Starting phenix.real_space_refine on Tue Nov 18 00:57:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_8782.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_8782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_8782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_8782.map" model { file = "/net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_8782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w81_8782/11_2025/5w81_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-2.0-5881/lib/python3.9/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: 2.31, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 387.2 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: 0.41 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: 1.64 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1507 1.33 - 1.45: 2524 1.45 - 1.57: 5462 1.57 - 1.69: 10 1.69 - 1.81: 94 Bond restraints: 9597 Sorted by residual: bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 bond pdb=" C4 ATP A1502 " pdb=" C5 ATP A1502 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.486 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP A1502 " pdb=" C6 ATP A1502 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C5 ATP A1502 " pdb=" N7 ATP A1502 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.48e+01 ... (remaining 9592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 12902 4.06 - 8.11: 73 8.11 - 12.17: 6 12.17 - 16.22: 0 16.22 - 20.28: 4 Bond angle restraints: 12985 Sorted by residual: angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 119.59 20.28 1.00e+00 1.00e+00 4.11e+02 angle pdb=" PB ATP A1502 " pdb=" O3B ATP A1502 " pdb=" PG ATP A1502 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 119.66 17.17 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PA ATP A1502 " pdb=" O3A ATP A1502 " pdb=" PB ATP A1502 " ideal model delta sigma weight residual 136.83 120.27 16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" C5 ATP A1501 " pdb=" C4 ATP A1501 " pdb=" N3 ATP A1501 " ideal model delta sigma weight residual 126.80 118.54 8.26 1.00e+00 1.00e+00 6.82e+01 ... (remaining 12980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 5258 17.38 - 34.75: 379 34.75 - 52.13: 117 52.13 - 69.51: 24 69.51 - 86.88: 3 Dihedral angle restraints: 5781 sinusoidal: 2362 harmonic: 3419 Sorted by residual: dihedral pdb=" CA TRP A1205 " pdb=" C TRP A1205 " pdb=" N PRO A1206 " pdb=" CA PRO A1206 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" C ILE A 332 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta harmonic sigma weight residual -122.00 -132.57 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" CA GLU A 218 " pdb=" C GLU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1002 0.053 - 0.106: 347 0.106 - 0.159: 98 0.159 - 0.212: 34 0.212 - 0.265: 9 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CA GLU A1406 " pdb=" N GLU A1406 " pdb=" C GLU A1406 " pdb=" CB GLU A1406 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU A 115 " pdb=" N GLU A 115 " pdb=" C GLU A 115 " pdb=" CB GLU A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS A1335 " pdb=" N LYS A1335 " pdb=" C LYS A1335 " pdb=" CB LYS A1335 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1487 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 324 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 325 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1448 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C LEU A1448 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A1448 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS A1449 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1057 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A1058 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " -0.021 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 13 2.53 - 3.12: 6394 3.12 - 3.72: 13963 3.72 - 4.31: 19019 4.31 - 4.90: 31491 Nonbonded interactions: 70880 Sorted by model distance: nonbonded pdb=" O2B ATP A1502 " pdb="MG MG A1504 " model vdw 1.940 2.170 nonbonded pdb=" O2B ATP A1501 " pdb="MG MG A1503 " model vdw 1.994 2.170 nonbonded pdb=" OE1 GLN A1292 " pdb="MG MG A1504 " model vdw 2.016 2.170 nonbonded pdb=" OG SER A 464 " pdb="MG MG A1503 " model vdw 2.148 2.170 nonbonded pdb=" O ARG A1453 " pdb=" OG SER A1457 " model vdw 2.155 3.040 ... (remaining 70875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 9597 Z= 0.593 Angle : 1.261 20.279 12985 Z= 0.900 Chirality : 0.064 0.265 1490 Planarity : 0.004 0.044 1589 Dihedral : 13.886 86.881 3569 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00801 ( 9597) covalent geometry : angle 1.26080 (12985) hydrogen bonds : bond 0.26241 ( 502) hydrogen bonds : angle 8.67122 ( 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 : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.7173 (t0) cc_final: 0.6927 (t0) REVERT: A 60 GLU cc_start: 0.6832 (tm-30) cc_final: 0.5829 (tm-30) REVERT: A 70 LEU cc_start: 0.7632 (tp) cc_final: 0.7405 (tt) REVERT: A 77 CYS cc_start: 0.6213 (p) cc_final: 0.5951 (p) REVERT: A 100 PRO cc_start: 0.9136 (Cg_exo) cc_final: 0.8888 (Cg_endo) REVERT: A 204 ILE cc_start: 0.4869 (mm) cc_final: 0.4560 (mt) REVERT: A 326 HIS cc_start: 0.8549 (t70) cc_final: 0.8325 (t-90) REVERT: A 384 MET cc_start: 0.6948 (mmp) cc_final: 0.6201 (mmm) REVERT: A 458 SER cc_start: 0.8544 (m) cc_final: 0.7877 (t) REVERT: A 461 SER cc_start: 0.8350 (m) cc_final: 0.7562 (t) REVERT: A 497 MET cc_start: 0.5461 (mtp) cc_final: 0.5168 (ttm) REVERT: A 513 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8321 (tp30) REVERT: A 527 GLU cc_start: 0.7911 (tt0) cc_final: 0.7553 (mp0) REVERT: A 578 ASP cc_start: 0.7289 (m-30) cc_final: 0.6669 (m-30) REVERT: A 625 PHE cc_start: 0.7618 (t80) cc_final: 0.7313 (t80) REVERT: A 854 ASN cc_start: 0.7330 (t0) cc_final: 0.6649 (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: 0.1107 time to fit residues: 44.5994 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 : 0.362 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 288 ASN A1062 HIS A1210 GLN A1372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120781 restraints weight = 17795.965| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.28 r_work: 0.3445 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9597 Z= 0.170 Angle : 0.709 8.873 12985 Z= 0.359 Chirality : 0.045 0.285 1490 Planarity : 0.005 0.071 1589 Dihedral : 8.267 87.416 1335 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.05 % Allowed : 12.35 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.87 (0.23), residues: 1163 helix: 0.19 (0.17), residues: 736 sheet: -2.06 (0.55), residues: 76 loop : -1.70 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 335 TYR 0.022 0.002 TYR A 921 PHE 0.019 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 covalent geometry : bond 0.00377 ( 9597) covalent geometry : angle 0.70939 (12985) hydrogen bonds : bond 0.04555 ( 502) hydrogen bonds : angle 4.51392 ( 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 243 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.360 Fit side-chains REVERT: A 7 GLU cc_start: 0.7094 (tp30) cc_final: 0.6550 (mp0) REVERT: A 26 LYS cc_start: 0.7662 (ttmm) cc_final: 0.7239 (ttpp) REVERT: A 453 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 527 GLU cc_start: 0.8121 (tt0) cc_final: 0.7880 (mp0) REVERT: A 619 HIS cc_start: 0.7940 (t-170) cc_final: 0.7622 (t-90) REVERT: A 977 THR cc_start: 0.8519 (t) cc_final: 0.8073 (m) REVERT: A 1249 SER cc_start: 0.9424 (t) cc_final: 0.9182 (t) REVERT: A 1303 MET cc_start: 0.8307 (mtp) cc_final: 0.8070 (mtp) REVERT: A 1374 SER cc_start: 0.9077 (m) cc_final: 0.8750 (p) REVERT: A 1383 LYS cc_start: 0.8514 (ttpp) cc_final: 0.8195 (tptt) REVERT: A 1437 HIS cc_start: 0.7801 (m-70) cc_final: 0.7231 (m-70) REVERT: A 1458 MET cc_start: 0.4735 (tpp) cc_final: 0.4442 (tpp) outliers start: 41 outliers final: 20 residues processed: 230 average time/residue: 0.0892 time to fit residues: 29.5078 Evaluate side-chains 176 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 312 PHE 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 1121 LEU Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1262 VAL Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 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: 9.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** A1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110407 restraints weight = 18601.015| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.20 r_work: 0.3315 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.8253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9597 Z= 0.248 Angle : 0.766 10.245 12985 Z= 0.392 Chirality : 0.045 0.217 1490 Planarity : 0.005 0.060 1589 Dihedral : 8.528 88.669 1335 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 5.34 % Allowed : 15.12 % Favored : 79.55 % 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: -0.71 (0.23), residues: 1163 helix: 0.31 (0.18), residues: 737 sheet: -2.10 (0.57), residues: 66 loop : -1.64 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1240 TYR 0.017 0.002 TYR A1022 PHE 0.024 0.002 PHE A 625 TRP 0.017 0.002 TRP A 278 HIS 0.015 0.002 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 9597) covalent geometry : angle 0.76610 (12985) hydrogen bonds : bond 0.06339 ( 502) hydrogen bonds : angle 4.86386 ( 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 249 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7731 (tp30) cc_final: 0.6806 (mp0) REVERT: A 51 GLU cc_start: 0.9038 (pp20) cc_final: 0.8652 (pp20) REVERT: A 311 TYR cc_start: 0.8094 (t80) cc_final: 0.7705 (t80) REVERT: A 491 SER cc_start: 0.9429 (OUTLIER) cc_final: 0.8960 (p) REVERT: A 979 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7367 (ttt90) REVERT: A 999 MET cc_start: 0.8146 (tpt) cc_final: 0.7889 (mmm) REVERT: A 1047 GLN cc_start: 0.8116 (tt0) cc_final: 0.7911 (mt0) REVERT: A 1231 LEU cc_start: 0.8762 (tt) cc_final: 0.8462 (mm) REVERT: A 1368 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7916 (mt) REVERT: A 1402 GLU cc_start: 0.8044 (tp30) cc_final: 0.7661 (tm-30) REVERT: A 1416 MET cc_start: 0.8597 (tmm) cc_final: 0.7268 (tmm) REVERT: A 1418 ASP cc_start: 0.7689 (t0) cc_final: 0.7480 (t0) REVERT: A 1437 HIS cc_start: 0.8278 (m-70) cc_final: 0.7896 (m-70) outliers start: 54 outliers final: 29 residues processed: 240 average time/residue: 0.0945 time to fit residues: 32.2139 Evaluate side-chains 185 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU 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 294 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 495 TRP 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 609 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1116 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 1368 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: 7.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A1004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.135462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112583 restraints weight = 18454.430| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.25 r_work: 0.3349 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.8649 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= 0.136 Angle : 0.633 12.659 12985 Z= 0.312 Chirality : 0.040 0.202 1490 Planarity : 0.004 0.061 1589 Dihedral : 7.912 80.424 1335 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.85 % Rotamer: Outliers : 3.75 % Allowed : 19.07 % 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: -0.06 (0.24), residues: 1163 helix: 0.80 (0.19), residues: 744 sheet: -1.66 (0.59), residues: 66 loop : -1.40 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1170 TYR 0.010 0.001 TYR A 514 PHE 0.031 0.001 PHE A 625 TRP 0.009 0.001 TRP A 203 HIS 0.009 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9597) covalent geometry : angle 0.63279 (12985) hydrogen bonds : bond 0.04577 ( 502) hydrogen bonds : angle 4.25696 ( 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 227 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.402 Fit side-chains REVERT: A 48 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7853 (mm) REVERT: A 51 GLU cc_start: 0.9016 (pp20) cc_final: 0.8680 (pp20) REVERT: A 138 LEU cc_start: 0.9147 (tp) cc_final: 0.8786 (tp) REVERT: A 208 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 282 MET cc_start: 0.8325 (tpp) cc_final: 0.8090 (mmt) REVERT: A 374 GLU cc_start: 0.8035 (tt0) cc_final: 0.7637 (tp30) REVERT: A 491 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.8846 (p) REVERT: A 979 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7440 (mtp85) REVERT: A 1047 GLN cc_start: 0.8094 (tt0) cc_final: 0.7863 (mt0) REVERT: A 1406 GLU cc_start: 0.7598 (pm20) cc_final: 0.7358 (tm-30) REVERT: A 1415 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9244 (pp) REVERT: A 1416 MET cc_start: 0.8589 (tmm) cc_final: 0.7436 (tmm) REVERT: A 1418 ASP cc_start: 0.7790 (t0) cc_final: 0.7423 (t0) REVERT: A 1437 HIS cc_start: 0.8297 (m-70) cc_final: 0.7798 (m-70) outliers start: 38 outliers final: 20 residues processed: 216 average time/residue: 0.0966 time to fit residues: 29.4634 Evaluate side-chains 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 355 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 617 LEU 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 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 1380 VAL Chi-restraints excluded: chain A residue 1415 LEU 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: 0.0270 chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 114 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 22 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116037 restraints weight = 18529.873| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.31 r_work: 0.3390 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9597 Z= 0.111 Angle : 0.585 11.562 12985 Z= 0.286 Chirality : 0.038 0.195 1490 Planarity : 0.004 0.062 1589 Dihedral : 7.506 82.332 1335 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 2.77 % Allowed : 20.55 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.24), residues: 1163 helix: 1.10 (0.19), residues: 736 sheet: -1.38 (0.54), residues: 75 loop : -1.45 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 304 TYR 0.013 0.001 TYR A 927 PHE 0.031 0.001 PHE A 625 TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9597) covalent geometry : angle 0.58494 (12985) hydrogen bonds : bond 0.03773 ( 502) hydrogen bonds : angle 3.91145 ( 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 225 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7764 (mm) REVERT: A 51 GLU cc_start: 0.8987 (pp20) cc_final: 0.8622 (pp20) REVERT: A 138 LEU cc_start: 0.9006 (tp) cc_final: 0.8787 (tp) REVERT: A 293 GLU cc_start: 0.8524 (tt0) cc_final: 0.8197 (tt0) REVERT: A 374 GLU cc_start: 0.8013 (tt0) cc_final: 0.7636 (tp30) REVERT: A 491 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8775 (p) REVERT: A 979 ARG cc_start: 0.7968 (tpp80) cc_final: 0.7598 (mtp180) REVERT: A 1231 LEU cc_start: 0.8630 (tt) cc_final: 0.8271 (mm) REVERT: A 1265 ASP cc_start: 0.8620 (m-30) cc_final: 0.8373 (m-30) REVERT: A 1416 MET cc_start: 0.8580 (tmm) cc_final: 0.7104 (tmm) REVERT: A 1418 ASP cc_start: 0.7839 (t0) cc_final: 0.7490 (t0) REVERT: A 1437 HIS cc_start: 0.8248 (m-70) cc_final: 0.7794 (m-70) outliers start: 28 outliers final: 13 residues processed: 215 average time/residue: 0.0975 time to fit residues: 29.5965 Evaluate side-chains 179 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU 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 1336 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A1047 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109261 restraints weight = 18587.114| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.24 r_work: 0.3293 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.9340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9597 Z= 0.164 Angle : 0.644 11.393 12985 Z= 0.317 Chirality : 0.040 0.191 1490 Planarity : 0.004 0.065 1589 Dihedral : 7.614 75.887 1335 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 3.75 % Allowed : 20.16 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.24), residues: 1163 helix: 1.04 (0.19), residues: 740 sheet: -1.19 (0.58), residues: 65 loop : -1.54 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1170 TYR 0.012 0.001 TYR A 927 PHE 0.027 0.001 PHE A 625 TRP 0.008 0.001 TRP A 18 HIS 0.005 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9597) covalent geometry : angle 0.64355 (12985) hydrogen bonds : bond 0.04760 ( 502) hydrogen bonds : angle 4.21833 ( 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 213 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.398 Fit side-chains REVERT: A 48 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7859 (mm) REVERT: A 51 GLU cc_start: 0.9057 (pp20) cc_final: 0.8659 (pp20) REVERT: A 102 LEU cc_start: 0.9238 (tp) cc_final: 0.8968 (tp) REVERT: A 109 SER cc_start: 0.6879 (OUTLIER) cc_final: 0.6574 (p) REVERT: A 138 LEU cc_start: 0.9115 (tp) cc_final: 0.8790 (tp) REVERT: A 193 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: A 225 PHE cc_start: 0.7473 (t80) cc_final: 0.7266 (t80) REVERT: A 313 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (t80) REVERT: A 316 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 491 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8827 (p) REVERT: A 979 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7414 (mtp85) REVERT: A 1231 LEU cc_start: 0.8768 (tt) cc_final: 0.8386 (mm) REVERT: A 1265 ASP cc_start: 0.8555 (m-30) cc_final: 0.8272 (m-30) REVERT: A 1416 MET cc_start: 0.8618 (tmm) cc_final: 0.7124 (tmm) REVERT: A 1418 ASP cc_start: 0.7921 (t0) cc_final: 0.7601 (t0) REVERT: A 1437 HIS cc_start: 0.8350 (m-70) cc_final: 0.7857 (m-70) outliers start: 38 outliers final: 22 residues processed: 199 average time/residue: 0.0945 time to fit residues: 26.7474 Evaluate side-chains 186 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1166 ARG Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1422 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112660 restraints weight = 18665.471| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.29 r_work: 0.3328 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.9499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9597 Z= 0.120 Angle : 0.607 13.827 12985 Z= 0.294 Chirality : 0.039 0.185 1490 Planarity : 0.004 0.052 1589 Dihedral : 7.185 76.219 1335 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.06 % Allowed : 21.94 % Favored : 75.00 % 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: 0.28 (0.24), residues: 1163 helix: 1.15 (0.19), residues: 743 sheet: -1.08 (0.59), residues: 65 loop : -1.60 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 304 TYR 0.027 0.001 TYR A 850 PHE 0.030 0.001 PHE A 625 TRP 0.006 0.001 TRP A 203 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9597) covalent geometry : angle 0.60746 (12985) hydrogen bonds : bond 0.04163 ( 502) hydrogen bonds : angle 4.01055 ( 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 213 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.405 Fit side-chains REVERT: A 24 MET cc_start: 0.8679 (mtp) cc_final: 0.8432 (mtm) REVERT: A 48 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (mm) REVERT: A 51 GLU cc_start: 0.9066 (pp20) cc_final: 0.8682 (pp20) REVERT: A 102 LEU cc_start: 0.9194 (tp) cc_final: 0.8810 (tp) REVERT: A 110 PHE cc_start: 0.7840 (t80) cc_final: 0.7269 (t80) REVERT: A 193 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8541 (m-30) REVERT: A 299 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6595 (mtpt) REVERT: A 316 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 345 MET cc_start: 0.8561 (mtt) cc_final: 0.8233 (mmp) REVERT: A 380 GLU cc_start: 0.8420 (tt0) cc_final: 0.8102 (tp30) REVERT: A 451 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 491 SER cc_start: 0.9307 (OUTLIER) cc_final: 0.8798 (p) REVERT: A 979 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7474 (mtp85) REVERT: A 1231 LEU cc_start: 0.8735 (tt) cc_final: 0.8316 (mm) REVERT: A 1265 ASP cc_start: 0.8558 (m-30) cc_final: 0.8312 (m-30) REVERT: A 1419 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8069 (pptt) REVERT: A 1428 ILE cc_start: 0.8447 (mp) cc_final: 0.8173 (tp) REVERT: A 1437 HIS cc_start: 0.8286 (m-70) cc_final: 0.7837 (m-70) outliers start: 31 outliers final: 17 residues processed: 206 average time/residue: 0.0924 time to fit residues: 27.3329 Evaluate side-chains 187 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 193 ASP 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 355 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1166 ARG Chi-restraints excluded: chain A residue 1419 LYS Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 57 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A1403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112371 restraints weight = 18561.191| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.29 r_work: 0.3340 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.9686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9597 Z= 0.125 Angle : 0.633 13.887 12985 Z= 0.306 Chirality : 0.039 0.181 1490 Planarity : 0.004 0.047 1589 Dihedral : 6.834 77.158 1335 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.06 % Allowed : 22.53 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.24), residues: 1163 helix: 1.20 (0.19), residues: 738 sheet: -0.95 (0.61), residues: 65 loop : -1.59 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1170 TYR 0.027 0.001 TYR A 850 PHE 0.031 0.001 PHE A 625 TRP 0.006 0.001 TRP A 203 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9597) covalent geometry : angle 0.63264 (12985) hydrogen bonds : bond 0.04189 ( 502) hydrogen bonds : angle 3.96929 ( 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: 31 poor density : 176 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8660 (mtp) cc_final: 0.8441 (mtm) REVERT: A 33 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7019 (ttp-170) REVERT: A 48 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 51 GLU cc_start: 0.9063 (pp20) cc_final: 0.8696 (pp20) REVERT: A 102 LEU cc_start: 0.9153 (tp) cc_final: 0.8898 (tp) REVERT: A 110 PHE cc_start: 0.7788 (t80) cc_final: 0.7256 (t80) REVERT: A 193 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8542 (m-30) REVERT: A 299 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6637 (mtpt) REVERT: A 316 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 345 MET cc_start: 0.8544 (mtt) cc_final: 0.8165 (mmm) REVERT: A 380 GLU cc_start: 0.8448 (tt0) cc_final: 0.8129 (tp30) REVERT: A 451 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 491 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8787 (p) REVERT: A 979 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7381 (mtp85) REVERT: A 1231 LEU cc_start: 0.8722 (tt) cc_final: 0.8275 (mm) REVERT: A 1265 ASP cc_start: 0.8505 (m-30) cc_final: 0.8281 (m-30) REVERT: A 1416 MET cc_start: 0.8570 (tmm) cc_final: 0.7141 (tmm) REVERT: A 1437 HIS cc_start: 0.8237 (m-70) cc_final: 0.7812 (m-70) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.0956 time to fit residues: 27.0364 Evaluate side-chains 192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 193 ASP 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 355 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112209 restraints weight = 18571.179| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.29 r_work: 0.3342 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.9833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9597 Z= 0.127 Angle : 0.635 14.736 12985 Z= 0.308 Chirality : 0.039 0.179 1490 Planarity : 0.004 0.046 1589 Dihedral : 6.651 79.178 1335 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.16 % Allowed : 22.83 % Favored : 74.01 % 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: 0.39 (0.24), residues: 1163 helix: 1.21 (0.19), residues: 738 sheet: -0.82 (0.62), residues: 65 loop : -1.53 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 336 TYR 0.029 0.001 TYR A 850 PHE 0.032 0.001 PHE A 625 TRP 0.008 0.001 TRP A 402 HIS 0.003 0.000 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9597) covalent geometry : angle 0.63492 (12985) hydrogen bonds : bond 0.04126 ( 502) hydrogen bonds : angle 3.96459 ( 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 209 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7842 (mtp85) cc_final: 0.6923 (ttp-170) REVERT: A 48 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7848 (mm) REVERT: A 51 GLU cc_start: 0.9070 (pp20) cc_final: 0.8709 (pp20) REVERT: A 102 LEU cc_start: 0.9189 (tp) cc_final: 0.8935 (tp) REVERT: A 109 SER cc_start: 0.6496 (OUTLIER) cc_final: 0.6189 (p) REVERT: A 193 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: A 299 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6616 (mtpt) REVERT: A 304 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.7963 (ttm-80) REVERT: A 316 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 345 MET cc_start: 0.8533 (mtt) cc_final: 0.8278 (mmp) REVERT: A 380 GLU cc_start: 0.8457 (tt0) cc_final: 0.8111 (tp30) REVERT: A 451 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 471 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 491 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 979 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7387 (mtp85) REVERT: A 1231 LEU cc_start: 0.8740 (tt) cc_final: 0.8341 (mm) REVERT: A 1265 ASP cc_start: 0.8477 (m-30) cc_final: 0.8260 (m-30) REVERT: A 1437 HIS cc_start: 0.8257 (m-70) cc_final: 0.7842 (m-70) outliers start: 32 outliers final: 20 residues processed: 202 average time/residue: 0.0939 time to fit residues: 26.9910 Evaluate side-chains 195 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 SER 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 299 LYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109613 restraints weight = 18676.562| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.26 r_work: 0.3305 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.9994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9597 Z= 0.158 Angle : 0.668 14.470 12985 Z= 0.323 Chirality : 0.040 0.178 1490 Planarity : 0.004 0.056 1589 Dihedral : 6.667 77.628 1335 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.96 % Allowed : 22.73 % Favored : 74.31 % 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: 1.14 (0.19), residues: 743 sheet: -0.90 (0.62), residues: 65 loop : -1.54 (0.28), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1170 TYR 0.011 0.001 TYR A 927 PHE 0.031 0.001 PHE A 625 TRP 0.008 0.001 TRP A 402 HIS 0.004 0.001 HIS A 608 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9597) covalent geometry : angle 0.66768 (12985) hydrogen bonds : bond 0.04599 ( 502) hydrogen bonds : angle 4.10752 ( 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 204 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8623 (mtm) cc_final: 0.8407 (mtp) REVERT: A 33 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7019 (ttp-170) REVERT: A 48 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 51 GLU cc_start: 0.9105 (pp20) cc_final: 0.8752 (pp20) REVERT: A 102 LEU cc_start: 0.9231 (tp) cc_final: 0.8999 (tp) REVERT: A 109 SER cc_start: 0.6459 (OUTLIER) cc_final: 0.6166 (p) REVERT: A 188 ASN cc_start: 0.7865 (m-40) cc_final: 0.7450 (m-40) REVERT: A 193 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: A 316 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8132 (tp) REVERT: A 345 MET cc_start: 0.8512 (mtt) cc_final: 0.8273 (mmp) REVERT: A 380 GLU cc_start: 0.8412 (tt0) cc_final: 0.8166 (tp30) REVERT: A 451 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 471 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8873 (mp) REVERT: A 491 SER cc_start: 0.9335 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 979 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7424 (mtp85) REVERT: A 1231 LEU cc_start: 0.8682 (tt) cc_final: 0.8267 (mm) REVERT: A 1265 ASP cc_start: 0.8493 (m-30) cc_final: 0.8273 (m-30) REVERT: A 1437 HIS cc_start: 0.8320 (m-70) cc_final: 0.7879 (m-70) outliers start: 30 outliers final: 22 residues processed: 198 average time/residue: 0.0925 time to fit residues: 26.1583 Evaluate side-chains 194 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 109 SER 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 316 ILE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 844 TRP Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 990 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1269 SER Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1422 VAL Chi-restraints excluded: chain A residue 1423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111181 restraints weight = 18561.011| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.27 r_work: 0.3326 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 1.0110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9597 Z= 0.132 Angle : 0.654 14.747 12985 Z= 0.315 Chirality : 0.039 0.180 1490 Planarity : 0.004 0.044 1589 Dihedral : 6.615 81.063 1335 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 2.87 % Allowed : 23.02 % 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: 0.41 (0.24), residues: 1163 helix: 1.23 (0.19), residues: 740 sheet: -0.92 (0.60), residues: 65 loop : -1.50 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1170 TYR 0.010 0.001 TYR A 927 PHE 0.031 0.001 PHE A 625 TRP 0.009 0.001 TRP A 402 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9597) covalent geometry : angle 0.65394 (12985) hydrogen bonds : bond 0.04257 ( 502) hydrogen bonds : angle 4.01395 ( 1497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.90 seconds wall clock time: 42 minutes 27.10 seconds (2547.10 seconds total)