Starting phenix.real_space_refine on Wed Feb 4 22:52:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxs_70993/02_2026/9oxs_70993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxs_70993/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9oxs_70993/02_2026/9oxs_70993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxs_70993/02_2026/9oxs_70993.map" model { file = "/net/cci-nas-00/data/ceres_data/9oxs_70993/02_2026/9oxs_70993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxs_70993/02_2026/9oxs_70993.cif" } 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-2.0-5952/lib/python3.9/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: 3.00, per 1000 atoms: 0.23 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: 0.98 Conformation dependent library (CDL) restraints added in 611.9 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: 0.67 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: 3.02 Time building geometry restraints manager: 1.30 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: 1088 0.027 - 0.055: 639 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 covalent geometry : bond 0.00356 (13586) covalent geometry : angle 0.57338 (18444) hydrogen bonds : bond 0.24617 ( 348) hydrogen bonds : angle 10.50578 ( 930) metal coordination : bond 0.00766 ( 12) metal coordination : angle 2.70971 ( 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 : 0.582 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: 0.1135 time to fit residues: 29.3938 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 : 0.414 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.155529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129733 restraints weight = 14287.964| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.77 r_work: 0.3383 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13598 Z= 0.183 Angle : 0.624 8.024 18453 Z= 0.318 Chirality : 0.045 0.151 2054 Planarity : 0.005 0.051 2326 Dihedral : 6.311 58.180 1864 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.24 % Allowed : 26.37 % Favored : 69.38 % 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: -1.92 (0.20), residues: 1615 helix: -0.46 (0.50), residues: 103 sheet: -1.20 (0.21), residues: 583 loop : -1.39 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.012 0.001 TYR A 189 PHE 0.017 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 covalent geometry : bond 0.00443 (13586) covalent geometry : angle 0.62142 (18444) hydrogen bonds : bond 0.04644 ( 348) hydrogen bonds : angle 7.20909 ( 930) metal coordination : bond 0.00918 ( 12) metal coordination : angle 2.71876 ( 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 231 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 1418 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6377 (tt) REVERT: B 98 MET cc_start: 0.8543 (ptp) cc_final: 0.8179 (ptp) REVERT: B 103 MET cc_start: 0.7744 (mmp) cc_final: 0.7309 (mmm) REVERT: B 192 MET cc_start: 0.6711 (mmt) cc_final: 0.5985 (mmp) REVERT: B 230 ASP cc_start: 0.6616 (t0) cc_final: 0.6172 (p0) REVERT: C 85 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6196 (tm) outliers start: 61 outliers final: 36 residues processed: 210 average time/residue: 0.1197 time to fit residues: 36.8663 Evaluate side-chains 199 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP 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 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 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 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 1254 GLU Chi-restraints excluded: chain A residue 1301 ASP Chi-restraints excluded: chain A residue 1384 LEU 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 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 342 VAL Chi-restraints excluded: chain B residue 374 HIS 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 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: 0.9980 chunk 53 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.160684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137139 restraints weight = 14353.462| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.66 r_work: 0.3463 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13598 Z= 0.129 Angle : 0.560 7.948 18453 Z= 0.285 Chirality : 0.044 0.144 2054 Planarity : 0.004 0.052 2326 Dihedral : 5.965 58.025 1859 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.76 % Allowed : 27.35 % Favored : 68.89 % 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: -1.79 (0.21), residues: 1615 helix: -0.42 (0.48), residues: 108 sheet: -1.08 (0.21), residues: 590 loop : -1.32 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.009 0.001 TYR A 189 PHE 0.018 0.001 PHE A 208 TRP 0.013 0.001 TRP B 359 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd covalent geometry : bond 0.00310 (13586) covalent geometry : angle 0.55816 (18444) hydrogen bonds : bond 0.03712 ( 348) hydrogen bonds : angle 6.48438 ( 930) metal coordination : bond 0.00711 ( 12) metal coordination : angle 2.16568 ( 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 224 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 GLU cc_start: 0.7032 (mp0) cc_final: 0.6430 (mp0) REVERT: A 1109 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7117 (ptp90) REVERT: A 1418 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6483 (tt) REVERT: B 192 MET cc_start: 0.6486 (mmp) cc_final: 0.5549 (mmp) REVERT: B 230 ASP cc_start: 0.6557 (t0) cc_final: 0.6146 (p0) REVERT: C 85 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6144 (tm) REVERT: C 90 MET cc_start: 0.5024 (pmm) cc_final: 0.3654 (ptt) outliers start: 54 outliers final: 36 residues processed: 203 average time/residue: 0.1172 time to fit residues: 34.3255 Evaluate side-chains 197 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP 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 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 709 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1109 ARG 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 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 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 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 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: 0.0570 chunk 133 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 620 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.162559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139011 restraints weight = 14231.589| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.66 r_work: 0.3490 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1429 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= 0.114 Angle : 0.536 7.678 18453 Z= 0.271 Chirality : 0.043 0.141 2054 Planarity : 0.004 0.053 2326 Dihedral : 5.791 57.986 1859 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.73 % Allowed : 26.24 % Favored : 69.03 % 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: -1.71 (0.21), residues: 1615 helix: -0.23 (0.49), residues: 108 sheet: -1.02 (0.21), residues: 609 loop : -1.29 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.009 0.001 TYR A 189 PHE 0.023 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 covalent geometry : bond 0.00273 (13586) covalent geometry : angle 0.53496 (18444) hydrogen bonds : bond 0.03332 ( 348) hydrogen bonds : angle 6.06663 ( 930) metal coordination : bond 0.00650 ( 12) metal coordination : angle 1.90462 ( 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 242 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7769 (tt) REVERT: A 464 GLU cc_start: 0.6709 (mp0) cc_final: 0.6353 (mp0) REVERT: A 579 ARG cc_start: 0.7624 (mmt90) cc_final: 0.7354 (mtt-85) REVERT: A 1418 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6455 (tt) REVERT: B 132 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8094 (mtp-110) REVERT: B 133 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7598 (ptp90) REVERT: B 192 MET cc_start: 0.6398 (mmp) cc_final: 0.5257 (mmp) REVERT: B 230 ASP cc_start: 0.6538 (t0) cc_final: 0.6080 (p0) REVERT: C 85 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6161 (tm) REVERT: C 90 MET cc_start: 0.4954 (pmm) cc_final: 0.3665 (ptt) outliers start: 68 outliers final: 46 residues processed: 219 average time/residue: 0.1100 time to fit residues: 35.0639 Evaluate side-chains 217 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 285 SER 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 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 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 966 MET Chi-restraints excluded: chain A residue 1040 THR 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 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 133 ARG 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 195 VAL Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 225 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 121 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 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 = 0.3862 r_free = 0.3862 target = 0.160705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135960 restraints weight = 14198.755| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.69 r_work: 0.3462 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1440 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= 0.147 Angle : 0.563 8.751 18453 Z= 0.283 Chirality : 0.044 0.142 2054 Planarity : 0.004 0.053 2326 Dihedral : 5.895 58.090 1859 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.43 % Allowed : 25.89 % Favored : 68.68 % 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: -0.26 (0.49), residues: 108 sheet: -1.03 (0.21), residues: 610 loop : -1.30 (0.20), residues: 897 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 0.029 0.001 PHE A 208 TRP 0.011 0.001 TRP B 359 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00358 (13586) covalent geometry : angle 0.56164 (18444) hydrogen bonds : bond 0.03426 ( 348) hydrogen bonds : angle 6.05511 ( 930) metal coordination : bond 0.00667 ( 12) metal coordination : angle 2.07663 ( 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 244 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 166 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7804 (tt) REVERT: A 579 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7373 (mtt-85) REVERT: A 860 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6974 (pmm-80) REVERT: A 1414 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5820 (mt-10) REVERT: A 1418 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6459 (tt) REVERT: B 79 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8294 (ttt) REVERT: B 132 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8243 (mtp-110) REVERT: B 133 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7674 (ptp90) REVERT: B 192 MET cc_start: 0.6489 (mmp) cc_final: 0.5169 (mmt) REVERT: B 372 MET cc_start: 0.7855 (ttp) cc_final: 0.7555 (ptp) REVERT: C 75 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6853 (mt) REVERT: C 85 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6202 (tm) REVERT: C 90 MET cc_start: 0.4904 (pmm) cc_final: 0.3818 (ptt) outliers start: 78 outliers final: 57 residues processed: 218 average time/residue: 0.1160 time to fit residues: 36.7579 Evaluate side-chains 227 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 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 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 1414 GLU 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 197 MET 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 307 SER 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: 2.9990 chunk 21 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.160122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135168 restraints weight = 14182.524| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.70 r_work: 0.3449 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1425 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= 0.157 Angle : 0.580 8.847 18453 Z= 0.290 Chirality : 0.044 0.142 2054 Planarity : 0.004 0.054 2326 Dihedral : 5.978 58.127 1859 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.57 % Allowed : 25.96 % 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: -1.71 (0.21), residues: 1615 helix: -0.33 (0.49), residues: 108 sheet: -0.98 (0.21), residues: 592 loop : -1.31 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1295 TYR 0.010 0.001 TYR A 189 PHE 0.036 0.002 PHE A 208 TRP 0.011 0.001 TRP B 359 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00385 (13586) covalent geometry : angle 0.57769 (18444) hydrogen bonds : bond 0.03465 ( 348) hydrogen bonds : angle 6.05533 ( 930) metal coordination : bond 0.00691 ( 12) metal coordination : angle 2.17039 ( 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 249 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7809 (tt) REVERT: A 393 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7895 (tp) REVERT: A 579 ARG cc_start: 0.7646 (mmt90) cc_final: 0.7411 (mtt-85) REVERT: A 860 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6941 (pmm-80) REVERT: A 1414 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5891 (mt-10) REVERT: A 1418 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6516 (tt) REVERT: B 79 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8342 (ttt) REVERT: B 98 MET cc_start: 0.8491 (ptp) cc_final: 0.8137 (ptp) REVERT: B 132 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8218 (mtp-110) REVERT: B 133 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7659 (ptp90) REVERT: B 192 MET cc_start: 0.6373 (mmp) cc_final: 0.4906 (mmp) REVERT: B 372 MET cc_start: 0.7805 (ttp) cc_final: 0.7516 (ptp) REVERT: C 75 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6879 (mt) REVERT: C 85 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6191 (tm) REVERT: C 90 MET cc_start: 0.5132 (pmm) cc_final: 0.4094 (ptt) outliers start: 80 outliers final: 60 residues processed: 222 average time/residue: 0.1186 time to fit residues: 38.3596 Evaluate side-chains 234 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 375 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 393 LEU 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 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 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 1414 GLU 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 197 MET 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 307 SER 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: 0.7980 chunk 93 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133529 restraints weight = 14346.577| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.65 r_work: 0.3432 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1383 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= 0.203 Angle : 0.635 10.136 18453 Z= 0.317 Chirality : 0.046 0.148 2054 Planarity : 0.005 0.054 2326 Dihedral : 6.205 58.256 1859 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.57 % Allowed : 26.10 % 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: -1.85 (0.21), residues: 1615 helix: -0.51 (0.48), residues: 108 sheet: -1.13 (0.21), residues: 613 loop : -1.34 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 891 TYR 0.011 0.002 TYR A 189 PHE 0.056 0.002 PHE A 877 TRP 0.012 0.002 TRP A1193 HIS 0.007 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00497 (13586) covalent geometry : angle 0.63219 (18444) hydrogen bonds : bond 0.03712 ( 348) hydrogen bonds : angle 6.19610 ( 930) metal coordination : bond 0.00794 ( 12) metal coordination : angle 2.53620 ( 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 246 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 166 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 159 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 289 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7449 (mt) REVERT: A 393 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7947 (tp) REVERT: A 579 ARG cc_start: 0.7696 (mmt90) cc_final: 0.7418 (mtt-85) REVERT: A 860 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6718 (pmm-80) REVERT: A 1414 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5913 (mt-10) REVERT: A 1418 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6593 (tt) REVERT: B 79 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (ttt) REVERT: B 103 MET cc_start: 0.8092 (mmp) cc_final: 0.7298 (mmm) REVERT: B 132 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8305 (mtp-110) REVERT: B 133 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7763 (ptp90) REVERT: B 192 MET cc_start: 0.6371 (mmp) cc_final: 0.4685 (mmt) REVERT: B 230 ASP cc_start: 0.6622 (t0) cc_final: 0.6177 (p0) REVERT: B 372 MET cc_start: 0.7816 (ttp) cc_final: 0.7500 (ptp) REVERT: C 75 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6944 (mt) REVERT: C 85 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6253 (tm) outliers start: 80 outliers final: 60 residues processed: 221 average time/residue: 0.1252 time to fit residues: 39.6129 Evaluate side-chains 237 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 167 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 235 GLN 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 339 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 393 LEU 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 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 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 1414 GLU 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 197 MET 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 307 SER 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 377 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 139 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 158 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135363 restraints weight = 14129.673| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.67 r_work: 0.3469 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13598 Z= 0.101 Angle : 0.531 10.180 18453 Z= 0.268 Chirality : 0.043 0.139 2054 Planarity : 0.004 0.058 2326 Dihedral : 5.786 57.960 1859 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.87 % Allowed : 27.21 % Favored : 67.92 % 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: -0.20 (0.50), residues: 108 sheet: -1.01 (0.21), residues: 605 loop : -1.32 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1295 TYR 0.009 0.001 TYR A1281 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 covalent geometry : bond 0.00237 (13586) covalent geometry : angle 0.52998 (18444) hydrogen bonds : bond 0.03080 ( 348) hydrogen bonds : angle 5.72140 ( 930) metal coordination : bond 0.00539 ( 12) metal coordination : angle 1.70908 ( 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 247 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.504 Fit side-chains REVERT: A 159 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 289 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 860 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6856 (pmm-80) REVERT: A 1418 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6330 (tt) REVERT: B 79 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8336 (ttt) REVERT: B 98 MET cc_start: 0.8290 (ptp) cc_final: 0.7865 (ptp) REVERT: B 132 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8068 (mtp-110) REVERT: B 133 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7512 (ptp90) REVERT: B 192 MET cc_start: 0.6340 (mmp) cc_final: 0.4667 (mmt) REVERT: B 372 MET cc_start: 0.7755 (ttp) cc_final: 0.7533 (ptp) REVERT: C 75 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6735 (mt) REVERT: C 85 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6158 (tm) outliers start: 70 outliers final: 52 residues processed: 221 average time/residue: 0.1164 time to fit residues: 36.8560 Evaluate side-chains 227 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 275 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 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 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 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 1384 LEU Chi-restraints excluded: chain A residue 1385 HIS 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 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 MET 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 307 SER Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 342 VAL 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: 6.9990 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 156 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 0.0170 chunk 49 optimal weight: 4.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.159191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133441 restraints weight = 14246.659| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.78 r_work: 0.3437 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13598 Z= 0.132 Angle : 0.560 10.549 18453 Z= 0.280 Chirality : 0.043 0.142 2054 Planarity : 0.004 0.054 2326 Dihedral : 5.855 58.052 1859 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.31 % Allowed : 27.77 % Favored : 67.92 % 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: -1.66 (0.21), residues: 1615 helix: -0.28 (0.50), residues: 108 sheet: -0.89 (0.21), residues: 588 loop : -1.33 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 579 TYR 0.009 0.001 TYR A 189 PHE 0.041 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 covalent geometry : bond 0.00321 (13586) covalent geometry : angle 0.55868 (18444) hydrogen bonds : bond 0.03205 ( 348) hydrogen bonds : angle 5.77139 ( 930) metal coordination : bond 0.00618 ( 12) metal coordination : angle 1.90527 ( 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 231 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 0.530 Fit side-chains REVERT: A 159 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7751 (tt) REVERT: A 289 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7419 (mt) REVERT: A 393 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 860 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6891 (pmm-80) REVERT: A 927 ARG cc_start: 0.6868 (ttm170) cc_final: 0.6621 (ttm170) REVERT: A 1418 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6417 (tt) REVERT: B 79 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8352 (ttt) REVERT: B 132 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8135 (mtp-110) REVERT: B 133 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7624 (ptp90) REVERT: B 192 MET cc_start: 0.6439 (mmp) cc_final: 0.4816 (mmt) REVERT: B 372 MET cc_start: 0.7777 (ttp) cc_final: 0.7570 (ptp) REVERT: C 75 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6779 (mt) REVERT: C 85 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6223 (tm) outliers start: 62 outliers final: 51 residues processed: 208 average time/residue: 0.1165 time to fit residues: 35.2493 Evaluate side-chains 223 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 275 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 339 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 393 LEU 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 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 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 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 170 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 MET 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 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: 4.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132247 restraints weight = 14437.212| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.73 r_work: 0.3420 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13598 Z= 0.246 Angle : 0.689 10.615 18453 Z= 0.342 Chirality : 0.047 0.155 2054 Planarity : 0.005 0.053 2326 Dihedral : 6.396 58.359 1859 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.18 % Allowed : 27.97 % Favored : 67.85 % 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: -1.91 (0.21), residues: 1615 helix: -0.69 (0.48), residues: 108 sheet: -1.17 (0.21), residues: 612 loop : -1.37 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1049 TYR 0.012 0.002 TYR A 989 PHE 0.041 0.002 PHE A 208 TRP 0.014 0.002 TRP A 952 HIS 0.008 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00604 (13586) covalent geometry : angle 0.68606 (18444) hydrogen bonds : bond 0.03893 ( 348) hydrogen bonds : angle 6.28835 ( 930) metal coordination : bond 0.00854 ( 12) metal coordination : angle 2.71114 ( 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 223 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 163 time to evaluate : 0.500 Fit side-chains REVERT: A 159 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7863 (tt) REVERT: A 289 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7485 (mt) REVERT: A 393 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (tp) REVERT: A 860 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7218 (pmm-80) REVERT: A 927 ARG cc_start: 0.6865 (ttm170) cc_final: 0.6633 (ttm170) REVERT: A 1418 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6705 (tt) REVERT: B 79 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8372 (ttt) REVERT: B 192 MET cc_start: 0.6450 (mmp) cc_final: 0.4536 (mmt) REVERT: B 230 ASP cc_start: 0.6647 (t0) cc_final: 0.6168 (p0) REVERT: B 372 MET cc_start: 0.7783 (ttp) cc_final: 0.7535 (ptp) REVERT: C 75 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6950 (mt) REVERT: C 85 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6317 (tm) outliers start: 60 outliers final: 50 residues processed: 202 average time/residue: 0.1119 time to fit residues: 32.7096 Evaluate side-chains 216 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 158 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 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 393 LEU 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 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 895 VAL Chi-restraints excluded: chain A residue 897 HIS 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 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 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 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 197 MET 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 307 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 367 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 118 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 158 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.160317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134563 restraints weight = 14146.010| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.78 r_work: 0.3450 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13598 Z= 0.107 Angle : 0.547 10.533 18453 Z= 0.276 Chirality : 0.043 0.142 2054 Planarity : 0.004 0.057 2326 Dihedral : 5.899 57.973 1859 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.18 % Allowed : 28.04 % Favored : 67.78 % 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: -1.77 (0.21), residues: 1615 helix: -0.29 (0.50), residues: 108 sheet: -0.99 (0.21), residues: 596 loop : -1.38 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.009 0.001 TYR A 189 PHE 0.038 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 covalent geometry : bond 0.00252 (13586) covalent geometry : angle 0.54525 (18444) hydrogen bonds : bond 0.03111 ( 348) hydrogen bonds : angle 5.77154 ( 930) metal coordination : bond 0.00650 ( 12) metal coordination : angle 1.82067 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3208.96 seconds wall clock time: 55 minutes 43.01 seconds (3343.01 seconds total)