7681 (ttm) REVERT: A 1437 HIS cc_start: 0.8083 (m-70) cc_final: 0.7574 (m-70) outliers start: 34 outliers final: 20 residues processed: 232 average time/residue: 0.1998 time to fit residues: 65.9451 Evaluate side-chains 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 223 ASN A 291 GLN A 620 ASN A1004 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117631 restraints weight = 18101.603| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.34 r_work: 0.3417 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.7601 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= 0.178 Angle : 0.594 8.361 12985 Z= 0.296 Chirality : 0.040 0.198 1490 Planarity : 0.004 0.067 1589 Dihedral : 7.496 88.389 1335 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.26 % Allowed : 19.57 % Favored : 77.17 % 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: 0.11 (0.24), residues: 1163 helix: 0.95 (0.19), residues: 747 sheet: -1.43 (0.56), residues: 75 loop : -1.45 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1124 HIS 0.005 0.001 HIS A 200 PHE 0.023 0.001 PHE A 136 TYR 0.011 0.001 TYR A 850 ARG 0.005 0.001 ARG A1447 *********************** 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 221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7426 (tp30) cc_final: 0.6626 (mp0) REVERT: A 48 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7628 (mm) REVERT: A 51 GLU cc_start: 0.8952 (pp20) cc_final: 0.8673 (pp20) REVERT: A 132 PHE cc_start: 0.7970 (t80) cc_final: 0.7698 (t80) REVERT: A 138 LEU cc_start: 0.8851 (tp) cc_final: 0.8615 (tt) REVERT: A 161 ILE cc_start: 0.7885 (tt) cc_final: 0.7622 (tt) REVERT: A 191 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8025 (ttpp) REVERT: A 233 LEU cc_start: 0.8401 (tp) cc_final: 0.8180 (mm) REVERT: A 491 SER cc_start: 0.9382 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 999 MET cc_start: 0.8109 (tpt) cc_final: 0.7853 (mmm) REVERT: A 1265 ASP cc_start: 0.8475 (m-30) cc_final: 0.7988 (m-30) REVERT: A 1416 MET cc_start: 0.7738 (ttp) cc_final: 0.7213 (tmm) REVERT: A 1417 MET cc_start: 0.8077 (ttm) cc_final: 0.7797 (ttm) REVERT: A 1437 HIS cc_start: 0.8134 (m-70) cc_final: 0.7673 (m-70) outliers start: 33 outliers final: 13 residues processed: 213 average time/residue: 0.1947 time to fit residues: 59.1351 Evaluate side-chains 180 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1114 LEU Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112274 restraints weight = 18430.068| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.30 r_work: 0.3337 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.8543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9597 Z= 0.217 Angle : 0.617 12.564 12985 Z= 0.308 Chirality : 0.040 0.192 1490 Planarity : 0.004 0.067 1589 Dihedral : 7.299 88.568 1335 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 3.95 % Allowed : 20.36 % Favored : 75.69 % 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: 0.16 (0.24), residues: 1163 helix: 1.04 (0.19), residues: 734 sheet: -1.19 (0.61), residues: 65 loop : -1.52 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.005 0.001 HIS A 608 PHE 0.029 0.001 PHE A 625 TYR 0.017 0.002 TYR A 850 ARG 0.005 0.001 ARG A1447 *********************** 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 219 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.086 Fit side-chains REVERT: A 48 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 51 GLU cc_start: 0.9014 (pp20) cc_final: 0.8698 (pp20) REVERT: A 102 LEU cc_start: 0.9243 (tp) cc_final: 0.8981 (tp) REVERT: A 304 ARG cc_start: 0.8256 (ttt180) cc_final: 0.7930 (ttm-80) REVERT: A 491 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.8874 (p) REVERT: A 617 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9048 (tt) REVERT: A 999 MET cc_start: 0.8153 (tpt) cc_final: 0.7943 (mmm) REVERT: A 1265 ASP cc_start: 0.8508 (m-30) cc_final: 0.8243 (m-30) REVERT: A 1406 GLU cc_start: 0.8166 (pt0) cc_final: 0.7963 (pm20) REVERT: A 1416 MET cc_start: 0.7962 (ttp) cc_final: 0.7445 (tmm) REVERT: A 1418 ASP cc_start: 0.7974 (t0) cc_final: 0.7674 (t0) REVERT: A 1437 HIS cc_start: 0.8321 (m-70) cc_final: 0.7834 (m-70) outliers start: 40 outliers final: 26 residues processed: 207 average time/residue: 0.1969 time to fit residues: 58.4706 Evaluate side-chains 191 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112499 restraints weight = 18181.879| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.26 r_work: 0.3339 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.9064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9597 Z= 0.192 Angle : 0.611 13.157 12985 Z= 0.299 Chirality : 0.039 0.191 1490 Planarity : 0.004 0.076 1589 Dihedral : 6.774 87.317 1335 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 3.46 % Allowed : 22.13 % Favored : 74.41 % 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: 0.24 (0.24), residues: 1163 helix: 1.11 (0.19), residues: 734 sheet: -1.08 (0.63), residues: 66 loop : -1.53 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 203 HIS 0.004 0.001 HIS A 608 PHE 0.028 0.001 PHE A 625 TYR 0.008 0.001 TYR A 514 ARG 0.003 0.000 ARG A1447 *********************** 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 215 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.984 Fit side-chains REVERT: A 24 MET cc_start: 0.8718 (mtp) cc_final: 0.8507 (mtm) REVERT: A 48 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7827 (mm) REVERT: A 51 GLU cc_start: 0.9011 (pp20) cc_final: 0.8699 (pp20) REVERT: A 102 LEU cc_start: 0.9272 (tp) cc_final: 0.9029 (tp) REVERT: A 193 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 304 ARG cc_start: 0.8351 (ttt180) cc_final: 0.8024 (ttm-80) REVERT: A 491 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.8921 (p) REVERT: A 999 MET cc_start: 0.8153 (tpt) cc_final: 0.7942 (mmm) REVERT: A 1166 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6870 (mmm-85) REVERT: A 1265 ASP cc_start: 0.8480 (m-30) cc_final: 0.8242 (m-30) REVERT: A 1322 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8483 (pt0) REVERT: A 1406 GLU cc_start: 0.8116 (pt0) cc_final: 0.7599 (tm-30) REVERT: A 1437 HIS cc_start: 0.8343 (m-70) cc_final: 0.7853 (m-70) outliers start: 35 outliers final: 18 residues processed: 206 average time/residue: 0.2055 time to fit residues: 59.6414 Evaluate side-chains 183 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111695 restraints weight = 18451.104| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.30 r_work: 0.3334 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.9367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9597 Z= 0.192 Angle : 0.612 16.255 12985 Z= 0.300 Chirality : 0.039 0.187 1490 Planarity : 0.004 0.082 1589 Dihedral : 6.604 83.604 1335 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 3.66 % Allowed : 21.94 % Favored : 74.41 % 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: 0.31 (0.24), residues: 1163 helix: 1.19 (0.19), residues: 733 sheet: -0.80 (0.64), residues: 65 loop : -1.60 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.003 0.001 HIS A 200 PHE 0.029 0.001 PHE A 625 TYR 0.012 0.001 TYR A 927 ARG 0.005 0.000 ARG A 554 *********************** 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 207 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.996 Fit side-chains REVERT: A 33 ARG cc_start: 0.7917 (mtp85) cc_final: 0.6984 (ttp-170) REVERT: A 47 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8407 (p0) REVERT: A 48 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 51 GLU cc_start: 0.9038 (pp20) cc_final: 0.8704 (pp20) REVERT: A 102 LEU cc_start: 0.9302 (tp) cc_final: 0.8989 (tp) REVERT: A 193 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8553 (m-30) REVERT: A 208 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 304 ARG cc_start: 0.8472 (ttt180) cc_final: 0.8159 (ttm-80) REVERT: A 491 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.8911 (p) REVERT: A 617 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8995 (tt) REVERT: A 1162 ASP cc_start: 0.8804 (t0) cc_final: 0.8557 (t0) REVERT: A 1166 ARG cc_start: 0.7358 (mmt180) cc_final: 0.6985 (mmm-85) REVERT: A 1322 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8400 (pt0) REVERT: A 1406 GLU cc_start: 0.8169 (pt0) cc_final: 0.7735 (tm-30) REVERT: A 1416 MET cc_start: 0.8426 (tmm) cc_final: 0.8188 (tmm) REVERT: A 1418 ASP cc_start: 0.8169 (t0) cc_final: 0.7961 (t0) REVERT: A 1437 HIS cc_start: 0.8320 (m-70) cc_final: 0.7855 (m-70) outliers start: 37 outliers final: 22 residues processed: 194 average time/residue: 0.2143 time to fit residues: 58.1938 Evaluate side-chains 185 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113005 restraints weight = 18764.348| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.36 r_work: 0.3351 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.9531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9597 Z= 0.169 Angle : 0.617 16.101 12985 Z= 0.301 Chirality : 0.039 0.184 1490 Planarity : 0.004 0.085 1589 Dihedral : 6.519 83.594 1335 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 2.57 % Allowed : 24.21 % Favored : 73.22 % 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: 0.47 (0.24), residues: 1163 helix: 1.30 (0.19), residues: 731 sheet: -0.62 (0.65), residues: 65 loop : -1.54 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1106 HIS 0.004 0.001 HIS A 608 PHE 0.032 0.001 PHE A 625 TYR 0.009 0.001 TYR A 927 ARG 0.004 0.000 ARG A 554 *********************** 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 207 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.009 Fit side-chains REVERT: A 33 ARG cc_start: 0.7900 (mtp85) cc_final: 0.6930 (ttp-170) REVERT: A 47 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8351 (p0) REVERT: A 48 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 51 GLU cc_start: 0.9037 (pp20) cc_final: 0.8698 (pp20) REVERT: A 102 LEU cc_start: 0.9233 (tp) cc_final: 0.8996 (tp) REVERT: A 138 LEU cc_start: 0.9156 (tp) cc_final: 0.8692 (tp) REVERT: A 193 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8500 (m-30) REVERT: A 208 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 304 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8136 (ttm-80) REVERT: A 617 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8910 (tt) REVERT: A 1052 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 1162 ASP cc_start: 0.8739 (t0) cc_final: 0.8461 (t0) REVERT: A 1166 ARG cc_start: 0.7278 (mmt180) cc_final: 0.6878 (mmm-85) REVERT: A 1322 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8352 (pt0) REVERT: A 1406 GLU cc_start: 0.8173 (pt0) cc_final: 0.7719 (tm-30) REVERT: A 1416 MET cc_start: 0.8385 (tmm) cc_final: 0.8177 (tmm) REVERT: A 1437 HIS cc_start: 0.8327 (m-70) cc_final: 0.7851 (m-70) outliers start: 26 outliers final: 16 residues processed: 201 average time/residue: 0.2105 time to fit residues: 59.6312 Evaluate side-chains 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112600 restraints weight = 18487.446| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.33 r_work: 0.3345 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.9664 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= 0.191 Angle : 0.628 15.462 12985 Z= 0.307 Chirality : 0.039 0.179 1490 Planarity : 0.004 0.087 1589 Dihedral : 6.557 85.969 1335 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 2.27 % Allowed : 24.70 % Favored : 73.02 % 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: 0.40 (0.24), residues: 1163 helix: 1.22 (0.19), residues: 737 sheet: -0.61 (0.65), residues: 65 loop : -1.55 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.004 0.001 HIS A 200 PHE 0.031 0.001 PHE A 625 TYR 0.008 0.001 TYR A 922 ARG 0.006 0.000 ARG A 336 *********************** 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 193 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7816 (mtp85) cc_final: 0.6874 (ttp-170) REVERT: A 47 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (p0) REVERT: A 48 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7858 (mm) REVERT: A 51 GLU cc_start: 0.9067 (pp20) cc_final: 0.8713 (pp20) REVERT: A 102 LEU cc_start: 0.9215 (tp) cc_final: 0.8983 (tp) REVERT: A 193 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: A 304 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8112 (ttm-80) REVERT: A 491 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 617 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 1052 GLU cc_start: 0.8587 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 1281 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8180 (tm-30) REVERT: A 1322 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8351 (pt0) REVERT: A 1406 GLU cc_start: 0.8275 (pt0) cc_final: 0.7838 (tm-30) REVERT: A 1416 MET cc_start: 0.8547 (tmm) cc_final: 0.8320 (tmm) REVERT: A 1418 ASP cc_start: 0.8033 (t0) cc_final: 0.7718 (t0) REVERT: A 1437 HIS cc_start: 0.8371 (m-70) cc_final: 0.7883 (m-70) REVERT: A 1446 GLU cc_start: 0.8363 (pp20) cc_final: 0.7612 (tm-30) outliers start: 23 outliers final: 17 residues processed: 187 average time/residue: 0.2099 time to fit residues: 56.6107 Evaluate side-chains 187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 109 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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** ** A1046 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 = 0.3794 r_free = 0.3794 target = 0.136292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113111 restraints weight = 18637.805| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.37 r_work: 0.3357 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.9803 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= 0.176 Angle : 0.627 14.690 12985 Z= 0.305 Chirality : 0.039 0.183 1490 Planarity : 0.004 0.088 1589 Dihedral : 6.578 86.673 1335 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 2.67 % Allowed : 24.51 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1163 helix: 1.22 (0.19), residues: 740 sheet: -0.51 (0.65), residues: 65 loop : -1.49 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.004 0.001 HIS A 200 PHE 0.033 0.001 PHE A 625 TYR 0.007 0.001 TYR A 516 ARG 0.006 0.000 ARG A 336 ********************** 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 202 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7786 (mtp85) cc_final: 0.6831 (ttp-170) REVERT: A 47 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8387 (p0) REVERT: A 48 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7844 (mm) REVERT: A 51 GLU cc_start: 0.9057 (pp20) cc_final: 0.8692 (pp20) REVERT: A 102 LEU cc_start: 0.9163 (tp) cc_final: 0.8947 (tp) REVERT: A 193 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8552 (m-30) REVERT: A 293 GLU cc_start: 0.8470 (tt0) cc_final: 0.7826 (tt0) REVERT: A 304 ARG cc_start: 0.8420 (ttt180) cc_final: 0.8149 (ttm-80) REVERT: A 491 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8773 (p) REVERT: A 617 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8961 (tt) REVERT: A 1052 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8430 (tm-30) REVERT: A 1166 ARG cc_start: 0.7463 (mmt180) cc_final: 0.7124 (mmt180) REVERT: A 1281 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8150 (tm-30) REVERT: A 1322 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8385 (pt0) REVERT: A 1406 GLU cc_start: 0.8274 (pt0) cc_final: 0.7517 (tm-30) REVERT: A 1416 MET cc_start: 0.8471 (tmm) cc_final: 0.7317 (tmm) REVERT: A 1418 ASP cc_start: 0.8082 (t0) cc_final: 0.7730 (t0) REVERT: A 1437 HIS cc_start: 0.8337 (m-70) cc_final: 0.7859 (m-70) REVERT: A 1446 GLU cc_start: 0.8309 (pp20) cc_final: 0.7635 (tm-30) outliers start: 27 outliers final: 17 residues processed: 192 average time/residue: 0.1885 time to fit residues: 52.2440 Evaluate side-chains 191 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1360 SER Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 3.9990 chunk 99 optimal weight: 0.0070 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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** A1047 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112587 restraints weight = 18462.173| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.35 r_work: 0.3341 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.9918 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= 0.184 Angle : 0.633 14.162 12985 Z= 0.309 Chirality : 0.039 0.182 1490 Planarity : 0.004 0.087 1589 Dihedral : 6.547 84.767 1335 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 2.47 % Allowed : 25.10 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1163 helix: 1.26 (0.19), residues: 739 sheet: -0.48 (0.65), residues: 65 loop : -1.45 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.004 0.001 HIS A 608 PHE 0.031 0.001 PHE A 625 TYR 0.010 0.001 TYR A 927 ARG 0.005 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4750.75 seconds wall clock time: 82 minutes 17.47 seconds (4937.47 seconds total)