Starting phenix.real_space_refine on Fri Sep 11 13:54:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_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_8782/09_2026/5w81_8782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.cif" model { file = "/net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w81_8782/09_2026/5w81_8782.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP: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: 1.94, per 1000 atoms: 0.21 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: 0.62 Conformation dependent library (CDL) restraints added in 233.5 milliseconds 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: 0.29 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: 1.65 Time building geometry restraints manager: 0.80 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 - 14.79: 5121 14.79 - 29.57: 414 29.57 - 44.36: 137 44.36 - 59.15: 41 59.15 - 73.93: 6 Dihedral angle restraints: 5719 sinusoidal: 2300 harmonic: 3419 Sorted by residual: dihedral pdb=" CA TRP A1205 " pdb=" C TRP A1205 " pdb=" N PRO A1206 " pdb=" CA PRO A1206 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C ILE A 332 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta harmonic sigma weight residual -122.00 -132.57 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" CA GLU A 218 " pdb=" C GLU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1002 0.053 - 0.106: 347 0.106 - 0.159: 98 0.159 - 0.212: 34 0.212 - 0.265: 9 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA GLU A1406 " pdb=" N GLU A1406 " pdb=" C GLU A1406 " pdb=" CB GLU A1406 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU A 115 " pdb=" N GLU A 115 " pdb=" C GLU A 115 " pdb=" CB GLU A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS A1335 " pdb=" N LYS A1335 " pdb=" C LYS A1335 " pdb=" CB LYS A1335 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1487 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 325 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1448 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C LEU A1448 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A1448 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A1449 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1057 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A1058 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.021 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 8.980 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 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= 0.593 Angle : 1.261 20.279 12985 Z= 0.900 Chirality : 0.064 0.265 1490 Planarity : 0.004 0.044 1589 Dihedral : 13.302 73.931 3507 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG A 554 TYR 0.015 0.002 TYR A 922 PHE 0.017 0.002 PHE A 136 TRP 0.011 0.001 TRP A 402 HIS 0.005 0.001 HIS A1087 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.59 ( 9597) covalent geometry : angle 1.26080 / 0.90 (12985) hydrogen bonds : bond 0.26241 / 17.24 ( 502) hydrogen bonds : angle 8.67122 / 6.21 ( 1497) *********************** 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 : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7172 (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: 0.7619 (t80) cc_final: 0.7313 (t80) REVERT: A 854 ASN cc_start: 0.7330 (t0) cc_final: 0.6649 (t0) REVERT: A 1008 VAL cc_start: 0.6781 (t) cc_final: 0.6438 (t) REVERT: A 1231 LEU cc_start: 0.8450 (tt) cc_final: 0.8207 (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: 0.7954 (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: 0.8263 (p) REVERT: A 1416 MET cc_start: 0.7109 (ttp) cc_final: 0.6826 (tmm) REVERT: A 1428 ILE cc_start: 0.8161 (mm) cc_final: 0.7428 (mp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1010 time to fit residues: 41.0540 Evaluate side-chains 176 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 223 ASN A 288 ASN A1062 HIS A1210 GLN A1372 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120740 restraints weight = 17791.107| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.27 r_work: 0.3446 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9597 Z= 0.192 Angle : 0.702 7.988 12985 Z= 0.357 Chirality : 0.044 0.291 1490 Planarity : 0.005 0.071 1589 Dihedral : 5.518 74.377 1273 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.85 % Allowed : 12.45 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.23), residues: 1163 helix: 0.12 (0.17), residues: 736 sheet: -2.09 (0.55), residues: 76 loop : -1.69 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 335 TYR 0.022 0.002 TYR A 921 PHE 0.018 0.002 PHE A 136 TRP 0.015 0.002 TRP A1275 HIS 0.009 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 9597) covalent geometry : angle 0.70201 / 0.36 (12985) hydrogen bonds : bond 0.04700 / 3.12 ( 502) hydrogen bonds : angle 4.53535 / 3.30 ( 1497) *********************** 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 240 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.357 Fit side-chains REVERT: A 7 GLU cc_start: 0.7100 (tp30) cc_final: 0.6526 (mp0) REVERT: A 26 LYS cc_start: 0.7687 (ttmm) cc_final: 0.7269 (ttpp) REVERT: A 453 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 527 GLU cc_start: 0.8129 (tt0) cc_final: 0.7874 (mp0) REVERT: A 619 HIS cc_start: 0.7922 (t-170) cc_final: 0.7610 (t-90) REVERT: A 977 THR cc_start: 0.8514 (t) cc_final: 0.8071 (m) REVERT: A 1249 SER cc_start: 0.9397 (t) cc_final: 0.9144 (t) REVERT: A 1374 SER cc_start: 0.9082 (m) cc_final: 0.8752 (p) REVERT: A 1383 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8186 (tptt) REVERT: A 1437 HIS cc_start: 0.7791 (m-70) cc_final: 0.7219 (m-70) REVERT: A 1458 MET cc_start: 0.4728 (tpp) cc_final: 0.4456 (tpp) outliers start: 39 outliers final: 18 residues processed: 227 average time/residue: 0.0793 time to fit residues: 26.4519 Evaluate side-chains 172 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1007 VAL 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 1422 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 97 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110955 restraints weight = 18198.521| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.28 r_work: 0.3306 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9597 Z= 0.204 Angle : 0.712 10.721 12985 Z= 0.364 Chirality : 0.043 0.221 1490 Planarity : 0.005 0.060 1589 Dihedral : 5.458 62.757 1273 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 4.84 % Allowed : 15.32 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1163 helix: 0.48 (0.18), residues: 744 sheet: -2.04 (0.57), residues: 65 loop : -1.62 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1240 TYR 0.015 0.002 TYR A1022 PHE 0.027 0.002 PHE A 625 TRP 0.017 0.002 TRP A 278 HIS 0.014 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 9597) covalent geometry : angle 0.71162 / 0.36 (12985) hydrogen bonds : bond 0.05994 / 3.93 ( 502) hydrogen bonds : angle 4.69587 / 3.39 ( 1497) *********************** 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 245 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7678 (tp30) cc_final: 0.6722 (mp0) REVERT: A 51 GLU cc_start: 0.8998 (pp20) cc_final: 0.8610 (pp20) REVERT: A 311 TYR cc_start: 0.7906 (t80) cc_final: 0.7534 (t80) REVERT: A 491 SER cc_start: 0.9382 (OUTLIER) cc_final: 0.8864 (p) REVERT: A 854 ASN cc_start: 0.7461 (t0) cc_final: 0.7229 (t0) REVERT: A 979 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7250 (ttt90) REVERT: A 986 LYS cc_start: 0.7536 (tppt) cc_final: 0.7186 (ttmm) REVERT: A 999 MET cc_start: 0.8047 (tpt) cc_final: 0.7794 (mmm) REVERT: A 1231 LEU cc_start: 0.8790 (tt) cc_final: 0.8462 (mm) REVERT: A 1416 MET cc_start: 0.8491 (tmm) cc_final: 0.7150 (tmm) REVERT: A 1418 ASP cc_start: 0.7814 (t0) cc_final: 0.7610 (t0) REVERT: A 1437 HIS cc_start: 0.8345 (m-70) cc_final: 0.7944 (m-70) outliers start: 49 outliers final: 26 residues processed: 234 average time/residue: 0.0923 time to fit residues: 31.1737 Evaluate side-chains 187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 349 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 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 1007 VAL Chi-restraints excluded: chain A residue 1028 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 1213 VAL Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1327 THR Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1422 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 75 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 291 GLN A1004 GLN A1047 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113640 restraints weight = 18451.253| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.24 r_work: 0.3361 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.8486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9597 Z= 0.134 Angle : 0.635 12.297 12985 Z= 0.308 Chirality : 0.040 0.204 1490 Planarity : 0.004 0.062 1589 Dihedral : 5.172 73.409 1273 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.51 % Rotamer: Outliers : 3.95 % Allowed : 18.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1163 helix: 0.88 (0.19), residues: 750 sheet: -1.73 (0.55), residues: 75 loop : -1.40 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 304 TYR 0.009 0.001 TYR A 859 PHE 0.032 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.007 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9597) covalent geometry : angle 0.63490 / 0.31 (12985) hydrogen bonds : bond 0.04431 / 2.90 ( 502) hydrogen bonds : angle 4.20403 / 3.07 ( 1497) *********************** 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 230 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9014 (pp20) cc_final: 0.8698 (pp20) REVERT: A 193 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8448 (m-30) REVERT: A 208 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7428 (tm-30) REVERT: A 282 MET cc_start: 0.8271 (tpp) cc_final: 0.8032 (mmt) REVERT: A 491 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 979 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7481 (mtp85) REVERT: A 1165 MET cc_start: 0.8666 (tpp) cc_final: 0.8381 (tpp) REVERT: A 1231 LEU cc_start: 0.8715 (tt) cc_final: 0.8379 (mm) REVERT: A 1303 MET cc_start: 0.8778 (mtp) cc_final: 0.8380 (ttp) REVERT: A 1368 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7842 (mt) REVERT: A 1416 MET cc_start: 0.8600 (tmm) cc_final: 0.7386 (tmm) REVERT: A 1417 MET cc_start: 0.8678 (ttm) cc_final: 0.8150 (ttm) REVERT: A 1418 ASP cc_start: 0.7787 (t0) cc_final: 0.7434 (t0) REVERT: A 1437 HIS cc_start: 0.8252 (m-70) cc_final: 0.7773 (m-70) outliers start: 40 outliers final: 19 residues processed: 217 average time/residue: 0.0892 time to fit residues: 27.8584 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 456 THR 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 620 ASN 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 1116 VAL Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1422 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 115 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 620 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113731 restraints weight = 18525.736| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.27 r_work: 0.3372 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.8849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9597 Z= 0.117 Angle : 0.595 12.092 12985 Z= 0.289 Chirality : 0.039 0.191 1490 Planarity : 0.004 0.064 1589 Dihedral : 4.930 73.763 1273 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 2.87 % Allowed : 21.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.24), residues: 1163 helix: 1.15 (0.19), residues: 739 sheet: -1.39 (0.56), residues: 75 loop : -1.31 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.012 0.001 TYR A 927 PHE 0.031 0.001 PHE A 625 TRP 0.008 0.001 TRP A 203 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9597) covalent geometry : angle 0.59477 / 0.29 (12985) hydrogen bonds : bond 0.04054 / 2.62 ( 502) hydrogen bonds : angle 3.99071 / 2.94 ( 1497) *********************** 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 221 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.369 Fit side-chains REVERT: A 51 GLU cc_start: 0.9026 (pp20) cc_final: 0.8657 (pp20) REVERT: A 102 LEU cc_start: 0.9253 (tp) cc_final: 0.8860 (tp) REVERT: A 193 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: A 491 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 979 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7590 (mtp180) REVERT: A 1265 ASP cc_start: 0.8534 (m-30) cc_final: 0.8282 (m-30) REVERT: A 1402 GLU cc_start: 0.7679 (tp30) cc_final: 0.7409 (tm-30) REVERT: A 1416 MET cc_start: 0.8571 (tmm) cc_final: 0.7445 (tmm) REVERT: A 1417 MET cc_start: 0.8638 (ttm) cc_final: 0.8133 (ttm) REVERT: A 1418 ASP cc_start: 0.7893 (t0) cc_final: 0.7608 (t0) REVERT: A 1437 HIS cc_start: 0.8296 (m-70) cc_final: 0.7852 (m-70) outliers start: 29 outliers final: 14 residues processed: 212 average time/residue: 0.0941 time to fit residues: 28.4736 Evaluate side-chains 185 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 193 ASP 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 295 LYS Chi-restraints excluded: chain A residue 456 THR 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 844 TRP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1336 LEU 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 72 optimal weight: 3.9990 chunk 56 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113425 restraints weight = 18493.821| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.30 r_work: 0.3365 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.9063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9597 Z= 0.119 Angle : 0.601 12.060 12985 Z= 0.289 Chirality : 0.039 0.184 1490 Planarity : 0.004 0.070 1589 Dihedral : 4.849 70.479 1273 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 3.26 % Allowed : 20.85 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1163 helix: 1.18 (0.19), residues: 739 sheet: -1.30 (0.58), residues: 65 loop : -1.54 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 304 TYR 0.008 0.001 TYR A 516 PHE 0.030 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9597) covalent geometry : angle 0.60090 / 0.29 (12985) hydrogen bonds : bond 0.03971 / 2.57 ( 502) hydrogen bonds : angle 3.94657 / 2.91 ( 1497) *********************** 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 212 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.385 Fit side-chains REVERT: A 51 GLU cc_start: 0.9032 (pp20) cc_final: 0.8666 (pp20) REVERT: A 102 LEU cc_start: 0.9258 (tp) cc_final: 0.9017 (tp) REVERT: A 109 SER cc_start: 0.6721 (OUTLIER) cc_final: 0.6516 (t) REVERT: A 193 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: A 293 GLU cc_start: 0.8608 (tt0) cc_final: 0.8305 (tt0) REVERT: A 295 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7543 (mmtt) REVERT: A 345 MET cc_start: 0.8354 (mmp) cc_final: 0.8098 (mmm) REVERT: A 491 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.8792 (p) REVERT: A 979 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7541 (mtp85) REVERT: A 1231 LEU cc_start: 0.8697 (tt) cc_final: 0.8385 (mm) REVERT: A 1265 ASP cc_start: 0.8519 (m-30) cc_final: 0.8276 (m-30) REVERT: A 1416 MET cc_start: 0.8531 (tmm) cc_final: 0.7044 (tmm) REVERT: A 1417 MET cc_start: 0.8671 (ttm) cc_final: 0.7971 (ttm) REVERT: A 1418 ASP cc_start: 0.7858 (t0) cc_final: 0.7544 (t0) REVERT: A 1437 HIS cc_start: 0.8236 (m-70) cc_final: 0.7806 (m-70) outliers start: 33 outliers final: 20 residues processed: 201 average time/residue: 0.0939 time to fit residues: 27.1720 Evaluate side-chains 190 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 193 ASP 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 295 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 THR 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 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 1166 ARG Chi-restraints excluded: chain A residue 1249 SER 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 108 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.0270 chunk 76 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116285 restraints weight = 18537.665| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.32 r_work: 0.3386 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.9226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9597 Z= 0.108 Angle : 0.591 12.185 12985 Z= 0.282 Chirality : 0.038 0.182 1490 Planarity : 0.004 0.071 1589 Dihedral : 4.688 69.203 1273 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 2.27 % Allowed : 22.23 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1163 helix: 1.25 (0.19), residues: 737 sheet: -1.00 (0.62), residues: 65 loop : -1.50 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.014 0.001 TYR A 850 PHE 0.031 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.003 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9597) covalent geometry : angle 0.59063 / 0.28 (12985) hydrogen bonds : bond 0.03745 / 2.41 ( 502) hydrogen bonds : angle 3.83059 / 2.82 ( 1497) *********************** 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 209 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7849 (mtp85) cc_final: 0.6941 (ttp-170) REVERT: A 51 GLU cc_start: 0.9032 (pp20) cc_final: 0.8676 (pp20) REVERT: A 102 LEU cc_start: 0.9191 (tp) cc_final: 0.8963 (tp) REVERT: A 109 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6508 (t) REVERT: A 293 GLU cc_start: 0.8610 (tt0) cc_final: 0.8310 (tt0) REVERT: A 295 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7522 (mmtt) REVERT: A 345 MET cc_start: 0.8316 (mmp) cc_final: 0.8062 (mmm) REVERT: A 1022 TYR cc_start: 0.7952 (m-80) cc_final: 0.7695 (m-80) REVERT: A 1052 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 1231 LEU cc_start: 0.8692 (tt) cc_final: 0.8362 (mm) REVERT: A 1265 ASP cc_start: 0.8478 (m-30) cc_final: 0.8252 (m-30) REVERT: A 1416 MET cc_start: 0.8532 (tmm) cc_final: 0.7097 (tmm) REVERT: A 1417 MET cc_start: 0.8617 (ttm) cc_final: 0.7982 (ttm) REVERT: A 1418 ASP cc_start: 0.8010 (t0) cc_final: 0.7565 (t0) REVERT: A 1437 HIS cc_start: 0.8168 (m-70) cc_final: 0.7775 (m-70) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 0.0856 time to fit residues: 25.2883 Evaluate side-chains 186 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 109 SER 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 295 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1166 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 0.0010 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 103 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116715 restraints weight = 18404.825| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.31 r_work: 0.3401 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.9344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9597 Z= 0.108 Angle : 0.614 12.690 12985 Z= 0.287 Chirality : 0.039 0.181 1490 Planarity : 0.004 0.064 1589 Dihedral : 4.603 68.196 1273 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 2.47 % Allowed : 22.43 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1163 helix: 1.28 (0.19), residues: 738 sheet: -0.96 (0.60), residues: 65 loop : -1.43 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.007 0.001 TYR A 516 PHE 0.031 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.003 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9597) covalent geometry : angle 0.61405 / 0.29 (12985) hydrogen bonds : bond 0.03628 / 2.34 ( 502) hydrogen bonds : angle 3.79793 / 2.80 ( 1497) *********************** 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: 25 poor density : 182 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7893 (mtp85) cc_final: 0.6991 (ttp-170) REVERT: A 51 GLU cc_start: 0.9016 (pp20) cc_final: 0.8675 (pp20) REVERT: A 102 LEU cc_start: 0.9186 (tp) cc_final: 0.8966 (tp) REVERT: A 109 SER cc_start: 0.6767 (OUTLIER) cc_final: 0.6379 (p) REVERT: A 193 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: A 293 GLU cc_start: 0.8591 (tt0) cc_final: 0.8320 (tt0) REVERT: A 295 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7516 (mmtt) REVERT: A 304 ARG cc_start: 0.8352 (ttt-90) cc_final: 0.7862 (ttm-80) REVERT: A 345 MET cc_start: 0.8334 (mmp) cc_final: 0.8092 (mmm) REVERT: A 380 GLU cc_start: 0.8325 (tt0) cc_final: 0.8063 (tp30) REVERT: A 491 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 619 HIS cc_start: 0.8530 (t-90) cc_final: 0.8317 (t-90) REVERT: A 1022 TYR cc_start: 0.7911 (m-80) cc_final: 0.7701 (m-80) REVERT: A 1052 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 1416 MET cc_start: 0.8531 (tmm) cc_final: 0.7142 (tmm) REVERT: A 1417 MET cc_start: 0.8609 (ttm) cc_final: 0.7980 (ttm) REVERT: A 1418 ASP cc_start: 0.7996 (t0) cc_final: 0.7588 (t0) REVERT: A 1437 HIS cc_start: 0.8100 (m-70) cc_final: 0.7741 (m-70) outliers start: 25 outliers final: 14 residues processed: 198 average time/residue: 0.0875 time to fit residues: 25.2371 Evaluate side-chains 191 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER 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 453 LEU Chi-restraints excluded: chain A residue 456 THR 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 844 TRP 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 1085 LEU Chi-restraints excluded: chain A residue 1166 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111119 restraints weight = 18546.466| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.29 r_work: 0.3321 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.9596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9597 Z= 0.146 Angle : 0.667 12.885 12985 Z= 0.316 Chirality : 0.040 0.180 1490 Planarity : 0.004 0.063 1589 Dihedral : 4.852 67.968 1273 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 2.47 % Allowed : 23.42 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1163 helix: 1.24 (0.19), residues: 737 sheet: -0.93 (0.61), residues: 65 loop : -1.42 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.010 0.001 TYR A 307 PHE 0.029 0.001 PHE A 625 TRP 0.007 0.001 TRP A 18 HIS 0.009 0.001 HIS A1403 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9597) covalent geometry : angle 0.66666 / 0.32 (12985) hydrogen bonds : bond 0.04409 / 2.89 ( 502) hydrogen bonds : angle 3.98949 / 2.91 ( 1497) *********************** 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 208 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.354 Fit side-chains REVERT: A 33 ARG cc_start: 0.7882 (mtp85) cc_final: 0.6971 (ttp-170) REVERT: A 51 GLU cc_start: 0.9076 (pp20) cc_final: 0.8695 (pp20) REVERT: A 102 LEU cc_start: 0.9245 (tp) cc_final: 0.9042 (tp) REVERT: A 109 SER cc_start: 0.6849 (OUTLIER) cc_final: 0.6434 (p) REVERT: A 193 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: A 225 PHE cc_start: 0.7596 (t80) cc_final: 0.7394 (t80) REVERT: A 293 GLU cc_start: 0.8637 (tt0) cc_final: 0.8339 (tt0) REVERT: A 299 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6614 (mtpt) REVERT: A 345 MET cc_start: 0.8376 (mmp) cc_final: 0.8134 (mmm) REVERT: A 451 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 491 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.8818 (p) REVERT: A 979 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7644 (mtp180) REVERT: A 1085 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 1416 MET cc_start: 0.8555 (tmm) cc_final: 0.7159 (tmm) REVERT: A 1417 MET cc_start: 0.8679 (ttm) cc_final: 0.8037 (ttm) REVERT: A 1418 ASP cc_start: 0.8111 (t0) cc_final: 0.7657 (t0) REVERT: A 1437 HIS cc_start: 0.8222 (m-70) cc_final: 0.7788 (m-70) outliers start: 25 outliers final: 15 residues processed: 200 average time/residue: 0.0913 time to fit residues: 26.4035 Evaluate side-chains 190 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 THR 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 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1249 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 60 optimal weight: 0.0050 chunk 79 optimal weight: 0.9980 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114417 restraints weight = 18499.082| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.31 r_work: 0.3378 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.9718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9597 Z= 0.120 Angle : 0.666 14.687 12985 Z= 0.314 Chirality : 0.039 0.180 1490 Planarity : 0.004 0.061 1589 Dihedral : 4.746 68.779 1273 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 1.98 % Allowed : 24.41 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.24), residues: 1163 helix: 1.28 (0.19), residues: 738 sheet: -0.86 (0.61), residues: 65 loop : -1.40 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.008 0.001 TYR A 927 PHE 0.032 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.003 0.000 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9597) covalent geometry : angle 0.66640 / 0.31 (12985) hydrogen bonds : bond 0.03989 / 2.57 ( 502) hydrogen bonds : angle 3.82896 / 2.80 ( 1497) ********************** 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 201 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7007 (ttp-170) REVERT: A 51 GLU cc_start: 0.9079 (pp20) cc_final: 0.8718 (pp20) REVERT: A 56 GLU cc_start: 0.9245 (mp0) cc_final: 0.8933 (mp0) REVERT: A 109 SER cc_start: 0.6698 (OUTLIER) cc_final: 0.6343 (p) REVERT: A 193 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: A 293 GLU cc_start: 0.8596 (tt0) cc_final: 0.8318 (tt0) REVERT: A 345 MET cc_start: 0.8324 (mmp) cc_final: 0.8106 (mmm) REVERT: A 380 GLU cc_start: 0.8378 (tt0) cc_final: 0.8105 (tp30) REVERT: A 451 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 491 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8770 (p) REVERT: A 979 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7665 (mtp180) REVERT: A 1085 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8758 (tt) REVERT: A 1416 MET cc_start: 0.8528 (tmm) cc_final: 0.7161 (tmm) REVERT: A 1417 MET cc_start: 0.8645 (ttm) cc_final: 0.8015 (ttm) REVERT: A 1418 ASP cc_start: 0.8055 (t0) cc_final: 0.7656 (t0) REVERT: A 1437 HIS cc_start: 0.8147 (m-70) cc_final: 0.7747 (m-70) outliers start: 20 outliers final: 15 residues processed: 194 average time/residue: 0.0919 time to fit residues: 25.8047 Evaluate side-chains 192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 THR 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 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1249 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112600 restraints weight = 18586.262| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.29 r_work: 0.3333 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.9839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9597 Z= 0.132 Angle : 0.670 14.659 12985 Z= 0.317 Chirality : 0.040 0.176 1490 Planarity : 0.004 0.060 1589 Dihedral : 4.775 68.436 1273 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 2.37 % Allowed : 24.51 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1163 helix: 1.31 (0.19), residues: 737 sheet: -0.82 (0.62), residues: 65 loop : -1.37 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 304 TYR 0.009 0.001 TYR A 927 PHE 0.030 0.001 PHE A 625 TRP 0.007 0.001 TRP A 203 HIS 0.003 0.001 HIS A 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9597) covalent geometry : angle 0.67006 / 0.32 (12985) hydrogen bonds : bond 0.04196 / 2.71 ( 502) hydrogen bonds : angle 3.90411 / 2.85 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.38 seconds wall clock time: 41 minutes 16.70 seconds (2476.70 seconds total)