Starting phenix.real_space_refine on Fri Sep 11 18:14:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.map" model { file = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o2p_0611/09_2026/6o2p_0611.cif" } resolution = 3.3 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= 0.185 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 47 5.16 5 C 6387 2.51 5 N 1596 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9767 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1179, 9450 Classifications: {'peptide': 1179} Link IDs: {'PTRANS': 32, 'TRANS': 1146} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 232 Unusual residues: {' MG': 2, 'AJP': 1, 'ATP': 2, 'POV': 6, 'VX7': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 2.46, per 1000 atoms: 0.25 Number of scatterers: 9767 At special positions: 0 Unit cell: (102.942, 120.916, 111.929, 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 47 16.00 P 6 15.00 Mg 2 11.99 O 1729 8.00 N 1596 7.00 C 6387 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: 0.88 Conformation dependent library (CDL) restraints added in 364.5 milliseconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 71.6% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 4.124A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 45 through 64 removed outlier: 3.507A pdb=" N LEU A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.745A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.680A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.800A pdb=" N LEU A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 166 removed outlier: 3.581A pdb=" N ILE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.662A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.840A pdb=" N ASP A 173 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 199 removed outlier: 3.901A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 Proline residue: A 205 - end of helix removed outlier: 3.670A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 268 removed outlier: 4.112A pdb=" N CYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.719A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 329 removed outlier: 3.613A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.010A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 352 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.706A pdb=" N TRP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.845A pdb=" N GLY A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.687A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 606 through 613 removed outlier: 3.534A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.564A pdb=" N ILE A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.197A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 869 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 913 removed outlier: 3.908A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 927 removed outlier: 4.702A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 958 Proline residue: A 936 - end of helix removed outlier: 3.746A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.622A pdb=" N LEU A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 985 removed outlier: 3.681A pdb=" N ILE A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 removed outlier: 4.035A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1047 removed outlier: 3.950A pdb=" N VAL A1017 " --> pdb=" O PRO A1013 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.863A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.677A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1122 removed outlier: 3.536A pdb=" N THR A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1168 removed outlier: 3.605A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A1161 " --> pdb=" O MET A1157 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.697A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 4.867A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.508A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.671A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.779A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1409 removed outlier: 3.562A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 3.659A pdb=" N LEU A1430 " --> pdb=" O SER A1426 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A1434 " --> pdb=" O LEU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1441 removed outlier: 3.885A pdb=" N ILE A1441 " --> pdb=" O PHE A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1450 removed outlier: 4.310A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.652A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B 14 " --> pdb=" O UNK B 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.398A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 479 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 removed outlier: 6.361A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ASP A 572 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS A 491 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN A 452 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 602 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 5.776A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1210 " --> pdb=" O ILE A1234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1227 through 1230 removed outlier: 5.776A pdb=" N GLU A1228 " --> pdb=" O ALA A1217 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA A1217 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A1266 " --> pdb=" O LYS A1213 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 6.260A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP A1370 " --> pdb=" O GLY A1287 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A1289 " --> pdb=" O ASP A1370 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N CYS A1400 " --> pdb=" O LEU A1367 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1369 " --> pdb=" O CYS A1400 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A1240 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1590 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: 1.89 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1884 1.34 - 1.46: 2314 1.46 - 1.58: 5686 1.58 - 1.70: 10 1.70 - 1.82: 79 Bond restraints: 9973 Sorted by residual: bond pdb=" C29 POV A1508 " pdb="C210 POV A1508 " ideal model delta sigma weight residual 1.333 1.510 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.60e-03 1.35e+04 2.19e+01 bond pdb=" C02 VX7 A1512 " pdb=" C05 VX7 A1512 " ideal model delta sigma weight residual 1.535 1.454 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" N LEU A 935 " pdb=" CA LEU A 935 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.60e+01 bond pdb=" C15 VX7 A1512 " pdb=" N16 VX7 A1512 " ideal model delta sigma weight residual 1.329 1.409 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 9968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 11704 2.78 - 5.56: 1760 5.56 - 8.34: 28 8.34 - 11.12: 2 11.12 - 13.90: 2 Bond angle restraints: 13496 Sorted by residual: angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 132.08 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 129.74 7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 133.14 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 130.54 6.29 1.00e+00 1.00e+00 3.95e+01 angle pdb=" CA GLY A 480 " pdb=" C GLY A 480 " pdb=" O GLY A 480 " ideal model delta sigma weight residual 122.37 118.19 4.18 7.30e-01 1.88e+00 3.28e+01 ... (remaining 13491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.64: 5539 23.64 - 47.29: 278 47.29 - 70.93: 33 70.93 - 94.58: 5 94.58 - 118.22: 4 Dihedral angle restraints: 5859 sinusoidal: 2383 harmonic: 3476 Sorted by residual: dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C02 AJP A1511 " pdb=" C85 AJP A1511 " pdb=" O84 AJP A1511 " pdb=" C05 AJP A1511 " ideal model delta sinusoidal sigma weight residual -57.60 60.62 -118.22 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C16 AJP A1511 " pdb=" C17 AJP A1511 " pdb=" C18 AJP A1511 " pdb=" C19 AJP A1511 " ideal model delta sinusoidal sigma weight residual 54.20 -54.61 108.81 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 5856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.183: 1537 1.183 - 2.367: 0 2.367 - 3.550: 0 3.550 - 4.733: 4 4.733 - 5.916: 21 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C12 AJP A1511 " pdb=" C07 AJP A1511 " pdb=" C11 AJP A1511 " pdb=" C13 AJP A1511 " both_signs ideal model delta sigma weight residual False 3.01 -2.91 5.92 2.00e-01 2.50e+01 8.75e+02 chirality pdb=" C20 AJP A1511 " pdb=" C15 AJP A1511 " pdb=" C19 AJP A1511 " pdb=" C21 AJP A1511 " both_signs ideal model delta sigma weight residual False 2.96 -2.86 5.82 2.00e-01 2.50e+01 8.46e+02 chirality pdb=" C07 AJP A1511 " pdb=" C06 AJP A1511 " pdb=" C08 AJP A1511 " pdb=" C12 AJP A1511 " both_signs ideal model delta sigma weight residual False -2.73 2.75 -5.48 2.00e-01 2.50e+01 7.50e+02 ... (remaining 1559 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1508 " -0.029 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C29 POV A1508 " 0.029 2.00e-02 2.50e+03 pdb="C210 POV A1508 " 0.030 2.00e-02 2.50e+03 pdb="C211 POV A1508 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 161 " -0.020 2.00e-02 2.50e+03 1.18e-02 2.77e+00 pdb=" CG TYR A 161 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 161 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 161 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 161 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 161 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 161 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 161 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 VX7 A1512 " -0.011 2.00e-02 2.50e+03 1.43e-02 2.56e+00 pdb=" C12 VX7 A1512 " 0.025 2.00e-02 2.50e+03 pdb=" C14 VX7 A1512 " -0.015 2.00e-02 2.50e+03 pdb=" N11 VX7 A1512 " 0.006 2.00e-02 2.50e+03 pdb=" O13 VX7 A1512 " -0.006 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 12 2.51 - 3.11: 5869 3.11 - 3.70: 14528 3.70 - 4.30: 19877 4.30 - 4.90: 34756 Nonbonded interactions: 75042 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.908 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.029 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.051 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.111 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.115 2.170 ... (remaining 75037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.014 0.177 9973 Z= 1.068 Angle : 1.830 13.896 13496 Z= 1.376 Chirality : 0.642 5.916 1562 Planarity : 0.003 0.029 1630 Dihedral : 14.483 118.221 3611 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.16 % Allowed : 5.51 % Favored : 93.33 % 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: -3.17 (0.20), residues: 1169 helix: -1.71 (0.16), residues: 723 sheet: -2.53 (0.53), residues: 74 loop : -2.47 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 560 TYR 0.026 0.002 TYR A 161 PHE 0.019 0.002 PHE A 337 TRP 0.016 0.002 TRP A1274 HIS 0.006 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.01390 / 1.07 ( 9973) covalent geometry : angle 1.82955 / 1.38 (13496) hydrogen bonds : bond 0.27567 / 18.07 ( 535) hydrogen bonds : angle 8.25443 / 5.95 ( 1590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8640 (tt0) cc_final: 0.8383 (mm-30) REVERT: A 26 LYS cc_start: 0.7520 (tptp) cc_final: 0.6867 (tppt) REVERT: A 29 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7249 (ttm-80) REVERT: A 51 GLU cc_start: 0.8792 (tp30) cc_final: 0.8334 (pt0) REVERT: A 82 MET cc_start: 0.7882 (mmt) cc_final: 0.7378 (mpp) REVERT: A 216 TRP cc_start: 0.8128 (t60) cc_final: 0.7899 (t60) REVERT: A 220 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6174 (mm-40) REVERT: A 257 GLU cc_start: 0.7928 (tt0) cc_final: 0.7293 (tp30) REVERT: A 267 GLU cc_start: 0.8391 (tt0) cc_final: 0.8146 (tp30) REVERT: A 369 ASN cc_start: 0.7730 (m-40) cc_final: 0.7500 (m-40) REVERT: A 373 ASP cc_start: 0.8464 (t0) cc_final: 0.8120 (m-30) REVERT: A 443 ASP cc_start: 0.8463 (m-30) cc_final: 0.7665 (p0) REVERT: A 448 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 476 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8810 (mm-30) REVERT: A 487 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7636 (mtp180) REVERT: A 504 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7905 (mp0) REVERT: A 529 ASP cc_start: 0.9059 (m-30) cc_final: 0.8765 (m-30) REVERT: A 572 ASP cc_start: 0.8084 (t0) cc_final: 0.7795 (t0) REVERT: A 597 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7324 (m-40) REVERT: A 968 LYS cc_start: 0.7803 (mttm) cc_final: 0.7404 (mtmm) REVERT: A 1044 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7857 (tm-30) REVERT: A 1046 GLU cc_start: 0.8008 (tt0) cc_final: 0.7549 (tp30) REVERT: A 1104 GLU cc_start: 0.8486 (tt0) cc_final: 0.8259 (tt0) REVERT: A 1128 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.7657 (ptt180) REVERT: A 1279 LEU cc_start: 0.7876 (tp) cc_final: 0.7663 (tt) REVERT: A 1284 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8718 (tptp) REVERT: A 1308 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8525 (mm-30) REVERT: A 1317 LYS cc_start: 0.8576 (tptp) cc_final: 0.8376 (tptp) REVERT: A 1320 ASP cc_start: 0.8503 (p0) cc_final: 0.8211 (p0) REVERT: A 1340 VAL cc_start: 0.7465 (m) cc_final: 0.7153 (p) REVERT: A 1341 ASP cc_start: 0.8212 (t70) cc_final: 0.7557 (t0) REVERT: A 1394 ASP cc_start: 0.8802 (m-30) cc_final: 0.7906 (t0) REVERT: A 1419 ASN cc_start: 0.8622 (m110) cc_final: 0.8259 (p0) REVERT: A 1437 PHE cc_start: 0.8307 (t80) cc_final: 0.7791 (t80) outliers start: 12 outliers final: 3 residues processed: 297 average time/residue: 0.1276 time to fit residues: 50.5170 Evaluate side-chains 179 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 1129 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN A 505 ASN A 525 GLN A 552 GLN A1039 GLN A1238 GLN A1330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094418 restraints weight = 20239.563| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.09 r_work: 0.3084 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9973 Z= 0.146 Angle : 0.963 34.267 13496 Z= 0.393 Chirality : 0.092 2.000 1562 Planarity : 0.004 0.035 1630 Dihedral : 5.729 59.639 1363 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.03 % Allowed : 13.33 % Favored : 84.64 % 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: -0.12 (0.23), residues: 1169 helix: 0.79 (0.18), residues: 766 sheet: -2.15 (0.52), residues: 79 loop : -1.50 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 104 TYR 0.017 0.002 TYR A 517 PHE 0.017 0.001 PHE A 83 TRP 0.027 0.002 TRP A1204 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 ( 9973) covalent geometry : angle 0.96335 / 0.39 (13496) hydrogen bonds : bond 0.05859 / 3.76 ( 535) hydrogen bonds : angle 4.37582 / 3.09 ( 1590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7046 (mt-10) REVERT: A 38 TYR cc_start: 0.9183 (m-10) cc_final: 0.8973 (m-10) REVERT: A 56 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8603 (mm-30) REVERT: A 92 GLU cc_start: 0.8192 (tp30) cc_final: 0.7832 (tp30) REVERT: A 102 LEU cc_start: 0.9471 (tp) cc_final: 0.9244 (tp) REVERT: A 106 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 220 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7415 (mm-40) REVERT: A 257 GLU cc_start: 0.8717 (tt0) cc_final: 0.8198 (tp30) REVERT: A 487 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8380 (mtp180) REVERT: A 504 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8422 (mp0) REVERT: A 600 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8254 (ptp90) REVERT: A 968 LYS cc_start: 0.8499 (mttm) cc_final: 0.8033 (mtmm) REVERT: A 1046 GLU cc_start: 0.8557 (tt0) cc_final: 0.8101 (tp30) REVERT: A 1253 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8510 (tm) REVERT: A 1284 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8764 (tptp) REVERT: A 1340 VAL cc_start: 0.8348 (m) cc_final: 0.8124 (p) REVERT: A 1341 ASP cc_start: 0.8601 (t70) cc_final: 0.7967 (t0) REVERT: A 1394 ASP cc_start: 0.8346 (m-30) cc_final: 0.7809 (t0) REVERT: A 1437 PHE cc_start: 0.8994 (t80) cc_final: 0.8607 (t80) outliers start: 21 outliers final: 14 residues processed: 234 average time/residue: 0.0956 time to fit residues: 32.2828 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 HIS A 151 GLN A 199 HIS A1079 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.093645 restraints weight = 20252.441| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.16 r_work: 0.3065 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9973 Z= 0.128 Angle : 0.908 32.542 13496 Z= 0.364 Chirality : 0.093 2.003 1562 Planarity : 0.003 0.034 1630 Dihedral : 5.139 59.260 1357 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 16.71 % Favored : 80.97 % 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: 0.81 (0.25), residues: 1169 helix: 1.46 (0.19), residues: 772 sheet: -1.88 (0.55), residues: 72 loop : -1.07 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.014 0.001 TYR A 385 PHE 0.015 0.001 PHE A 81 TRP 0.013 0.001 TRP A 882 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9973) covalent geometry : angle 0.90794 / 0.36 (13496) hydrogen bonds : bond 0.05168 / 3.30 ( 535) hydrogen bonds : angle 3.96961 / 2.79 ( 1590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7759 (mm-30) cc_final: 0.6985 (mt-10) REVERT: A 56 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8655 (mm-30) REVERT: A 92 GLU cc_start: 0.8220 (tp30) cc_final: 0.7759 (tp30) REVERT: A 257 GLU cc_start: 0.8691 (tt0) cc_final: 0.8229 (tp30) REVERT: A 286 GLU cc_start: 0.8131 (tt0) cc_final: 0.7921 (tt0) REVERT: A 487 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8365 (mtp180) REVERT: A 504 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8313 (mp0) REVERT: A 600 ARG cc_start: 0.8685 (ptt-90) cc_final: 0.8279 (ptp90) REVERT: A 1028 MET cc_start: 0.8630 (mmp) cc_final: 0.8211 (mtm) REVERT: A 1046 GLU cc_start: 0.8538 (tt0) cc_final: 0.8193 (tp30) REVERT: A 1253 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8554 (tm) REVERT: A 1284 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8711 (tptp) REVERT: A 1320 ASP cc_start: 0.8100 (p0) cc_final: 0.7751 (p0) REVERT: A 1340 VAL cc_start: 0.8270 (m) cc_final: 0.8013 (p) REVERT: A 1341 ASP cc_start: 0.8557 (t70) cc_final: 0.7919 (t0) REVERT: A 1394 ASP cc_start: 0.8284 (m-30) cc_final: 0.7926 (m-30) REVERT: A 1419 ASN cc_start: 0.8948 (m110) cc_final: 0.8334 (t0) REVERT: A 1437 PHE cc_start: 0.8909 (t80) cc_final: 0.8639 (t80) outliers start: 24 outliers final: 14 residues processed: 194 average time/residue: 0.1035 time to fit residues: 28.5019 Evaluate side-chains 161 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092246 restraints weight = 20466.729| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.15 r_work: 0.3042 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9973 Z= 0.142 Angle : 0.907 32.739 13496 Z= 0.363 Chirality : 0.092 1.998 1562 Planarity : 0.003 0.033 1630 Dihedral : 5.152 65.900 1356 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.00 % Allowed : 17.97 % Favored : 79.03 % 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: 1.05 (0.25), residues: 1169 helix: 1.63 (0.19), residues: 770 sheet: -1.89 (0.51), residues: 74 loop : -0.86 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 29 TYR 0.014 0.001 TYR A 38 PHE 0.013 0.001 PHE A 81 TRP 0.014 0.001 TRP A1063 HIS 0.004 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9973) covalent geometry : angle 0.90735 / 0.36 (13496) hydrogen bonds : bond 0.05144 / 3.28 ( 535) hydrogen bonds : angle 3.89943 / 2.74 ( 1590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 92 GLU cc_start: 0.8353 (tp30) cc_final: 0.7914 (tp30) REVERT: A 216 TRP cc_start: 0.8899 (t60) cc_final: 0.8696 (t60) REVERT: A 257 GLU cc_start: 0.8702 (tt0) cc_final: 0.8324 (tp30) REVERT: A 485 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8403 (t) REVERT: A 487 ARG cc_start: 0.8941 (mtt180) cc_final: 0.8392 (mtp180) REVERT: A 504 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8313 (mp0) REVERT: A 600 ARG cc_start: 0.8576 (ptt-90) cc_final: 0.8138 (ptp90) REVERT: A 871 LEU cc_start: 0.9261 (mt) cc_final: 0.8957 (mm) REVERT: A 1028 MET cc_start: 0.8626 (mmp) cc_final: 0.8231 (mtm) REVERT: A 1046 GLU cc_start: 0.8511 (tt0) cc_final: 0.8261 (tp30) REVERT: A 1253 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8655 (tm) REVERT: A 1284 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8741 (tptp) REVERT: A 1340 VAL cc_start: 0.8287 (m) cc_final: 0.8048 (p) REVERT: A 1341 ASP cc_start: 0.8636 (t70) cc_final: 0.7992 (t0) REVERT: A 1394 ASP cc_start: 0.8240 (m-30) cc_final: 0.7863 (m-30) REVERT: A 1419 ASN cc_start: 0.9039 (m110) cc_final: 0.8394 (t0) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.0974 time to fit residues: 25.1174 Evaluate side-chains 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 62 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.092900 restraints weight = 20445.666| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.17 r_work: 0.3057 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9973 Z= 0.123 Angle : 0.889 32.330 13496 Z= 0.352 Chirality : 0.092 2.002 1562 Planarity : 0.003 0.033 1630 Dihedral : 5.028 69.383 1356 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 19.03 % Favored : 77.39 % 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: 1.23 (0.25), residues: 1169 helix: 1.72 (0.19), residues: 772 sheet: -1.68 (0.55), residues: 69 loop : -0.73 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 29 TYR 0.016 0.001 TYR A 385 PHE 0.017 0.001 PHE A 200 TRP 0.012 0.001 TRP A 882 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9973) covalent geometry : angle 0.88946 / 0.35 (13496) hydrogen bonds : bond 0.04765 / 3.05 ( 535) hydrogen bonds : angle 3.79671 / 2.65 ( 1590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7987 (mm-30) cc_final: 0.6806 (mt-10) REVERT: A 56 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8689 (mm-30) REVERT: A 60 GLU cc_start: 0.8705 (tp30) cc_final: 0.8461 (tp30) REVERT: A 92 GLU cc_start: 0.8378 (tp30) cc_final: 0.7923 (tp30) REVERT: A 257 GLU cc_start: 0.8649 (tt0) cc_final: 0.8293 (tp30) REVERT: A 485 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8434 (t) REVERT: A 487 ARG cc_start: 0.8939 (mtt180) cc_final: 0.8386 (mtp180) REVERT: A 504 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8283 (mp0) REVERT: A 600 ARG cc_start: 0.8642 (ptt-90) cc_final: 0.8252 (ptp90) REVERT: A 871 LEU cc_start: 0.9275 (mt) cc_final: 0.9059 (mm) REVERT: A 913 TYR cc_start: 0.8158 (p90) cc_final: 0.7844 (p90) REVERT: A 1028 MET cc_start: 0.8585 (mmp) cc_final: 0.8211 (mtm) REVERT: A 1253 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8655 (tm) REVERT: A 1284 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8749 (tptp) REVERT: A 1341 ASP cc_start: 0.8603 (t70) cc_final: 0.7903 (t0) REVERT: A 1363 LYS cc_start: 0.8926 (tptp) cc_final: 0.8594 (tptp) REVERT: A 1394 ASP cc_start: 0.8255 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1419 ASN cc_start: 0.9036 (m110) cc_final: 0.8393 (t0) outliers start: 37 outliers final: 19 residues processed: 182 average time/residue: 0.0969 time to fit residues: 25.7100 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092919 restraints weight = 20402.509| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.14 r_work: 0.3058 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9973 Z= 0.125 Angle : 0.896 32.386 13496 Z= 0.357 Chirality : 0.092 1.999 1562 Planarity : 0.003 0.032 1630 Dihedral : 5.035 73.687 1356 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.29 % Allowed : 20.00 % Favored : 76.71 % 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: 1.38 (0.25), residues: 1169 helix: 1.78 (0.19), residues: 770 sheet: -1.28 (0.56), residues: 79 loop : -0.57 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.016 0.001 TYR A 385 PHE 0.012 0.001 PHE A 200 TRP 0.016 0.001 TRP A1063 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9973) covalent geometry : angle 0.89562 / 0.36 (13496) hydrogen bonds : bond 0.04764 / 3.04 ( 535) hydrogen bonds : angle 3.77235 / 2.63 ( 1590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8050 (mm-30) cc_final: 0.6881 (mt-10) REVERT: A 56 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8707 (mm-30) REVERT: A 60 GLU cc_start: 0.8685 (tp30) cc_final: 0.8451 (tp30) REVERT: A 92 GLU cc_start: 0.8376 (tp30) cc_final: 0.7928 (tp30) REVERT: A 207 GLN cc_start: 0.8594 (tp40) cc_final: 0.7799 (tp40) REVERT: A 257 GLU cc_start: 0.8680 (tt0) cc_final: 0.8362 (tp30) REVERT: A 485 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 487 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8419 (mtp180) REVERT: A 504 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 539 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 600 ARG cc_start: 0.8610 (ptt-90) cc_final: 0.8233 (ptp90) REVERT: A 871 LEU cc_start: 0.9308 (mt) cc_final: 0.9082 (mm) REVERT: A 993 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (t0) REVERT: A 1028 MET cc_start: 0.8596 (mmp) cc_final: 0.8219 (mtm) REVERT: A 1253 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8664 (tm) REVERT: A 1284 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8764 (tptp) REVERT: A 1341 ASP cc_start: 0.8606 (t70) cc_final: 0.7902 (t0) REVERT: A 1394 ASP cc_start: 0.8151 (m-30) cc_final: 0.7763 (m-30) REVERT: A 1419 ASN cc_start: 0.9014 (m110) cc_final: 0.8387 (t0) REVERT: A 1439 GLN cc_start: 0.8701 (mm110) cc_final: 0.8412 (tt0) outliers start: 34 outliers final: 20 residues processed: 182 average time/residue: 0.0927 time to fit residues: 24.7252 Evaluate side-chains 169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.091091 restraints weight = 20440.222| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.02 r_work: 0.3036 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9973 Z= 0.144 Angle : 0.905 32.567 13496 Z= 0.363 Chirality : 0.092 1.995 1562 Planarity : 0.003 0.033 1630 Dihedral : 5.227 80.016 1356 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 20.29 % Favored : 76.52 % 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: 1.38 (0.25), residues: 1169 helix: 1.76 (0.19), residues: 772 sheet: -1.44 (0.57), residues: 69 loop : -0.51 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.023 0.001 TYR A 517 PHE 0.012 0.001 PHE A 200 TRP 0.020 0.001 TRP A1063 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9973) covalent geometry : angle 0.90460 / 0.36 (13496) hydrogen bonds : bond 0.05071 / 3.26 ( 535) hydrogen bonds : angle 3.88088 / 2.72 ( 1590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8145 (mm-30) cc_final: 0.6965 (mt-10) REVERT: A 56 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8713 (mm-30) REVERT: A 60 GLU cc_start: 0.8690 (tp30) cc_final: 0.8474 (tp30) REVERT: A 92 GLU cc_start: 0.8403 (tp30) cc_final: 0.7933 (tp30) REVERT: A 207 GLN cc_start: 0.8625 (tp40) cc_final: 0.7833 (tp40) REVERT: A 216 TRP cc_start: 0.9009 (t60) cc_final: 0.8809 (t60) REVERT: A 257 GLU cc_start: 0.8681 (tt0) cc_final: 0.8368 (tp30) REVERT: A 485 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8456 (t) REVERT: A 487 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8428 (mtp180) REVERT: A 504 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8253 (mp0) REVERT: A 539 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8205 (tp) REVERT: A 600 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.8268 (ptp90) REVERT: A 871 LEU cc_start: 0.9318 (mt) cc_final: 0.9089 (mm) REVERT: A 993 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8665 (t0) REVERT: A 1028 MET cc_start: 0.8607 (mmp) cc_final: 0.8229 (mtm) REVERT: A 1166 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 1253 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8682 (tm) REVERT: A 1284 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8769 (tptp) REVERT: A 1321 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8390 (tm-30) REVERT: A 1341 ASP cc_start: 0.8694 (t70) cc_final: 0.8021 (t0) REVERT: A 1394 ASP cc_start: 0.8180 (m-30) cc_final: 0.7760 (m-30) REVERT: A 1419 ASN cc_start: 0.9031 (m110) cc_final: 0.8372 (t0) REVERT: A 1439 GLN cc_start: 0.8702 (mm110) cc_final: 0.8438 (tt0) outliers start: 33 outliers final: 24 residues processed: 171 average time/residue: 0.0939 time to fit residues: 23.4873 Evaluate side-chains 169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 HIS A1038 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092202 restraints weight = 20458.963| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.14 r_work: 0.3038 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9973 Z= 0.134 Angle : 0.909 32.584 13496 Z= 0.363 Chirality : 0.092 1.996 1562 Planarity : 0.003 0.032 1630 Dihedral : 5.204 81.396 1356 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.38 % Allowed : 20.29 % Favored : 76.33 % 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: 1.39 (0.25), residues: 1169 helix: 1.75 (0.19), residues: 770 sheet: -1.35 (0.59), residues: 69 loop : -0.47 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.030 0.001 TYR A 517 PHE 0.014 0.001 PHE A 319 TRP 0.021 0.001 TRP A1063 HIS 0.004 0.001 HIS A 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9973) covalent geometry : angle 0.90944 / 0.36 (13496) hydrogen bonds : bond 0.04930 / 3.15 ( 535) hydrogen bonds : angle 3.85299 / 2.68 ( 1590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7214 (mt-10) REVERT: A 56 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 92 GLU cc_start: 0.8389 (tp30) cc_final: 0.7935 (tp30) REVERT: A 257 GLU cc_start: 0.8673 (tt0) cc_final: 0.8354 (tp30) REVERT: A 485 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8429 (t) REVERT: A 487 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8416 (mtp180) REVERT: A 504 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8216 (mp0) REVERT: A 539 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 600 ARG cc_start: 0.8633 (ptt-90) cc_final: 0.8281 (ptp90) REVERT: A 871 LEU cc_start: 0.9316 (mt) cc_final: 0.9089 (mm) REVERT: A 993 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8649 (t0) REVERT: A 1028 MET cc_start: 0.8608 (mmp) cc_final: 0.8218 (mtm) REVERT: A 1166 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8206 (t80) REVERT: A 1253 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8687 (tm) REVERT: A 1284 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8770 (tptp) REVERT: A 1321 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8410 (tm-30) REVERT: A 1341 ASP cc_start: 0.8674 (t70) cc_final: 0.7977 (t0) REVERT: A 1394 ASP cc_start: 0.8196 (m-30) cc_final: 0.7965 (m-30) REVERT: A 1419 ASN cc_start: 0.9033 (m110) cc_final: 0.8379 (t0) REVERT: A 1439 GLN cc_start: 0.8712 (mm110) cc_final: 0.8444 (tt0) outliers start: 35 outliers final: 23 residues processed: 172 average time/residue: 0.0904 time to fit residues: 22.9109 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 856 HIS Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 0.0050 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090061 restraints weight = 20694.046| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.05 r_work: 0.3035 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9973 Z= 0.169 Angle : 0.924 32.786 13496 Z= 0.374 Chirality : 0.092 1.991 1562 Planarity : 0.003 0.032 1630 Dihedral : 5.393 85.213 1356 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.38 % Allowed : 20.39 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.24 (0.25), residues: 1169 helix: 1.63 (0.19), residues: 778 sheet: -1.31 (0.57), residues: 75 loop : -0.56 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.028 0.001 TYR A 517 PHE 0.015 0.001 PHE A 319 TRP 0.027 0.001 TRP A1063 HIS 0.005 0.001 HIS A 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9973) covalent geometry : angle 0.92372 / 0.37 (13496) hydrogen bonds : bond 0.05293 / 3.38 ( 535) hydrogen bonds : angle 3.97874 / 2.77 ( 1590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7401 (mt-10) REVERT: A 56 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8677 (mm-30) REVERT: A 92 GLU cc_start: 0.8497 (tp30) cc_final: 0.7988 (tp30) REVERT: A 207 GLN cc_start: 0.8660 (tp40) cc_final: 0.7933 (tp40) REVERT: A 257 GLU cc_start: 0.8698 (tt0) cc_final: 0.8356 (tp30) REVERT: A 331 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8704 (tp) REVERT: A 348 MET cc_start: 0.8723 (tpt) cc_final: 0.8512 (tpt) REVERT: A 485 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8487 (t) REVERT: A 487 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8405 (mtp180) REVERT: A 504 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8235 (mp0) REVERT: A 539 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 871 LEU cc_start: 0.9313 (mt) cc_final: 0.9088 (mm) REVERT: A 993 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8661 (t0) REVERT: A 1016 PHE cc_start: 0.8549 (t80) cc_final: 0.8342 (t80) REVERT: A 1028 MET cc_start: 0.8635 (mmp) cc_final: 0.8218 (mtm) REVERT: A 1166 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8290 (t80) REVERT: A 1253 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8675 (tm) REVERT: A 1284 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8774 (tptp) REVERT: A 1341 ASP cc_start: 0.8720 (t70) cc_final: 0.8059 (t0) REVERT: A 1394 ASP cc_start: 0.8130 (m-30) cc_final: 0.7845 (m-30) REVERT: A 1419 ASN cc_start: 0.9064 (m110) cc_final: 0.8399 (t0) REVERT: A 1439 GLN cc_start: 0.8731 (mm110) cc_final: 0.8496 (tt0) outliers start: 35 outliers final: 25 residues processed: 172 average time/residue: 0.0980 time to fit residues: 24.6583 Evaluate side-chains 174 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 0.2980 chunk 110 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0050 chunk 10 optimal weight: 3.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 HIS ** A1012 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 = 0.3474 r_free = 0.3474 target = 0.110507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094408 restraints weight = 20032.695| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.06 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9973 Z= 0.111 Angle : 0.896 32.450 13496 Z= 0.357 Chirality : 0.092 1.998 1562 Planarity : 0.003 0.033 1630 Dihedral : 5.096 83.876 1356 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.32 % Allowed : 21.35 % Favored : 76.33 % 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: 1.36 (0.25), residues: 1169 helix: 1.73 (0.19), residues: 779 sheet: -1.37 (0.55), residues: 77 loop : -0.53 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.027 0.001 TYR A 517 PHE 0.013 0.001 PHE A 319 TRP 0.035 0.001 TRP A 216 HIS 0.001 0.000 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9973) covalent geometry : angle 0.89634 / 0.36 (13496) hydrogen bonds : bond 0.04342 / 2.79 ( 535) hydrogen bonds : angle 3.79574 / 2.62 ( 1590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7342 (mt-10) REVERT: A 56 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 92 GLU cc_start: 0.8338 (tp30) cc_final: 0.7895 (tp30) REVERT: A 207 GLN cc_start: 0.8538 (tp40) cc_final: 0.7817 (tp40) REVERT: A 257 GLU cc_start: 0.8684 (tt0) cc_final: 0.8405 (tp30) REVERT: A 265 MET cc_start: 0.8013 (tpp) cc_final: 0.7790 (tpp) REVERT: A 331 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 485 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8435 (t) REVERT: A 487 ARG cc_start: 0.8908 (mtt180) cc_final: 0.8367 (mtp180) REVERT: A 504 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 600 ARG cc_start: 0.8578 (ptt-90) cc_final: 0.8253 (ptp90) REVERT: A 993 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8619 (t0) REVERT: A 1000 ILE cc_start: 0.8920 (mt) cc_final: 0.8683 (mp) REVERT: A 1028 MET cc_start: 0.8546 (mmp) cc_final: 0.8162 (mtm) REVERT: A 1104 GLU cc_start: 0.8718 (tt0) cc_final: 0.8278 (tt0) REVERT: A 1166 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 1253 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8670 (tm) REVERT: A 1284 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8713 (tptp) REVERT: A 1341 ASP cc_start: 0.8535 (t70) cc_final: 0.7778 (t0) REVERT: A 1394 ASP cc_start: 0.8060 (m-30) cc_final: 0.7823 (m-30) REVERT: A 1419 ASN cc_start: 0.9038 (m110) cc_final: 0.8385 (t0) REVERT: A 1439 GLN cc_start: 0.8733 (mm110) cc_final: 0.8522 (tt0) outliers start: 24 outliers final: 16 residues processed: 173 average time/residue: 0.0923 time to fit residues: 23.3879 Evaluate side-chains 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 856 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.107550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.091414 restraints weight = 20617.514| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.06 r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9973 Z= 0.145 Angle : 0.919 32.587 13496 Z= 0.370 Chirality : 0.092 1.993 1562 Planarity : 0.003 0.032 1630 Dihedral : 5.253 87.057 1356 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.61 % Allowed : 22.42 % Favored : 74.98 % 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: 1.42 (0.25), residues: 1169 helix: 1.74 (0.19), residues: 779 sheet: -1.06 (0.55), residues: 85 loop : -0.44 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.026 0.002 TYR A 517 PHE 0.023 0.001 PHE A 83 TRP 0.031 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9973) covalent geometry : angle 0.91931 / 0.37 (13496) hydrogen bonds : bond 0.04964 / 3.17 ( 535) hydrogen bonds : angle 3.91952 / 2.74 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.77 seconds wall clock time: 39 minutes 1.24 seconds (2341.24 seconds total)