Starting phenix.real_space_refine on Tue Jul 29 00:28:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o2p_0611/07_2025/6o2p_0611.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o2p_0611/07_2025/6o2p_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_0611/07_2025/6o2p_0611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o2p_0611/07_2025/6o2p_0611.map" model { file = "/net/cci-nas-00/data/ceres_data/6o2p_0611/07_2025/6o2p_0611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o2p_0611/07_2025/6o2p_0611.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.185 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 255 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 7.13, per 1000 atoms: 0.73 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.27 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: 3.30 Time building geometry restraints manager: 3.11 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 - 34.87: 5850 34.87 - 69.75: 162 69.75 - 104.62: 26 104.62 - 139.49: 53 139.49 - 174.36: 12 Dihedral angle restraints: 6103 sinusoidal: 2627 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=" C12 AJP A1511 " pdb=" C10 AJP A1511 " pdb=" C11 AJP A1511 " pdb=" O82 AJP A1511 " ideal model delta sinusoidal sigma weight residual 287.38 113.02 174.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C06 AJP A1511 " pdb=" C07 AJP A1511 " pdb=" C12 AJP A1511 " pdb=" C13 AJP A1511 " ideal model delta sinusoidal sigma weight residual 109.15 -82.00 -168.85 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 6100 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: 3.520 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.280 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 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 : 22.920 174.362 3855 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 0.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (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 TRP 0.016 0.002 TRP A1274 HIS 0.006 0.002 HIS A 146 PHE 0.019 0.002 PHE A 337 TYR 0.026 0.002 TYR A 161 ARG 0.003 0.001 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.27567 ( 535) hydrogen bonds : angle 8.25443 ( 1590) covalent geometry : bond 0.01390 ( 9973) covalent geometry : angle 1.82955 (13496) *********************** 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 : 1.026 Fit side-chains 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: 0.6881 (tppt) REVERT: A 29 ARG cc_start: 0.7606 (ptp-170) cc_final: 0.7260 (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: 0.7377 (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: 0.8282 (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: 0.2675 time to fit residues: 104.2964 Evaluate side-chains 181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3470 r_free = 0.3470 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093281 restraints weight = 19993.972| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.06 r_work: 0.3063 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2952 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= 0.150 Angle : 0.977 35.241 13496 Z= 0.400 Chirality : 0.092 2.029 1562 Planarity : 0.004 0.036 1630 Dihedral : 18.437 179.989 1607 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.93 % Allowed : 14.01 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1169 helix: 0.72 (0.18), residues: 767 sheet: -2.13 (0.52), residues: 79 loop : -1.57 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1204 HIS 0.008 0.001 HIS A 199 PHE 0.017 0.001 PHE A 81 TYR 0.018 0.002 TYR A 517 ARG 0.006 0.001 ARG A 104 Details of bonding type rmsd hydrogen bonds : bond 0.06293 ( 535) hydrogen bonds : angle 4.46311 ( 1590) covalent geometry : bond 0.00321 ( 9973) covalent geometry : angle 0.97746 (13496) *********************** 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 235 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8590 (mm-30) REVERT: A 60 GLU cc_start: 0.8793 (tp30) cc_final: 0.8579 (tp30) REVERT: A 92 GLU cc_start: 0.8196 (tp30) cc_final: 0.7820 (tp30) REVERT: A 102 LEU cc_start: 0.9474 (tp) cc_final: 0.9259 (tp) REVERT: A 106 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 220 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 257 GLU cc_start: 0.8714 (tt0) cc_final: 0.8176 (tp30) REVERT: A 487 ARG cc_start: 0.8925 (mtt180) cc_final: 0.8397 (mtp180) REVERT: A 504 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8433 (mp0) REVERT: A 572 ASP cc_start: 0.8890 (t0) cc_final: 0.8687 (t0) REVERT: A 600 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.8281 (ptp90) REVERT: A 968 LYS cc_start: 0.8514 (mttm) cc_final: 0.8044 (mtmm) REVERT: A 1046 GLU cc_start: 0.8573 (tt0) cc_final: 0.8105 (tp30) REVERT: A 1104 GLU cc_start: 0.9018 (tt0) cc_final: 0.8796 (tt0) REVERT: A 1253 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8419 (tm) REVERT: A 1284 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8763 (tptp) REVERT: A 1317 LYS cc_start: 0.8557 (tptp) cc_final: 0.8298 (tppt) REVERT: A 1318 VAL cc_start: 0.9357 (t) cc_final: 0.9076 (p) REVERT: A 1320 ASP cc_start: 0.8259 (p0) cc_final: 0.7415 (p0) REVERT: A 1340 VAL cc_start: 0.8318 (m) cc_final: 0.8096 (p) REVERT: A 1341 ASP cc_start: 0.8622 (t70) cc_final: 0.7985 (t0) REVERT: A 1394 ASP cc_start: 0.8344 (m-30) cc_final: 0.7748 (t0) REVERT: A 1437 PHE cc_start: 0.9005 (t80) cc_final: 0.8615 (t80) outliers start: 20 outliers final: 15 residues processed: 230 average time/residue: 0.2428 time to fit residues: 78.8573 Evaluate side-chains 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 1094 SER 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 51 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3471 r_free = 0.3471 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093678 restraints weight = 20383.803| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.07 r_work: 0.3074 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9973 Z= 0.127 Angle : 0.925 33.486 13496 Z= 0.370 Chirality : 0.090 1.992 1562 Planarity : 0.003 0.041 1630 Dihedral : 17.605 179.505 1601 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.80 % Allowed : 16.04 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1169 helix: 1.41 (0.19), residues: 778 sheet: -2.17 (0.53), residues: 62 loop : -1.01 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 882 HIS 0.004 0.001 HIS A 199 PHE 0.015 0.001 PHE A 81 TYR 0.016 0.001 TYR A 38 ARG 0.006 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 535) hydrogen bonds : angle 3.97983 ( 1590) covalent geometry : bond 0.00274 ( 9973) covalent geometry : angle 0.92463 (13496) *********************** 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 202 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7080 (mt-10) REVERT: A 56 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8647 (mm-30) REVERT: A 92 GLU cc_start: 0.8238 (tp30) cc_final: 0.7824 (tp30) REVERT: A 257 GLU cc_start: 0.8705 (tt0) cc_final: 0.8251 (tp30) REVERT: A 286 GLU cc_start: 0.8138 (tt0) cc_final: 0.7929 (tt0) REVERT: A 485 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8365 (t) REVERT: A 487 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8400 (mtp180) REVERT: A 504 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8339 (mp0) REVERT: A 572 ASP cc_start: 0.8919 (t0) cc_final: 0.8715 (t0) REVERT: A 600 ARG cc_start: 0.8688 (ptt-90) cc_final: 0.8287 (ptp90) REVERT: A 1028 MET cc_start: 0.8628 (mmp) cc_final: 0.8217 (mtm) REVERT: A 1046 GLU cc_start: 0.8541 (tt0) cc_final: 0.8200 (tp30) REVERT: A 1253 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8606 (tm) REVERT: A 1284 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8699 (tptp) REVERT: A 1340 VAL cc_start: 0.8287 (m) cc_final: 0.8037 (p) REVERT: A 1341 ASP cc_start: 0.8583 (t70) cc_final: 0.7951 (t0) REVERT: A 1394 ASP cc_start: 0.8254 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1419 ASN cc_start: 0.8954 (m110) cc_final: 0.8364 (t0) REVERT: A 1437 PHE cc_start: 0.8907 (t80) cc_final: 0.8635 (t80) outliers start: 29 outliers final: 17 residues processed: 197 average time/residue: 0.2746 time to fit residues: 76.8408 Evaluate side-chains 165 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 318 VAL 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 982 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 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 15 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 41 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094153 restraints weight = 19865.247| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.04 r_work: 0.3089 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4091 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= 0.120 Angle : 0.907 33.684 13496 Z= 0.362 Chirality : 0.089 1.999 1562 Planarity : 0.003 0.033 1630 Dihedral : 17.003 176.424 1600 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.29 % Allowed : 17.58 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1169 helix: 1.64 (0.19), residues: 773 sheet: -1.73 (0.52), residues: 69 loop : -0.76 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1063 HIS 0.004 0.001 HIS A 199 PHE 0.012 0.001 PHE A 81 TYR 0.015 0.001 TYR A 385 ARG 0.006 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 535) hydrogen bonds : angle 3.78924 ( 1590) covalent geometry : bond 0.00259 ( 9973) covalent geometry : angle 0.90689 (13496) *********************** 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 192 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8667 (mm-30) REVERT: A 60 GLU cc_start: 0.8718 (tp30) cc_final: 0.8470 (tp30) REVERT: A 92 GLU cc_start: 0.8284 (tp30) cc_final: 0.7910 (tp30) REVERT: A 257 GLU cc_start: 0.8682 (tt0) cc_final: 0.8316 (tp30) REVERT: A 378 GLN cc_start: 0.7779 (tt0) cc_final: 0.7389 (tp40) REVERT: A 485 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8387 (t) REVERT: A 487 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8418 (mtp180) REVERT: A 504 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8287 (mp0) REVERT: A 600 ARG cc_start: 0.8672 (ptt-90) cc_final: 0.8237 (ptp90) REVERT: A 1028 MET cc_start: 0.8598 (mmp) cc_final: 0.8235 (mtm) REVERT: A 1046 GLU cc_start: 0.8476 (tt0) cc_final: 0.8242 (tp30) REVERT: A 1104 GLU cc_start: 0.8803 (tt0) cc_final: 0.8390 (tt0) REVERT: A 1253 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (tm) REVERT: A 1284 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8697 (tptp) REVERT: A 1341 ASP cc_start: 0.8596 (t70) cc_final: 0.7880 (t0) REVERT: A 1394 ASP cc_start: 0.8229 (m-30) cc_final: 0.7865 (m-30) REVERT: A 1419 ASN cc_start: 0.8969 (m110) cc_final: 0.8361 (t0) outliers start: 34 outliers final: 15 residues processed: 184 average time/residue: 0.3183 time to fit residues: 83.6163 Evaluate side-chains 165 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 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 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 1167 ILE 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 1322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A1375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092569 restraints weight = 20071.748| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.10 r_work: 0.3047 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9973 Z= 0.137 Angle : 0.908 33.869 13496 Z= 0.364 Chirality : 0.089 2.002 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.837 176.788 1600 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.19 % Allowed : 19.23 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1169 helix: 1.77 (0.19), residues: 770 sheet: -1.49 (0.54), residues: 73 loop : -0.64 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.012 0.001 PHE A 81 TYR 0.010 0.001 TYR A 304 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 535) hydrogen bonds : angle 3.85167 ( 1590) covalent geometry : bond 0.00310 ( 9973) covalent geometry : angle 0.90814 (13496) *********************** 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 183 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8086 (mm-30) cc_final: 0.6968 (mt-10) REVERT: A 56 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8716 (mm-30) REVERT: A 92 GLU cc_start: 0.8394 (tp30) cc_final: 0.7976 (tp30) REVERT: A 257 GLU cc_start: 0.8627 (tt0) cc_final: 0.8272 (tp30) REVERT: A 485 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8431 (t) REVERT: A 487 ARG cc_start: 0.8928 (mtt180) cc_final: 0.8386 (mtp180) REVERT: A 504 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8283 (mp0) REVERT: A 600 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.8256 (ptp90) REVERT: A 871 LEU cc_start: 0.9266 (mt) cc_final: 0.8941 (mm) REVERT: A 913 TYR cc_start: 0.8150 (p90) cc_final: 0.7875 (p90) REVERT: A 1028 MET cc_start: 0.8618 (mmp) cc_final: 0.8243 (mtm) REVERT: A 1104 GLU cc_start: 0.8748 (tt0) cc_final: 0.8294 (tt0) REVERT: A 1253 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (tm) REVERT: A 1284 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8712 (tptp) REVERT: A 1340 VAL cc_start: 0.8238 (m) cc_final: 0.7990 (p) REVERT: A 1341 ASP cc_start: 0.8618 (t70) cc_final: 0.7981 (t0) REVERT: A 1363 LYS cc_start: 0.8898 (tptp) cc_final: 0.8568 (tptp) REVERT: A 1394 ASP cc_start: 0.8252 (m-30) cc_final: 0.7863 (m-30) REVERT: A 1419 ASN cc_start: 0.9048 (m110) cc_final: 0.8399 (t0) outliers start: 33 outliers final: 25 residues processed: 177 average time/residue: 0.2653 time to fit residues: 67.1600 Evaluate side-chains 170 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 265 MET 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 982 ILE Chi-restraints excluded: chain A residue 1005 ILE 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 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A1375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090914 restraints weight = 20407.002| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.07 r_work: 0.3020 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9973 Z= 0.156 Angle : 0.916 34.244 13496 Z= 0.371 Chirality : 0.089 2.008 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.772 177.188 1600 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.67 % Allowed : 19.13 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1169 helix: 1.73 (0.19), residues: 770 sheet: -1.33 (0.55), residues: 73 loop : -0.57 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1063 HIS 0.003 0.001 HIS A1085 PHE 0.012 0.001 PHE A 81 TYR 0.011 0.001 TYR A 304 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 535) hydrogen bonds : angle 3.93733 ( 1590) covalent geometry : bond 0.00364 ( 9973) covalent geometry : angle 0.91564 (13496) *********************** 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 186 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8125 (mm-30) cc_final: 0.6933 (mt-10) REVERT: A 56 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8713 (mm-30) REVERT: A 92 GLU cc_start: 0.8456 (tp30) cc_final: 0.8030 (tp30) REVERT: A 257 GLU cc_start: 0.8643 (tt0) cc_final: 0.8291 (tp30) REVERT: A 485 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8466 (t) REVERT: A 487 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8387 (mtp180) REVERT: A 504 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8251 (mp0) REVERT: A 539 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8245 (tp) REVERT: A 600 ARG cc_start: 0.8667 (ptt-90) cc_final: 0.8326 (ptp90) REVERT: A 1028 MET cc_start: 0.8638 (mmp) cc_final: 0.8239 (mtm) REVERT: A 1104 GLU cc_start: 0.8751 (tt0) cc_final: 0.8272 (tt0) REVERT: A 1166 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8334 (t80) REVERT: A 1253 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8647 (tm) REVERT: A 1284 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8764 (tptp) REVERT: A 1340 VAL cc_start: 0.8223 (m) cc_final: 0.7979 (p) REVERT: A 1341 ASP cc_start: 0.8713 (t70) cc_final: 0.8095 (t0) REVERT: A 1394 ASP cc_start: 0.8169 (m-30) cc_final: 0.7794 (m-30) REVERT: A 1419 ASN cc_start: 0.9057 (m110) cc_final: 0.8411 (t0) REVERT: A 1439 GLN cc_start: 0.8724 (mm110) cc_final: 0.8422 (tt0) outliers start: 38 outliers final: 26 residues processed: 179 average time/residue: 0.2300 time to fit residues: 59.2017 Evaluate side-chains 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain A residue 108 SER 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 452 GLN 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 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1095 THR 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 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.090415 restraints weight = 20543.299| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.11 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9973 Z= 0.163 Angle : 0.926 34.299 13496 Z= 0.374 Chirality : 0.089 2.004 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.759 177.564 1600 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.48 % Allowed : 19.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1169 helix: 1.72 (0.19), residues: 770 sheet: -1.29 (0.56), residues: 73 loop : -0.52 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.012 0.001 PHE A1078 TYR 0.024 0.001 TYR A 517 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.05365 ( 535) hydrogen bonds : angle 3.96217 ( 1590) covalent geometry : bond 0.00381 ( 9973) covalent geometry : angle 0.92605 (13496) *********************** 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 179 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7002 (mt-10) REVERT: A 56 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 92 GLU cc_start: 0.8459 (tp30) cc_final: 0.8027 (tp30) REVERT: A 257 GLU cc_start: 0.8659 (tt0) cc_final: 0.8302 (tp30) REVERT: A 331 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 485 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8492 (t) REVERT: A 487 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8402 (mtp180) REVERT: A 504 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8217 (mp0) REVERT: A 539 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8249 (tp) REVERT: A 600 ARG cc_start: 0.8698 (ptt-90) cc_final: 0.8345 (ptp90) REVERT: A 1028 MET cc_start: 0.8652 (mmp) cc_final: 0.8238 (mtm) REVERT: A 1104 GLU cc_start: 0.8778 (tt0) cc_final: 0.8291 (tt0) REVERT: A 1137 MET cc_start: 0.8533 (mmm) cc_final: 0.8163 (mtt) REVERT: A 1166 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8329 (t80) REVERT: A 1253 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8660 (tm) REVERT: A 1284 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8742 (tptp) REVERT: A 1341 ASP cc_start: 0.8718 (t70) cc_final: 0.8068 (t0) REVERT: A 1394 ASP cc_start: 0.8215 (m-30) cc_final: 0.7996 (m-30) REVERT: A 1419 ASN cc_start: 0.9050 (m110) cc_final: 0.8392 (t0) REVERT: A 1439 GLN cc_start: 0.8716 (mm110) cc_final: 0.8435 (tt0) outliers start: 36 outliers final: 23 residues processed: 172 average time/residue: 0.2692 time to fit residues: 65.6302 Evaluate side-chains 162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 331 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 538 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE 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 1263 THR Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 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 73 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.0570 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 856 HIS A1038 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092786 restraints weight = 20555.139| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.08 r_work: 0.3067 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9973 Z= 0.120 Angle : 0.901 33.901 13496 Z= 0.360 Chirality : 0.089 1.998 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.575 176.916 1600 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.61 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1169 helix: 1.78 (0.19), residues: 775 sheet: -1.21 (0.56), residues: 75 loop : -0.62 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 216 HIS 0.002 0.001 HIS A1085 PHE 0.010 0.001 PHE A 81 TYR 0.029 0.001 TYR A 517 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 535) hydrogen bonds : angle 3.81001 ( 1590) covalent geometry : bond 0.00260 ( 9973) covalent geometry : angle 0.90142 (13496) *********************** 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 177 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7169 (mt-10) REVERT: A 60 GLU cc_start: 0.8658 (tp30) cc_final: 0.8382 (tp30) REVERT: A 75 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8369 (ttm170) REVERT: A 92 GLU cc_start: 0.8380 (tp30) cc_final: 0.7977 (tp30) REVERT: A 257 GLU cc_start: 0.8688 (tt0) cc_final: 0.8430 (tp30) REVERT: A 265 MET cc_start: 0.8141 (ttm) cc_final: 0.7870 (mtp) REVERT: A 281 MET cc_start: 0.8627 (mmm) cc_final: 0.7864 (mmm) REVERT: A 331 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 485 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8409 (t) REVERT: A 487 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8381 (mtp180) REVERT: A 504 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8212 (mp0) REVERT: A 539 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8233 (tp) REVERT: A 600 ARG cc_start: 0.8655 (ptt-90) cc_final: 0.8333 (ptp90) REVERT: A 1028 MET cc_start: 0.8603 (mmp) cc_final: 0.8214 (mtm) REVERT: A 1104 GLU cc_start: 0.8699 (tt0) cc_final: 0.8223 (tt0) REVERT: A 1137 MET cc_start: 0.8317 (mmm) cc_final: 0.8035 (mtt) REVERT: A 1166 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8236 (t80) REVERT: A 1253 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8660 (tm) REVERT: A 1284 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8727 (tptp) REVERT: A 1341 ASP cc_start: 0.8588 (t70) cc_final: 0.7867 (t0) REVERT: A 1394 ASP cc_start: 0.8209 (m-30) cc_final: 0.7897 (m-30) REVERT: A 1419 ASN cc_start: 0.9040 (m110) cc_final: 0.8396 (t0) REVERT: A 1439 GLN cc_start: 0.8739 (mm110) cc_final: 0.8487 (tt0) outliers start: 27 outliers final: 16 residues processed: 170 average time/residue: 0.3326 time to fit residues: 84.0089 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 331 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 539 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE 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 1322 VAL Chi-restraints excluded: chain A residue 1326 SER Chi-restraints excluded: chain A residue 1361 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091885 restraints weight = 20375.869| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.04 r_work: 0.3055 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9973 Z= 0.132 Angle : 0.917 33.932 13496 Z= 0.366 Chirality : 0.089 2.001 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.549 177.415 1600 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.71 % Allowed : 21.64 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1169 helix: 1.79 (0.19), residues: 776 sheet: -1.12 (0.57), residues: 75 loop : -0.59 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.024 0.001 PHE A 83 TYR 0.028 0.001 TYR A 517 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 535) hydrogen bonds : angle 3.83366 ( 1590) covalent geometry : bond 0.00301 ( 9973) covalent geometry : angle 0.91694 (13496) *********************** 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 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7372 (mt-10) REVERT: A 92 GLU cc_start: 0.8353 (tp30) cc_final: 0.7953 (tp30) REVERT: A 257 GLU cc_start: 0.8735 (tt0) cc_final: 0.8451 (tp30) REVERT: A 265 MET cc_start: 0.8161 (ttm) cc_final: 0.7942 (mtp) REVERT: A 281 MET cc_start: 0.8716 (mmm) cc_final: 0.7925 (mmm) REVERT: A 331 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 485 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8424 (t) REVERT: A 487 ARG cc_start: 0.8907 (mtt180) cc_final: 0.8393 (mtp180) REVERT: A 504 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8214 (mp0) REVERT: A 539 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8217 (tp) REVERT: A 600 ARG cc_start: 0.8675 (ptt-90) cc_final: 0.8362 (ptp90) REVERT: A 1028 MET cc_start: 0.8624 (mmp) cc_final: 0.8222 (mtm) REVERT: A 1104 GLU cc_start: 0.8699 (tt0) cc_final: 0.8214 (tt0) REVERT: A 1137 MET cc_start: 0.8378 (mmm) cc_final: 0.8020 (mtt) REVERT: A 1166 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8224 (t80) REVERT: A 1253 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8685 (tm) REVERT: A 1284 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8712 (tptp) REVERT: A 1341 ASP cc_start: 0.8668 (t70) cc_final: 0.7962 (t0) REVERT: A 1394 ASP cc_start: 0.8089 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1419 ASN cc_start: 0.9034 (m110) cc_final: 0.8379 (t0) REVERT: A 1439 GLN cc_start: 0.8748 (mm110) cc_final: 0.8529 (tt0) outliers start: 28 outliers final: 20 residues processed: 163 average time/residue: 0.2064 time to fit residues: 48.7450 Evaluate side-chains 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 331 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 539 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE 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 1203 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 1322 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 59 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094080 restraints weight = 20294.266| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.12 r_work: 0.3080 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4968 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= 0.119 Angle : 0.916 33.808 13496 Z= 0.366 Chirality : 0.089 2.002 1562 Planarity : 0.003 0.033 1630 Dihedral : 16.458 177.151 1600 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.42 % Allowed : 22.13 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1169 helix: 1.85 (0.19), residues: 774 sheet: -0.93 (0.54), residues: 85 loop : -0.49 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 216 HIS 0.002 0.001 HIS A1085 PHE 0.023 0.001 PHE A 83 TYR 0.026 0.001 TYR A 517 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 535) hydrogen bonds : angle 3.78996 ( 1590) covalent geometry : bond 0.00261 ( 9973) covalent geometry : angle 0.91631 (13496) ********************** 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 169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 2.313 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7338 (mt-10) REVERT: A 60 GLU cc_start: 0.8635 (tp30) cc_final: 0.8378 (tp30) REVERT: A 92 GLU cc_start: 0.8365 (tp30) cc_final: 0.7956 (tp30) REVERT: A 257 GLU cc_start: 0.8723 (tt0) cc_final: 0.8420 (tp30) REVERT: A 331 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 385 TYR cc_start: 0.7404 (t80) cc_final: 0.7153 (t80) REVERT: A 485 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8404 (t) REVERT: A 487 ARG cc_start: 0.8921 (mtt180) cc_final: 0.8377 (mtp180) REVERT: A 504 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 600 ARG cc_start: 0.8651 (ptt-90) cc_final: 0.8357 (ptp90) REVERT: A 1000 ILE cc_start: 0.8898 (mt) cc_final: 0.8648 (mp) REVERT: A 1028 MET cc_start: 0.8562 (mmp) cc_final: 0.8175 (mtm) REVERT: A 1104 GLU cc_start: 0.8650 (tt0) cc_final: 0.8180 (tt0) REVERT: A 1137 MET cc_start: 0.8279 (mmm) cc_final: 0.7985 (mtt) REVERT: A 1166 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8234 (t80) REVERT: A 1253 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (tm) REVERT: A 1284 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8680 (tptp) REVERT: A 1341 ASP cc_start: 0.8562 (t70) cc_final: 0.7831 (t0) REVERT: A 1394 ASP cc_start: 0.8063 (m-30) cc_final: 0.7846 (m-30) REVERT: A 1419 ASN cc_start: 0.9038 (m110) cc_final: 0.8371 (t0) REVERT: A 1439 GLN cc_start: 0.8751 (mm110) cc_final: 0.8540 (tt0) outliers start: 25 outliers final: 19 residues processed: 164 average time/residue: 0.3400 time to fit residues: 81.6230 Evaluate side-chains 162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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 331 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 590 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1005 ILE 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 1203 ILE Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 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 10 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093964 restraints weight = 20301.691| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.08 r_work: 0.3068 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9973 Z= 0.126 Angle : 0.917 33.845 13496 Z= 0.367 Chirality : 0.089 2.003 1562 Planarity : 0.003 0.032 1630 Dihedral : 16.460 177.494 1600 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 22.51 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.25), residues: 1169 helix: 1.88 (0.19), residues: 776 sheet: -0.84 (0.55), residues: 85 loop : -0.46 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 216 HIS 0.003 0.001 HIS A1085 PHE 0.021 0.001 PHE A 83 TYR 0.026 0.001 TYR A 913 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 535) hydrogen bonds : angle 3.81384 ( 1590) covalent geometry : bond 0.00282 ( 9973) covalent geometry : angle 0.91729 (13496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5711.79 seconds wall clock time: 107 minutes 1.28 seconds (6421.28 seconds total)