Starting phenix.real_space_refine on Fri Jul 3 10:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxs_70993/07_2026/9oxs_70993.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 Zn 3 6.06 5 P 7 5.49 5 S 88 5.16 5 C 8463 2.51 5 N 2300 2.21 5 O 2391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9275 Classifications: {'peptide': 1168} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1102} Chain breaks: 13 Chain: "B" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2937 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 905 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Classifications: {'DNA': 1, 'RNA': 6} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2} Link IDs: {'rna2p': 6} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12518 SG CYS C 41 32.361 90.732 97.691 1.00 71.55 S ATOM 12582 SG CYS C 49 29.216 90.974 99.925 1.00 70.83 S ATOM 12617 SG CYS C 55 31.152 87.771 99.698 1.00 79.87 S ATOM 12719 SG CYS C 68 47.774 81.930 108.724 1.00 69.33 S ATOM 12789 SG CYS C 76 44.065 80.721 108.243 1.00 65.02 S ATOM 12834 SG CYS C 82 44.986 84.324 109.641 1.00 73.17 S ATOM 12955 SG CYS C 96 64.429 78.867 111.298 1.00118.90 S ATOM 13035 SG CYS C 105 66.535 76.424 109.228 1.00124.87 S ATOM 13073 SG CYS C 110 63.543 78.207 107.632 1.00113.99 S Time building chain proxies: 2.86, per 1000 atoms: 0.22 Number of scatterers: 13252 At special positions: 0 Unit cell: (89.024, 107, 134.392, 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) Zn 3 29.99 S 88 16.00 P 7 15.00 O 2391 8.00 N 2300 7.00 C 8463 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: 1.00 Conformation dependent library (CDL) restraints added in 510.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 82 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 105 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " Number of angles added : 9 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3082 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 33 sheets defined 9.1% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 489 through 493 removed outlier: 4.065A pdb=" N ASN A 492 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.697A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1401 through 1405 Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1411 through 1423 Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.797A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.670A pdb=" N ASP B 78 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.729A pdb=" N ASP B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.508A pdb=" N ALA C 6 " --> pdb=" O GLN C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.595A pdb=" N ARG C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 96 through 101 Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.345A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1336 " --> pdb=" O LEU A1348 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1348 " --> pdb=" O THR A1336 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 6 " --> pdb=" O LEU A1347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.642A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.587A pdb=" N SER A 119 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A 107 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR A 117 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.778A pdb=" N LEU A 220 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 206 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 218 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE A 208 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 216 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 240 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 257 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 3.733A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN A 290 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ARG A 313 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.605A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 384 removed outlier: 3.725A pdb=" N LEU A 382 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS A 395 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL A 465 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR A 397 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE A 463 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 481 removed outlier: 3.700A pdb=" N VAL A 501 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 525 through 528 removed outlier: 3.516A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 990 " --> pdb=" O SER A 974 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.355A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 584 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.563A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 628 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS A 636 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 648 through 652 removed outlier: 3.527A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 667 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.685A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 854 removed outlier: 3.521A pdb=" N GLU A 848 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 931 through 934 Processing sheet with id=AB9, first strand: chain 'A' and resid 1021 through 1028 removed outlier: 6.581A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL A1025 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA A1035 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR A1027 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A1033 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1036 " --> pdb=" O GLN A1077 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1046 through 1048 Processing sheet with id=AC2, first strand: chain 'A' and resid 1102 through 1106 removed outlier: 6.655A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1159 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.962A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A1189 " --> pdb=" O ILE A1186 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 3.962A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A1189 " --> pdb=" O ILE A1186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1221 through 1222 removed outlier: 6.991A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.873A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.873A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.902A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 380 " --> pdb=" O GLY B 393 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 122 through 127 removed outlier: 6.232A pdb=" N PHE B 143 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE B 156 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 145 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 164 through 169 removed outlier: 6.596A pdb=" N ALA B 179 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 167 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 177 " --> pdb=" O MET B 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 184 through 188 removed outlier: 3.868A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 205 through 210 removed outlier: 3.960A pdb=" N GLU B 207 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 226 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.344A pdb=" N GLY B 262 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL B 250 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 260 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 259 " --> pdb=" O TRP B 273 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.521A pdb=" N LYS B 313 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 312 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 316 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLU B 323 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 334 through 339 removed outlier: 6.152A pdb=" N GLY B 350 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL B 337 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 348 " --> pdb=" O VAL B 337 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 930 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: 3.21 Time building geometry restraints manager: 1.37 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: 4242 1.34 - 1.46: 2615 1.46 - 1.58: 6577 1.58 - 1.70: 13 1.70 - 1.82: 139 Bond restraints: 13586 Sorted by residual: bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CA MET B 372 " pdb=" CB MET B 372 " ideal model delta sigma weight residual 1.531 1.548 -0.017 1.51e-02 4.39e+03 1.26e+00 bond pdb=" CB VAL B 367 " pdb=" CG1 VAL B 367 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CA SER A1031 " pdb=" CB SER A1031 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 9.59e-01 ... (remaining 13581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 17681 1.22 - 2.45: 594 2.45 - 3.67: 134 3.67 - 4.90: 33 4.90 - 6.12: 2 Bond angle restraints: 18444 Sorted by residual: angle pdb=" N SER A1031 " pdb=" CA SER A1031 " pdb=" CB SER A1031 " ideal model delta sigma weight residual 114.17 110.40 3.77 1.14e+00 7.69e-01 1.09e+01 angle pdb=" CA MET B 372 " pdb=" CB MET B 372 " pdb=" CG MET B 372 " ideal model delta sigma weight residual 114.10 120.22 -6.12 2.00e+00 2.50e-01 9.36e+00 angle pdb=" N ALA A 232 " pdb=" CA ALA A 232 " pdb=" C ALA A 232 " ideal model delta sigma weight residual 114.64 110.83 3.81 1.52e+00 4.33e-01 6.29e+00 angle pdb=" CA GLY A 277 " pdb=" C GLY A 277 " pdb=" N VAL A 278 " ideal model delta sigma weight residual 114.85 117.00 -2.15 9.50e-01 1.11e+00 5.10e+00 angle pdb=" N THR A 259 " pdb=" CA THR A 259 " pdb=" C THR A 259 " ideal model delta sigma weight residual 110.61 113.32 -2.71 1.25e+00 6.40e-01 4.70e+00 ... (remaining 18439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6874 17.84 - 35.68: 884 35.68 - 53.53: 255 53.53 - 71.37: 50 71.37 - 89.21: 19 Dihedral angle restraints: 8082 sinusoidal: 3314 harmonic: 4768 Sorted by residual: dihedral pdb=" CA VAL A 231 " pdb=" C VAL A 231 " pdb=" N ALA A 232 " pdb=" CA ALA A 232 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR B 213 " pdb=" C THR B 213 " pdb=" N ASP B 214 " pdb=" CA ASP B 214 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 8079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1087 0.027 - 0.055: 640 0.055 - 0.082: 140 0.082 - 0.110: 122 0.110 - 0.137: 65 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CA ILE A 472 " pdb=" N ILE A 472 " pdb=" C ILE A 472 " pdb=" CB ILE A 472 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE A 998 " pdb=" N ILE A 998 " pdb=" C ILE A 998 " pdb=" CB ILE A 998 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE A1222 " pdb=" N ILE A1222 " pdb=" C ILE A1222 " pdb=" CB ILE A1222 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 2051 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 271 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A 272 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 227 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 228 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 340 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 341 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 341 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 341 " 0.022 5.00e-02 4.00e+02 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 103 2.50 - 3.10: 8969 3.10 - 3.70: 19144 3.70 - 4.30: 29306 4.30 - 4.90: 51846 Nonbonded interactions: 109368 Sorted by model distance: nonbonded pdb=" OG SER B 170 " pdb=" OD2 ASP B 214 " model vdw 1.901 3.040 nonbonded pdb=" O LEU A 370 " pdb=" OG SER A 386 " model vdw 1.996 3.040 nonbonded pdb=" O THR A1436 " pdb=" OG1 THR A1440 " model vdw 2.041 3.040 nonbonded pdb=" O GLU A1030 " pdb=" OG SER A1031 " model vdw 2.072 3.040 nonbonded pdb=" O GLY A 276 " pdb=" OH TYR A 288 " model vdw 2.103 3.040 ... (remaining 109363 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: 1.940 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.004 0.037 13598 Z= 0.156 Angle : 0.576 6.120 18453 Z= 0.301 Chirality : 0.044 0.137 2054 Planarity : 0.004 0.043 2326 Dihedral : 17.581 89.209 5000 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.28 % Allowed : 28.11 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.21), residues: 1615 helix: -0.46 (0.53), residues: 96 sheet: -1.39 (0.22), residues: 585 loop : -1.43 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 579 TYR 0.012 0.001 TYR A 39 PHE 0.012 0.001 PHE A 934 TRP 0.008 0.001 TRP B 359 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13586) covalent geometry : angle 0.57338 / 0.30 (18444) hydrogen bonds : bond 0.24617 / 16.49 ( 348) hydrogen bonds : angle 10.50578 / 7.05 ( 930) metal coordination : bond 0.00766 / 0.43 ( 12) metal coordination : angle 2.70971 / 1.37 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 0.501 Fit side-chains REVERT: B 103 MET cc_start: 0.7313 (mmp) cc_final: 0.7109 (mmm) REVERT: C 58 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7464 (ttp80) outliers start: 4 outliers final: 3 residues processed: 174 average time/residue: 0.1028 time to fit residues: 26.8642 Evaluate side-chains 169 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain B residue 249 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1188 GLN A1405 ASN B 116 ASN C 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129509 restraints weight = 14298.591| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.78 r_work: 0.3382 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13598 Z= 0.189 Angle : 0.642 8.813 18453 Z= 0.328 Chirality : 0.046 0.166 2054 Planarity : 0.005 0.049 2326 Dihedral : 6.362 58.124 1864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.83 % Allowed : 26.03 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.20), residues: 1615 helix: -0.51 (0.50), residues: 103 sheet: -1.22 (0.21), residues: 582 loop : -1.38 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 74 TYR 0.012 0.001 TYR A 189 PHE 0.018 0.002 PHE A 934 TRP 0.016 0.002 TRP B 359 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13586) covalent geometry : angle 0.63906 / 0.33 (18444) hydrogen bonds : bond 0.05073 / 3.47 ( 348) hydrogen bonds : angle 7.64218 / 5.12 ( 930) metal coordination : bond 0.00744 / 0.47 ( 12) metal coordination : angle 2.80309 / 1.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.397 Fit side-chains REVERT: A 289 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7504 (mt) REVERT: A 1418 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6370 (tt) REVERT: B 98 MET cc_start: 0.8582 (ptp) cc_final: 0.8329 (ptp) REVERT: B 103 MET cc_start: 0.7650 (mmp) cc_final: 0.7229 (mmm) REVERT: B 230 ASP cc_start: 0.6639 (t0) cc_final: 0.6224 (p0) REVERT: C 58 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7564 (ttp80) REVERT: C 85 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6212 (tm) outliers start: 55 outliers final: 32 residues processed: 200 average time/residue: 0.1154 time to fit residues: 34.1271 Evaluate side-chains 197 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1165 GLU Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1301 ASP Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129476 restraints weight = 14437.782| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.79 r_work: 0.3393 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13598 Z= 0.178 Angle : 0.615 8.367 18453 Z= 0.312 Chirality : 0.045 0.156 2054 Planarity : 0.005 0.053 2326 Dihedral : 6.186 58.161 1859 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.73 % Allowed : 26.51 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.20), residues: 1615 helix: -0.63 (0.48), residues: 108 sheet: -1.20 (0.21), residues: 585 loop : -1.35 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.012 0.001 TYR A 189 PHE 0.018 0.002 PHE A 934 TRP 0.015 0.001 TRP B 359 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (13586) covalent geometry : angle 0.61220 / 0.31 (18444) hydrogen bonds : bond 0.04216 / 2.92 ( 348) hydrogen bonds : angle 6.92934 / 4.65 ( 930) metal coordination : bond 0.00809 / 0.52 ( 12) metal coordination : angle 2.71572 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 0.514 Fit side-chains REVERT: A 1235 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5579 (ttm-80) REVERT: A 1418 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6379 (tt) REVERT: B 103 MET cc_start: 0.7788 (mmp) cc_final: 0.7194 (mmm) REVERT: B 192 MET cc_start: 0.6756 (mmt) cc_final: 0.5883 (mmt) REVERT: B 230 ASP cc_start: 0.6624 (t0) cc_final: 0.6183 (p0) REVERT: C 85 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6174 (tm) outliers start: 68 outliers final: 45 residues processed: 216 average time/residue: 0.1256 time to fit residues: 39.6241 Evaluate side-chains 210 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1165 GLU Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128014 restraints weight = 14420.191| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.78 r_work: 0.3375 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13598 Z= 0.225 Angle : 0.657 8.830 18453 Z= 0.330 Chirality : 0.047 0.165 2054 Planarity : 0.005 0.056 2326 Dihedral : 6.299 58.308 1859 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.64 % Allowed : 26.24 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1615 helix: -0.68 (0.48), residues: 108 sheet: -1.32 (0.21), residues: 599 loop : -1.39 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1248 TYR 0.012 0.002 TYR A 189 PHE 0.022 0.002 PHE A 934 TRP 0.015 0.002 TRP B 359 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (13586) covalent geometry : angle 0.65340 / 0.33 (18444) hydrogen bonds : bond 0.04118 / 2.83 ( 348) hydrogen bonds : angle 6.77264 / 4.54 ( 930) metal coordination : bond 0.00878 / 0.56 ( 12) metal coordination : angle 3.00525 / 1.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 163 time to evaluate : 0.435 Fit side-chains REVERT: A 159 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 289 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 579 ARG cc_start: 0.7655 (mmt90) cc_final: 0.7409 (mtt-85) REVERT: A 860 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6870 (pmm-80) REVERT: A 869 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: A 1235 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.5576 (ttm-80) REVERT: A 1418 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6453 (tt) REVERT: B 192 MET cc_start: 0.6510 (mmp) cc_final: 0.5476 (mmt) REVERT: B 230 ASP cc_start: 0.6717 (t0) cc_final: 0.6226 (p0) REVERT: C 75 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6894 (mt) REVERT: C 85 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6228 (tm) REVERT: C 90 MET cc_start: 0.5137 (pmm) cc_final: 0.3887 (ptt) outliers start: 81 outliers final: 58 residues processed: 221 average time/residue: 0.1043 time to fit residues: 34.0860 Evaluate side-chains 224 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130285 restraints weight = 14223.626| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.79 r_work: 0.3382 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13598 Z= 0.146 Angle : 0.585 8.326 18453 Z= 0.296 Chirality : 0.044 0.150 2054 Planarity : 0.004 0.057 2326 Dihedral : 6.148 58.061 1859 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.50 % Allowed : 26.17 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.20), residues: 1615 helix: -0.49 (0.48), residues: 108 sheet: -1.21 (0.21), residues: 605 loop : -1.34 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.010 0.001 TYR A 189 PHE 0.018 0.001 PHE A 208 TRP 0.014 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13586) covalent geometry : angle 0.58251 / 0.30 (18444) hydrogen bonds : bond 0.03641 / 2.52 ( 348) hydrogen bonds : angle 6.47311 / 4.34 ( 930) metal coordination : bond 0.00720 / 0.45 ( 12) metal coordination : angle 2.45871 / 1.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 0.584 Fit side-chains REVERT: A 159 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7840 (tt) REVERT: A 579 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7360 (mtt-85) REVERT: A 860 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6910 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6392 (tt) REVERT: B 79 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8435 (ttt) REVERT: B 98 MET cc_start: 0.8501 (ptp) cc_final: 0.8084 (ptp) REVERT: B 133 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7520 (ptp90) REVERT: B 192 MET cc_start: 0.6523 (mmp) cc_final: 0.5302 (mmt) REVERT: B 230 ASP cc_start: 0.6690 (t0) cc_final: 0.6162 (p0) REVERT: C 75 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6815 (mt) REVERT: C 85 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6126 (tm) REVERT: C 90 MET cc_start: 0.5089 (pmm) cc_final: 0.3784 (ptt) outliers start: 79 outliers final: 59 residues processed: 220 average time/residue: 0.1164 time to fit residues: 37.7621 Evaluate side-chains 224 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 158 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 147 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 158 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135216 restraints weight = 14178.380| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.72 r_work: 0.3459 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13598 Z= 0.139 Angle : 0.579 8.170 18453 Z= 0.292 Chirality : 0.044 0.148 2054 Planarity : 0.004 0.056 2326 Dihedral : 6.080 58.045 1859 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.08 % Allowed : 26.44 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.21), residues: 1615 helix: -0.35 (0.49), residues: 108 sheet: -1.13 (0.21), residues: 605 loop : -1.33 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.010 0.001 TYR A 189 PHE 0.032 0.001 PHE A 208 TRP 0.012 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (13586) covalent geometry : angle 0.57723 / 0.29 (18444) hydrogen bonds : bond 0.03471 / 2.40 ( 348) hydrogen bonds : angle 6.29418 / 4.21 ( 930) metal coordination : bond 0.00690 / 0.43 ( 12) metal coordination : angle 2.30001 / 1.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 170 time to evaluate : 0.512 Fit side-chains REVERT: A 159 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 579 ARG cc_start: 0.7617 (mmt90) cc_final: 0.7396 (mtt-85) REVERT: A 860 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6907 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6530 (tt) REVERT: B 79 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8377 (ttt) REVERT: B 133 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7510 (ptp90) REVERT: B 192 MET cc_start: 0.6359 (mmp) cc_final: 0.5042 (mmt) REVERT: B 230 ASP cc_start: 0.6621 (t0) cc_final: 0.6209 (p0) REVERT: C 75 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6903 (mt) REVERT: C 85 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6117 (tm) REVERT: C 90 MET cc_start: 0.5078 (pmm) cc_final: 0.3835 (ptt) outliers start: 73 outliers final: 58 residues processed: 222 average time/residue: 0.1122 time to fit residues: 36.8447 Evaluate side-chains 228 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 0.0170 chunk 93 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN B 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.161077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136126 restraints weight = 14213.960| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.70 r_work: 0.3470 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13598 Z= 0.125 Angle : 0.560 7.833 18453 Z= 0.283 Chirality : 0.044 0.144 2054 Planarity : 0.004 0.056 2326 Dihedral : 5.981 58.006 1859 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.36 % Allowed : 26.44 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.21), residues: 1615 helix: -0.20 (0.49), residues: 108 sheet: -0.97 (0.21), residues: 590 loop : -1.36 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1049 TYR 0.010 0.001 TYR A 189 PHE 0.029 0.001 PHE A 208 TRP 0.012 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (13586) covalent geometry : angle 0.55843 / 0.28 (18444) hydrogen bonds : bond 0.03314 / 2.31 ( 348) hydrogen bonds : angle 6.13063 / 4.11 ( 930) metal coordination : bond 0.00634 / 0.39 ( 12) metal coordination : angle 2.11961 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 164 time to evaluate : 0.409 Fit side-chains REVERT: A 159 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 289 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7435 (mt) REVERT: A 579 ARG cc_start: 0.7632 (mmt90) cc_final: 0.7402 (mtt-85) REVERT: A 860 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6869 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6498 (tt) REVERT: B 79 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8362 (ttt) REVERT: B 133 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7539 (ptp90) REVERT: B 192 MET cc_start: 0.6485 (mmp) cc_final: 0.5096 (mmt) REVERT: B 230 ASP cc_start: 0.6617 (t0) cc_final: 0.6176 (p0) REVERT: C 75 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6874 (mt) REVERT: C 85 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6139 (tm) REVERT: C 90 MET cc_start: 0.5014 (pmm) cc_final: 0.3758 (ptt) outliers start: 77 outliers final: 60 residues processed: 220 average time/residue: 0.1125 time to fit residues: 36.1890 Evaluate side-chains 225 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 139 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135732 restraints weight = 14191.731| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.70 r_work: 0.3466 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13598 Z= 0.138 Angle : 0.570 9.576 18453 Z= 0.286 Chirality : 0.044 0.143 2054 Planarity : 0.004 0.055 2326 Dihedral : 5.971 58.067 1859 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.43 % Allowed : 26.44 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1615 helix: -0.18 (0.49), residues: 108 sheet: -0.99 (0.21), residues: 596 loop : -1.34 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1317 TYR 0.010 0.001 TYR A 189 PHE 0.030 0.001 PHE A 208 TRP 0.011 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13586) covalent geometry : angle 0.56769 / 0.29 (18444) hydrogen bonds : bond 0.03346 / 2.32 ( 348) hydrogen bonds : angle 6.06904 / 4.06 ( 930) metal coordination : bond 0.00653 / 0.41 ( 12) metal coordination : angle 2.16567 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 161 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 289 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 579 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7405 (mtt-85) REVERT: A 860 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6823 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6518 (tt) REVERT: B 133 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7661 (ptp90) REVERT: B 192 MET cc_start: 0.6377 (mmp) cc_final: 0.5037 (mmt) REVERT: B 230 ASP cc_start: 0.6618 (t0) cc_final: 0.6158 (p0) REVERT: C 75 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6896 (mt) REVERT: C 85 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6167 (tm) REVERT: C 90 MET cc_start: 0.4991 (pmm) cc_final: 0.3831 (ptt) outliers start: 78 outliers final: 59 residues processed: 217 average time/residue: 0.1029 time to fit residues: 33.2350 Evaluate side-chains 223 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 157 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 128 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 11 optimal weight: 0.0570 chunk 156 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.162045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137163 restraints weight = 14246.188| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.70 r_work: 0.3484 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13598 Z= 0.116 Angle : 0.555 9.706 18453 Z= 0.278 Chirality : 0.043 0.142 2054 Planarity : 0.004 0.056 2326 Dihedral : 5.883 57.970 1859 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.80 % Allowed : 26.93 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1615 helix: -0.06 (0.50), residues: 108 sheet: -0.88 (0.21), residues: 588 loop : -1.35 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1049 TYR 0.009 0.001 TYR A1281 PHE 0.034 0.001 PHE A 208 TRP 0.011 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13586) covalent geometry : angle 0.55366 / 0.28 (18444) hydrogen bonds : bond 0.03192 / 2.22 ( 348) hydrogen bonds : angle 5.92531 / 3.97 ( 930) metal coordination : bond 0.00590 / 0.37 ( 12) metal coordination : angle 1.92464 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 164 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 289 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7425 (mt) REVERT: A 579 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7397 (mtt-85) REVERT: A 587 GLN cc_start: 0.6621 (tm-30) cc_final: 0.5548 (mm110) REVERT: A 860 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6822 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6456 (tt) REVERT: B 133 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7576 (ptp90) REVERT: B 192 MET cc_start: 0.6354 (mmp) cc_final: 0.4946 (mmt) REVERT: C 75 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6814 (mt) REVERT: C 85 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6150 (tm) REVERT: C 90 MET cc_start: 0.4881 (pmm) cc_final: 0.3662 (ptt) outliers start: 69 outliers final: 59 residues processed: 213 average time/residue: 0.1124 time to fit residues: 35.2572 Evaluate side-chains 225 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1235 ARG Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1385 HIS Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1411 SER Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 36 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 HIS B 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136670 restraints weight = 14114.112| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.77 r_work: 0.3474 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13598 Z= 0.097 Angle : 0.529 10.302 18453 Z= 0.266 Chirality : 0.042 0.140 2054 Planarity : 0.004 0.057 2326 Dihedral : 5.726 57.896 1859 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.90 % Allowed : 27.70 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1615 helix: 0.12 (0.51), residues: 108 sheet: -0.78 (0.21), residues: 599 loop : -1.36 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1049 TYR 0.010 0.001 TYR A1281 PHE 0.031 0.001 PHE A 208 TRP 0.012 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (13586) covalent geometry : angle 0.52772 / 0.27 (18444) hydrogen bonds : bond 0.03002 / 2.09 ( 348) hydrogen bonds : angle 5.71560 / 3.84 ( 930) metal coordination : bond 0.00567 / 0.34 ( 12) metal coordination : angle 1.67350 / 0.77 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 168 time to evaluate : 0.440 Fit side-chains REVERT: A 159 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7735 (tt) REVERT: A 269 LEU cc_start: 0.8807 (mt) cc_final: 0.8143 (mp) REVERT: A 289 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7370 (mt) REVERT: A 579 ARG cc_start: 0.7666 (mmt90) cc_final: 0.7364 (mtt-85) REVERT: A 587 GLN cc_start: 0.6554 (tm-30) cc_final: 0.5552 (mt0) REVERT: A 860 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6841 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6326 (tt) REVERT: B 192 MET cc_start: 0.6434 (mmp) cc_final: 0.5091 (mmt) REVERT: C 85 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6140 (tm) REVERT: C 90 MET cc_start: 0.4807 (pmm) cc_final: 0.3649 (ptt) outliers start: 56 outliers final: 48 residues processed: 207 average time/residue: 0.1210 time to fit residues: 36.0668 Evaluate side-chains 214 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 860 ARG Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS Chi-restraints excluded: chain A residue 946 CYS Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1234 LEU Chi-restraints excluded: chain A residue 1254 GLU Chi-restraints excluded: chain A residue 1304 VAL Chi-restraints excluded: chain A residue 1369 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 76 CYS Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130635 restraints weight = 14232.987| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.76 r_work: 0.3402 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13598 Z= 0.213 Angle : 0.657 10.281 18453 Z= 0.324 Chirality : 0.047 0.300 2054 Planarity : 0.005 0.053 2326 Dihedral : 6.080 58.309 1859 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.38 % Allowed : 27.21 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1615 helix: -0.35 (0.48), residues: 108 sheet: -0.99 (0.21), residues: 596 loop : -1.34 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1049 TYR 0.013 0.002 TYR A 189 PHE 0.035 0.002 PHE A 208 TRP 0.012 0.002 TRP A1193 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.21 (13586) covalent geometry : angle 0.65460 / 0.32 (18444) hydrogen bonds : bond 0.03714 / 2.55 ( 348) hydrogen bonds : angle 6.06658 / 4.09 ( 930) metal coordination : bond 0.00798 / 0.50 ( 12) metal coordination : angle 2.53178 / 1.19 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3376.56 seconds wall clock time: 58 minutes 36.35 seconds (3516.35 seconds total)