Starting phenix.real_space_refine on Fri Sep 11 19:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.map" model { file = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6a95_6997/09_2026/6a95_6997.cif" } resolution = 2.6 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= 0.007 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: 5 Type Number sf(0) Gaussians S 73 5.16 5 Na 1 4.78 5 C 7262 2.51 5 N 1760 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11002 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1307, 10433 Classifications: {'peptide': 1307} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 1260} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 7, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 447 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 66 Unusual residues: {' NA': 1, '9SR': 1, 'NAG': 3} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.61, per 1000 atoms: 0.24 Number of scatterers: 11002 At special positions: 0 Unit cell: (127.647, 128.738, 120.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 Na 1 11.00 O 1906 8.00 N 1760 7.00 C 7262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 709 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1030 " distance=2.03 Simple disulfide: pdb=" SG CYS A1368 " - pdb=" SG CYS A1381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 52 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1605 " - " ASN A1015 " " NAG A1606 " - " ASN A 312 " " NAG A1607 " - " ASN A 308 " " NAG C 1 " - " ASN A 330 " " NAG D 1 " - " ASN A1034 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 537.1 milliseconds 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 67.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.556A pdb=" N ARG A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.887A pdb=" N SER A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.753A pdb=" N ILE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 159' Processing helix chain 'A' and resid 162 through 186 removed outlier: 3.652A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.527A pdb=" N VAL A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 removed outlier: 3.712A pdb=" N ARG A 230 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 231 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 239 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 240 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 4.294A pdb=" N ILE A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 281 removed outlier: 3.567A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.650A pdb=" N PHE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.628A pdb=" N TRP A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.783A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.834A pdb=" N PHE A 396 " --> pdb=" O HIS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 435 removed outlier: 3.506A pdb=" N LEU A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.848A pdb=" N ALA A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.597A pdb=" N LEU A 523 " --> pdb=" O PRO A 519 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 569 removed outlier: 3.637A pdb=" N TYR A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.540A pdb=" N LYS A 580 " --> pdb=" O PHE A 577 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 581' Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 608 through 623 removed outlier: 3.615A pdb=" N ARG A 613 " --> pdb=" O ARG A 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 614 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 615 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 618 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 621 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.599A pdb=" N ASN A 628 " --> pdb=" O TRP A 624 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 633 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 664 removed outlier: 3.685A pdb=" N PHE A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 678 Proline residue: A 675 - end of helix removed outlier: 3.792A pdb=" N ASP A 678 " --> pdb=" O PRO A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 3.622A pdb=" N ALA A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 3.652A pdb=" N ASP A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 731 through 742 removed outlier: 3.513A pdb=" N ASN A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 855 removed outlier: 3.861A pdb=" N ARG A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 875 Processing helix chain 'A' and resid 879 through 882 Processing helix chain 'A' and resid 883 through 912 removed outlier: 3.551A pdb=" N ASN A 888 " --> pdb=" O PRO A 884 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 894 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 941 removed outlier: 3.670A pdb=" N VAL A 929 " --> pdb=" O LEU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 removed outlier: 3.624A pdb=" N ARG A 951 " --> pdb=" O LEU A 947 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 952 " --> pdb=" O GLN A 948 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 947 through 952' Processing helix chain 'A' and resid 953 through 960 removed outlier: 4.015A pdb=" N ARG A 960 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 removed outlier: 3.546A pdb=" N LYS A 964 " --> pdb=" O PRO A 961 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 965' Processing helix chain 'A' and resid 967 through 977 removed outlier: 3.991A pdb=" N VAL A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1005 removed outlier: 3.514A pdb=" N ASN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 996 " --> pdb=" O PHE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1033 Processing helix chain 'A' and resid 1046 through 1059 removed outlier: 3.738A pdb=" N GLN A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1073 removed outlier: 3.720A pdb=" N ILE A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.807A pdb=" N PHE A1092 " --> pdb=" O MET A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.598A pdb=" N CYS A1109 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1117 " --> pdb=" O ASP A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1144 removed outlier: 3.785A pdb=" N THR A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1166 removed outlier: 3.652A pdb=" N LEU A1162 " --> pdb=" O HIS A1158 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1186 removed outlier: 3.640A pdb=" N MET A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A1179 " --> pdb=" O THR A1175 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A1180 " --> pdb=" O MET A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1190 Processing helix chain 'A' and resid 1195 through 1205 removed outlier: 3.502A pdb=" N VAL A1201 " --> pdb=" O GLU A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1223 removed outlier: 3.610A pdb=" N ILE A1212 " --> pdb=" O ILE A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1230 Processing helix chain 'A' and resid 1231 through 1249 removed outlier: 3.882A pdb=" N ILE A1235 " --> pdb=" O ASP A1231 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A1236 " --> pdb=" O PRO A1232 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.674A pdb=" N LEU A1267 " --> pdb=" O LEU A1263 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A1269 " --> pdb=" O ARG A1265 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1279 removed outlier: 3.695A pdb=" N TYR A1278 " --> pdb=" O ARG A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.512A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1321 removed outlier: 3.669A pdb=" N PHE A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1349 removed outlier: 3.522A pdb=" N GLN A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1352 No H-bonds generated for 'chain 'A' and resid 1350 through 1352' Processing helix chain 'A' and resid 1354 through 1363 removed outlier: 3.772A pdb=" N VAL A1358 " --> pdb=" O GLY A1354 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1361 " --> pdb=" O GLY A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1399 removed outlier: 4.085A pdb=" N SER A1393 " --> pdb=" O ALA A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1423 removed outlier: 4.080A pdb=" N ALA A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A1416 " --> pdb=" O ASP A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1437 removed outlier: 3.661A pdb=" N VAL A1436 " --> pdb=" O MET A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1459 removed outlier: 3.799A pdb=" N GLU A1458 " --> pdb=" O SER A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1469 through 1475 removed outlier: 4.093A pdb=" N LYS A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1484 No H-bonds generated for 'chain 'A' and resid 1482 through 1484' Processing helix chain 'A' and resid 1489 through 1504 removed outlier: 3.534A pdb=" N ASP A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1503 " --> pdb=" O ASP A1499 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A1504 " --> pdb=" O VAL A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1520 Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1012 Processing sheet with id=AA3, first strand: chain 'A' and resid 1447 through 1449 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 30 557 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.25 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: 3272 1.34 - 1.46: 2864 1.46 - 1.58: 5034 1.58 - 1.70: 3 1.70 - 1.83: 118 Bond restraints: 11291 Sorted by residual: bond pdb=" C13 9SR A1608 " pdb=" N14 9SR A1608 " ideal model delta sigma weight residual 1.281 1.487 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C03 9SR A1608 " pdb=" C21 9SR A1608 " ideal model delta sigma weight residual 1.528 1.634 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C02 9SR A1608 " pdb=" C03 9SR A1608 " ideal model delta sigma weight residual 1.540 1.452 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" N PRO A1159 " pdb=" CD PRO A1159 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" C HIS A1158 " pdb=" N PRO A1159 " ideal model delta sigma weight residual 1.335 1.390 -0.054 1.36e-02 5.41e+03 1.58e+01 ... (remaining 11286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 14871 2.63 - 5.25: 403 5.25 - 7.88: 64 7.88 - 10.51: 18 10.51 - 13.13: 2 Bond angle restraints: 15358 Sorted by residual: angle pdb=" N THR A1156 " pdb=" CA THR A1156 " pdb=" C THR A1156 " ideal model delta sigma weight residual 113.88 122.86 -8.98 1.23e+00 6.61e-01 5.33e+01 angle pdb=" N LEU A1162 " pdb=" CA LEU A1162 " pdb=" C LEU A1162 " ideal model delta sigma weight residual 111.36 105.30 6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" C THR A1156 " pdb=" CA THR A1156 " pdb=" CB THR A1156 " ideal model delta sigma weight residual 109.03 101.56 7.47 1.62e+00 3.81e-01 2.13e+01 angle pdb=" C THR A1426 " pdb=" N ASP A1427 " pdb=" CA ASP A1427 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" CA HIS A1158 " pdb=" C HIS A1158 " pdb=" N PRO A1159 " ideal model delta sigma weight residual 120.93 116.24 4.69 1.06e+00 8.90e-01 1.96e+01 ... (remaining 15353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 6129 15.29 - 30.59: 339 30.59 - 45.88: 78 45.88 - 61.17: 13 61.17 - 76.47: 7 Dihedral angle restraints: 6566 sinusoidal: 2557 harmonic: 4009 Sorted by residual: dihedral pdb=" CB CYS B 13 " pdb=" SG CYS B 13 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual -86.00 -155.67 69.67 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CA SER A 574 " pdb=" C SER A 574 " pdb=" N PRO A 575 " pdb=" CA PRO A 575 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TRP A 624 " pdb=" C TRP A 624 " pdb=" N PRO A 625 " pdb=" CA PRO A 625 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1612 0.097 - 0.193: 138 0.193 - 0.290: 11 0.290 - 0.386: 2 0.386 - 0.483: 1 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CG LEU A1054 " pdb=" CB LEU A1054 " pdb=" CD1 LEU A1054 " pdb=" CD2 LEU A1054 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.02e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 330 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1761 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1015 " 0.143 2.00e-02 2.50e+03 2.41e-01 7.25e+02 pdb=" CG ASN A1015 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN A1015 " 0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN A1015 " -0.423 2.00e-02 2.50e+03 pdb=" C1 NAG A1605 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 312 " 0.099 2.00e-02 2.50e+03 1.17e-01 1.72e+02 pdb=" CG ASN A 312 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 312 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 312 " -0.193 2.00e-02 2.50e+03 pdb=" C1 NAG A1606 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " -0.100 2.00e-02 2.50e+03 1.13e-01 1.59e+02 pdb=" CG ASN A 330 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " 0.180 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.136 2.00e-02 2.50e+03 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3779 2.86 - 3.37: 10222 3.37 - 3.88: 17543 3.88 - 4.39: 20290 4.39 - 4.90: 33888 Nonbonded interactions: 85722 Sorted by model distance: nonbonded pdb=" CG PRO A1155 " pdb=" NH1 ARG A1225 " model vdw 2.354 3.520 nonbonded pdb=" O ILE A1152 " pdb=" OH TYR A1164 " model vdw 2.362 3.040 nonbonded pdb=" OD2 ASP A 539 " pdb=" NZ LYS B 44 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP A 686 " pdb=" ND1 HIS A 689 " model vdw 2.373 3.120 nonbonded pdb=" O LEU A1346 " pdb=" OH TYR A1394 " model vdw 2.375 3.040 ... (remaining 85717 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.550 Find NCS groups from input model: 0.060 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:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.007 0.206 11306 Z= 0.324 Angle : 1.127 37.176 15395 Z= 0.563 Chirality : 0.060 0.483 1764 Planarity : 0.007 0.104 1893 Dihedral : 10.695 76.466 3956 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.15 % Favored : 92.48 % Rotamer: Outliers : 1.05 % Allowed : 5.36 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -5.57 (0.16), residues: 1356 helix: -4.07 (0.09), residues: 829 sheet: -2.33 (0.80), residues: 31 loop : -2.70 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG A 233 TYR 0.039 0.004 TYR A 933 PHE 0.035 0.003 PHE A 535 TRP 0.063 0.004 TRP A1063 HIS 0.012 0.003 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.32 (11291) covalent geometry : angle 1.06064 / 0.55 (15358) SS BOND : bond 0.00565 / 0.38 ( 8) SS BOND : angle 1.82012 / 1.18 ( 16) hydrogen bonds : bond 0.30950 / 21.98 ( 557) hydrogen bonds : angle 9.20108 / 6.49 ( 1590) link_BETA1-4 : bond 0.01968 / 0.94 ( 2) link_BETA1-4 : angle 6.42285 / 3.60 ( 6) link_NAG-ASN : bond 0.06067 / 3.92 ( 5) link_NAG-ASN : angle 11.51733 / 6.86 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.402 Fit side-chains REVERT: A 141 ILE cc_start: 0.8068 (tp) cc_final: 0.7849 (tt) REVERT: A 159 MET cc_start: 0.7000 (mtm) cc_final: 0.6745 (mtp) REVERT: A 259 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8086 (mptt) REVERT: A 424 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7932 (mtpp) REVERT: A 641 PHE cc_start: 0.8045 (m-80) cc_final: 0.7843 (m-80) REVERT: A 645 MET cc_start: 0.8260 (mmt) cc_final: 0.8021 (mmm) REVERT: A 856 LYS cc_start: 0.7736 (tppt) cc_final: 0.6896 (ptmt) REVERT: A 1147 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7580 (mttp) REVERT: A 1169 ASN cc_start: 0.7934 (t0) cc_final: 0.7510 (t0) REVERT: A 1225 ARG cc_start: 0.7567 (mpp-170) cc_final: 0.7170 (mpp80) REVERT: A 1230 LYS cc_start: 0.6800 (mptp) cc_final: 0.6333 (mmpt) REVERT: A 1300 PHE cc_start: 0.8212 (m-10) cc_final: 0.7333 (t80) REVERT: A 1322 MET cc_start: 0.8676 (ttp) cc_final: 0.8468 (ttm) REVERT: A 1369 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7322 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7351 (m-30) cc_final: 0.6847 (m-30) REVERT: A 1486 HIS cc_start: 0.7063 (m-70) cc_final: 0.6761 (m-70) REVERT: B 15 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7749 (mmmt) REVERT: B 28 LYS cc_start: 0.7667 (mttt) cc_final: 0.7459 (mttp) outliers start: 12 outliers final: 4 residues processed: 292 average time/residue: 0.5656 time to fit residues: 178.7212 Evaluate side-chains 187 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 183 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 532 ASN A 541 HIS A 555 ASN A 584 ASN A 661 GLN A 743 ASN A 859 GLN A 882 GLN A 888 ASN A 966 ASN A1077 HIS A1133 GLN ** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 ASN A1438 GLN B 29 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126123 restraints weight = 12257.442| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.81 r_work: 0.3202 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11306 Z= 0.151 Angle : 0.724 15.897 15395 Z= 0.365 Chirality : 0.044 0.312 1764 Planarity : 0.006 0.051 1893 Dihedral : 5.747 54.391 1557 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.49 % Favored : 93.29 % Rotamer: Outliers : 4.66 % Allowed : 10.19 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.84 (0.20), residues: 1356 helix: -1.46 (0.15), residues: 838 sheet: -2.38 (0.79), residues: 31 loop : -2.41 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 41 TYR 0.018 0.002 TYR A 933 PHE 0.016 0.002 PHE A 410 TRP 0.027 0.002 TRP A 624 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11291) covalent geometry : angle 0.69723 / 0.36 (15358) SS BOND : bond 0.00368 / 0.26 ( 8) SS BOND : angle 2.18821 / 1.51 ( 16) hydrogen bonds : bond 0.06681 / 4.87 ( 557) hydrogen bonds : angle 4.58385 / 3.14 ( 1590) link_BETA1-4 : bond 0.00813 / 0.39 ( 2) link_BETA1-4 : angle 3.76072 / 2.16 ( 6) link_NAG-ASN : bond 0.00372 / 0.22 ( 5) link_NAG-ASN : angle 5.37709 / 3.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.7026 (m-10) cc_final: 0.6798 (m-80) REVERT: A 214 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 219 ASP cc_start: 0.2663 (OUTLIER) cc_final: 0.2349 (m-30) REVERT: A 259 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8214 (mptt) REVERT: A 374 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7698 (mp) REVERT: A 424 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7845 (mtpp) REVERT: A 425 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7815 (ttp-170) REVERT: A 598 LEU cc_start: 0.8001 (mm) cc_final: 0.7698 (mm) REVERT: A 634 MET cc_start: 0.7444 (mmp) cc_final: 0.7226 (mtm) REVERT: A 665 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: A 671 MET cc_start: 0.8849 (ttp) cc_final: 0.8589 (ttm) REVERT: A 914 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 977 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8331 (mm-30) REVERT: A 1137 ARG cc_start: 0.8512 (ttt-90) cc_final: 0.8287 (tmt90) REVERT: A 1144 MET cc_start: 0.7962 (mtm) cc_final: 0.7671 (mpp) REVERT: A 1147 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7759 (mtmm) REVERT: A 1177 MET cc_start: 0.8426 (tpt) cc_final: 0.8217 (tpt) REVERT: A 1190 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: A 1226 HIS cc_start: 0.6872 (p-80) cc_final: 0.6653 (p-80) REVERT: A 1230 LYS cc_start: 0.7196 (mptp) cc_final: 0.6702 (mmpt) REVERT: A 1286 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7745 (ptp90) REVERT: A 1369 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7642 (mtp-110) REVERT: A 1429 ASP cc_start: 0.6731 (m-30) cc_final: 0.6515 (m-30) REVERT: A 1431 ASP cc_start: 0.7822 (m-30) cc_final: 0.7488 (m-30) REVERT: A 1443 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 1486 HIS cc_start: 0.7001 (m-70) cc_final: 0.6704 (m-70) REVERT: B 15 LYS cc_start: 0.8221 (mmtp) cc_final: 0.7750 (mmmt) REVERT: B 28 LYS cc_start: 0.7746 (mttt) cc_final: 0.7449 (mttp) REVERT: B 34 LYS cc_start: 0.8356 (ptpp) cc_final: 0.8125 (ptpt) REVERT: B 50 SER cc_start: 0.8892 (m) cc_final: 0.8629 (p) outliers start: 53 outliers final: 14 residues processed: 228 average time/residue: 0.4808 time to fit residues: 120.0588 Evaluate side-chains 194 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1133 GLN A1183 ASN A1227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117328 restraints weight = 12288.852| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.58 r_work: 0.3158 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11306 Z= 0.190 Angle : 0.782 20.854 15395 Z= 0.392 Chirality : 0.046 0.302 1764 Planarity : 0.005 0.038 1893 Dihedral : 5.619 47.558 1557 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 4.57 % Allowed : 12.57 % Favored : 82.86 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.55 (0.22), residues: 1356 helix: -0.26 (0.17), residues: 845 sheet: -2.42 (0.79), residues: 31 loop : -2.24 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 41 TYR 0.033 0.002 TYR A 933 PHE 0.015 0.002 PHE A 641 TRP 0.030 0.002 TRP A 624 HIS 0.007 0.002 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (11291) covalent geometry : angle 0.74960 / 0.38 (15358) SS BOND : bond 0.00474 / 0.30 ( 8) SS BOND : angle 4.67622 / 2.47 ( 16) hydrogen bonds : bond 0.06171 / 4.49 ( 557) hydrogen bonds : angle 4.26862 / 2.91 ( 1590) link_BETA1-4 : bond 0.00723 / 0.35 ( 2) link_BETA1-4 : angle 3.82964 / 2.18 ( 6) link_NAG-ASN : bond 0.00205 / 0.11 ( 5) link_NAG-ASN : angle 4.75465 / 3.23 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.8227 (t80) cc_final: 0.7910 (t80) REVERT: A 219 ASP cc_start: 0.2673 (OUTLIER) cc_final: 0.2364 (m-30) REVERT: A 259 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8239 (mptt) REVERT: A 424 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7870 (mtpp) REVERT: A 425 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7888 (ttp-170) REVERT: A 598 LEU cc_start: 0.8030 (mm) cc_final: 0.7756 (mm) REVERT: A 634 MET cc_start: 0.7321 (mmp) cc_final: 0.7016 (mtm) REVERT: A 665 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: A 671 MET cc_start: 0.8900 (ttp) cc_final: 0.8673 (ttm) REVERT: A 855 ASN cc_start: 0.7528 (t0) cc_final: 0.7166 (t0) REVERT: A 914 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8022 (t80) REVERT: A 977 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 1025 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7823 (mmt) REVERT: A 1147 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7687 (mtmm) REVERT: A 1177 MET cc_start: 0.8498 (tpt) cc_final: 0.8169 (tpt) REVERT: A 1190 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: A 1209 PHE cc_start: 0.8215 (m-10) cc_final: 0.7902 (m-80) REVERT: A 1226 HIS cc_start: 0.6870 (p-80) cc_final: 0.6622 (p-80) REVERT: A 1274 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7681 (mtt-85) REVERT: A 1286 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7728 (ptp90) REVERT: A 1369 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7565 (mtp-110) REVERT: A 1429 ASP cc_start: 0.6942 (m-30) cc_final: 0.6584 (m-30) REVERT: A 1431 ASP cc_start: 0.7961 (m-30) cc_final: 0.7647 (m-30) REVERT: A 1443 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 1486 HIS cc_start: 0.7016 (m-70) cc_final: 0.6740 (m-70) REVERT: B 15 LYS cc_start: 0.8261 (mmtp) cc_final: 0.7827 (mmmt) REVERT: B 28 LYS cc_start: 0.7812 (mttt) cc_final: 0.7460 (mttp) outliers start: 52 outliers final: 27 residues processed: 216 average time/residue: 0.5147 time to fit residues: 121.6958 Evaluate side-chains 207 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 42 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116070 restraints weight = 12305.200| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.56 r_work: 0.3071 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 11306 Z= 0.204 Angle : 0.753 21.360 15395 Z= 0.378 Chirality : 0.047 0.303 1764 Planarity : 0.004 0.046 1893 Dihedral : 5.581 51.547 1557 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 5.45 % Allowed : 13.01 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1356 helix: 0.28 (0.18), residues: 843 sheet: -2.26 (0.82), residues: 31 loop : -2.03 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 847 TYR 0.029 0.002 TYR A 933 PHE 0.019 0.002 PHE A 641 TRP 0.023 0.002 TRP A 624 HIS 0.007 0.002 HIS A 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (11291) covalent geometry : angle 0.72770 / 0.37 (15358) SS BOND : bond 0.00619 / 0.38 ( 8) SS BOND : angle 3.67144 / 1.78 ( 16) hydrogen bonds : bond 0.05850 / 4.27 ( 557) hydrogen bonds : angle 4.11522 / 2.81 ( 1590) link_BETA1-4 : bond 0.00628 / 0.30 ( 2) link_BETA1-4 : angle 3.74722 / 2.14 ( 6) link_NAG-ASN : bond 0.00258 / 0.13 ( 5) link_NAG-ASN : angle 4.45546 / 2.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.8257 (t80) cc_final: 0.7880 (t80) REVERT: A 216 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7475 (tp) REVERT: A 219 ASP cc_start: 0.2450 (OUTLIER) cc_final: 0.2151 (m-30) REVERT: A 259 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8204 (mptt) REVERT: A 424 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7814 (mtpp) REVERT: A 598 LEU cc_start: 0.7973 (mm) cc_final: 0.7690 (mm) REVERT: A 634 MET cc_start: 0.7407 (mmp) cc_final: 0.7011 (mtm) REVERT: A 665 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (mmm) REVERT: A 855 ASN cc_start: 0.7545 (t0) cc_final: 0.7186 (t0) REVERT: A 914 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 977 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 1025 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7802 (mmt) REVERT: A 1147 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7705 (mtmm) REVERT: A 1177 MET cc_start: 0.8478 (tpt) cc_final: 0.8113 (tpt) REVERT: A 1190 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: A 1226 HIS cc_start: 0.6917 (p-80) cc_final: 0.6706 (p-80) REVERT: A 1274 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: A 1429 ASP cc_start: 0.7087 (m-30) cc_final: 0.6618 (m-30) REVERT: A 1431 ASP cc_start: 0.8071 (m-30) cc_final: 0.7753 (m-30) REVERT: A 1443 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: A 1486 HIS cc_start: 0.7046 (m-70) cc_final: 0.6773 (m-70) REVERT: B 8 GLU cc_start: 0.6444 (tm-30) cc_final: 0.6121 (tt0) REVERT: B 15 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7833 (mmmt) REVERT: B 31 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7939 (pp) outliers start: 62 outliers final: 30 residues processed: 222 average time/residue: 0.4851 time to fit residues: 117.9302 Evaluate side-chains 214 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 117 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118864 restraints weight = 12326.277| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.55 r_work: 0.3174 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11306 Z= 0.128 Angle : 0.663 20.003 15395 Z= 0.331 Chirality : 0.042 0.283 1764 Planarity : 0.004 0.045 1893 Dihedral : 5.310 50.068 1557 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.78 % Favored : 92.99 % Rotamer: Outliers : 3.78 % Allowed : 15.11 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.23), residues: 1356 helix: 0.73 (0.18), residues: 843 sheet: -2.03 (0.82), residues: 31 loop : -1.92 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 847 TYR 0.018 0.001 TYR A1228 PHE 0.016 0.001 PHE A1102 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11291) covalent geometry : angle 0.63730 / 0.32 (15358) SS BOND : bond 0.00473 / 0.30 ( 8) SS BOND : angle 3.62438 / 1.83 ( 16) hydrogen bonds : bond 0.04800 / 3.53 ( 557) hydrogen bonds : angle 3.90184 / 2.67 ( 1590) link_BETA1-4 : bond 0.00464 / 0.22 ( 2) link_BETA1-4 : angle 3.55119 / 2.03 ( 6) link_NAG-ASN : bond 0.00347 / 0.18 ( 5) link_NAG-ASN : angle 3.96494 / 2.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 136 THR cc_start: 0.8278 (m) cc_final: 0.7990 (m) REVERT: A 189 PHE cc_start: 0.8273 (t80) cc_final: 0.7890 (t80) REVERT: A 216 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7408 (tp) REVERT: A 219 ASP cc_start: 0.2657 (OUTLIER) cc_final: 0.2369 (m-30) REVERT: A 259 LYS cc_start: 0.8805 (ttpp) cc_final: 0.8133 (mmtp) REVERT: A 424 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7728 (mtpp) REVERT: A 598 LEU cc_start: 0.7871 (mm) cc_final: 0.7610 (mm) REVERT: A 634 MET cc_start: 0.7373 (mmp) cc_final: 0.6957 (mtm) REVERT: A 855 ASN cc_start: 0.7257 (t0) cc_final: 0.6850 (t0) REVERT: A 914 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 977 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 1025 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7813 (mmt) REVERT: A 1033 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 1142 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8003 (mtt180) REVERT: A 1147 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7572 (mtmm) REVERT: A 1226 HIS cc_start: 0.6882 (p-80) cc_final: 0.6648 (p-80) REVERT: A 1429 ASP cc_start: 0.7049 (m-30) cc_final: 0.6728 (m-30) REVERT: A 1431 ASP cc_start: 0.8001 (m-30) cc_final: 0.7682 (m-30) REVERT: A 1443 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 1486 HIS cc_start: 0.7058 (m-70) cc_final: 0.6822 (m-70) REVERT: B 8 GLU cc_start: 0.6435 (tm-30) cc_final: 0.6053 (tt0) REVERT: B 14 LYS cc_start: 0.7596 (mmmm) cc_final: 0.7371 (mttp) REVERT: B 15 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7824 (mmmt) REVERT: B 31 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.7927 (pp) outliers start: 43 outliers final: 22 residues processed: 212 average time/residue: 0.5063 time to fit residues: 117.2452 Evaluate side-chains 205 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 127 optimal weight: 0.0070 chunk 115 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119350 restraints weight = 12294.097| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.57 r_work: 0.3182 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11306 Z= 0.121 Angle : 0.643 19.872 15395 Z= 0.321 Chirality : 0.042 0.269 1764 Planarity : 0.004 0.049 1893 Dihedral : 5.137 48.896 1556 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.93 % Favored : 92.92 % Rotamer: Outliers : 4.13 % Allowed : 15.11 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1356 helix: 1.03 (0.18), residues: 839 sheet: -2.31 (1.09), residues: 20 loop : -1.79 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 847 TYR 0.019 0.001 TYR A1228 PHE 0.016 0.001 PHE A 641 TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (11291) covalent geometry : angle 0.62118 / 0.31 (15358) SS BOND : bond 0.00557 / 0.34 ( 8) SS BOND : angle 3.40452 / 1.70 ( 16) hydrogen bonds : bond 0.04543 / 3.34 ( 557) hydrogen bonds : angle 3.79524 / 2.59 ( 1590) link_BETA1-4 : bond 0.00432 / 0.21 ( 2) link_BETA1-4 : angle 3.45916 / 1.97 ( 6) link_NAG-ASN : bond 0.00415 / 0.22 ( 5) link_NAG-ASN : angle 3.51448 / 2.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8156 (m) cc_final: 0.7865 (m) REVERT: A 189 PHE cc_start: 0.8303 (t80) cc_final: 0.7907 (t80) REVERT: A 216 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7387 (tp) REVERT: A 219 ASP cc_start: 0.2424 (OUTLIER) cc_final: 0.2106 (m-30) REVERT: A 259 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8084 (mmtp) REVERT: A 424 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7635 (mtpp) REVERT: A 598 LEU cc_start: 0.7881 (mm) cc_final: 0.7598 (mm) REVERT: A 634 MET cc_start: 0.7347 (mmp) cc_final: 0.6935 (mtm) REVERT: A 662 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 855 ASN cc_start: 0.7093 (t0) cc_final: 0.6672 (t0) REVERT: A 977 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 1025 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7856 (mmp) REVERT: A 1033 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7704 (mm-30) REVERT: A 1142 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8052 (mtt180) REVERT: A 1144 MET cc_start: 0.8012 (tpp) cc_final: 0.6708 (tmm) REVERT: A 1147 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7570 (mtmm) REVERT: A 1190 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: A 1429 ASP cc_start: 0.7049 (m-30) cc_final: 0.6716 (m-30) REVERT: A 1431 ASP cc_start: 0.7982 (m-30) cc_final: 0.7725 (m-30) REVERT: A 1443 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 1486 HIS cc_start: 0.7067 (m-70) cc_final: 0.6829 (m-70) REVERT: B 14 LYS cc_start: 0.7592 (mmmm) cc_final: 0.7372 (mttp) REVERT: B 15 LYS cc_start: 0.8187 (mmtp) cc_final: 0.7784 (mmmt) REVERT: B 31 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7996 (pp) outliers start: 47 outliers final: 22 residues processed: 218 average time/residue: 0.4927 time to fit residues: 117.5560 Evaluate side-chains 205 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1130 SER Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1443 GLU Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 21 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122479 restraints weight = 12326.780| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.88 r_work: 0.3089 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 11306 Z= 0.111 Angle : 0.634 19.167 15395 Z= 0.313 Chirality : 0.041 0.260 1764 Planarity : 0.004 0.047 1893 Dihedral : 5.039 47.043 1556 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 3.60 % Allowed : 15.91 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1356 helix: 1.27 (0.18), residues: 842 sheet: -2.28 (1.67), residues: 10 loop : -1.76 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 847 TYR 0.018 0.001 TYR A1228 PHE 0.017 0.001 PHE A 641 TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11291) covalent geometry : angle 0.61256 / 0.31 (15358) SS BOND : bond 0.00497 / 0.31 ( 8) SS BOND : angle 3.50531 / 1.72 ( 16) hydrogen bonds : bond 0.04227 / 3.12 ( 557) hydrogen bonds : angle 3.72764 / 2.55 ( 1590) link_BETA1-4 : bond 0.00416 / 0.20 ( 2) link_BETA1-4 : angle 3.32462 / 1.90 ( 6) link_NAG-ASN : bond 0.00479 / 0.25 ( 5) link_NAG-ASN : angle 3.23753 / 2.06 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8092 (m) cc_final: 0.7864 (m) REVERT: A 189 PHE cc_start: 0.8294 (t80) cc_final: 0.7907 (t80) REVERT: A 216 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7394 (tp) REVERT: A 219 ASP cc_start: 0.2726 (OUTLIER) cc_final: 0.2403 (m-30) REVERT: A 259 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8047 (mmtp) REVERT: A 424 LYS cc_start: 0.7972 (mmtp) cc_final: 0.7558 (mtpp) REVERT: A 598 LEU cc_start: 0.7825 (mm) cc_final: 0.7589 (mm) REVERT: A 634 MET cc_start: 0.7495 (mmp) cc_final: 0.6961 (mtm) REVERT: A 662 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (mt) REVERT: A 855 ASN cc_start: 0.6859 (t0) cc_final: 0.6507 (t0) REVERT: A 969 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: A 977 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8346 (mm-30) REVERT: A 1025 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7860 (mmt) REVERT: A 1033 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 1142 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.8039 (mtt180) REVERT: A 1144 MET cc_start: 0.7928 (tpp) cc_final: 0.6567 (tmm) REVERT: A 1147 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7520 (mtmm) REVERT: A 1177 MET cc_start: 0.8469 (tpt) cc_final: 0.8052 (tpt) REVERT: A 1190 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 1263 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 1285 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7872 (mmt) REVERT: A 1429 ASP cc_start: 0.7042 (m-30) cc_final: 0.6765 (m-30) REVERT: A 1431 ASP cc_start: 0.8029 (m-30) cc_final: 0.7760 (m-30) REVERT: A 1486 HIS cc_start: 0.7024 (m-70) cc_final: 0.6760 (m-70) REVERT: B 14 LYS cc_start: 0.7564 (mmmm) cc_final: 0.7323 (mttp) REVERT: B 15 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7735 (mmmt) REVERT: B 31 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7950 (pp) outliers start: 41 outliers final: 21 residues processed: 208 average time/residue: 0.5339 time to fit residues: 121.3822 Evaluate side-chains 202 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 47 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.166292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118985 restraints weight = 12257.126| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.55 r_work: 0.3177 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11306 Z= 0.130 Angle : 0.658 19.763 15395 Z= 0.327 Chirality : 0.042 0.261 1764 Planarity : 0.004 0.054 1893 Dihedral : 5.035 46.559 1556 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 3.60 % Allowed : 16.34 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1356 helix: 1.26 (0.18), residues: 851 sheet: -2.39 (1.09), residues: 20 loop : -1.77 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 847 TYR 0.018 0.001 TYR A1228 PHE 0.020 0.001 PHE A 641 TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11291) covalent geometry : angle 0.63622 / 0.32 (15358) SS BOND : bond 0.00440 / 0.27 ( 8) SS BOND : angle 3.79001 / 1.89 ( 16) hydrogen bonds : bond 0.04572 / 3.36 ( 557) hydrogen bonds : angle 3.77572 / 2.58 ( 1590) link_BETA1-4 : bond 0.00359 / 0.17 ( 2) link_BETA1-4 : angle 3.34719 / 1.90 ( 6) link_NAG-ASN : bond 0.00454 / 0.24 ( 5) link_NAG-ASN : angle 3.21397 / 2.01 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8132 (m) cc_final: 0.7900 (m) REVERT: A 189 PHE cc_start: 0.8314 (t80) cc_final: 0.7934 (t80) REVERT: A 216 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7487 (tp) REVERT: A 219 ASP cc_start: 0.2702 (OUTLIER) cc_final: 0.2351 (m-30) REVERT: A 259 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8099 (mmtp) REVERT: A 424 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7671 (mtpp) REVERT: A 598 LEU cc_start: 0.7906 (mm) cc_final: 0.7672 (mm) REVERT: A 631 MET cc_start: 0.8413 (mtp) cc_final: 0.8194 (mtt) REVERT: A 634 MET cc_start: 0.7334 (mmp) cc_final: 0.7021 (mtp) REVERT: A 855 ASN cc_start: 0.7003 (t0) cc_final: 0.6653 (t0) REVERT: A 969 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: A 977 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 1025 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7875 (mmp) REVERT: A 1033 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 1142 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8059 (mtt180) REVERT: A 1144 MET cc_start: 0.7965 (tpp) cc_final: 0.6622 (tmm) REVERT: A 1147 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7550 (mtmm) REVERT: A 1177 MET cc_start: 0.8455 (tpt) cc_final: 0.8026 (tpt) REVERT: A 1190 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: A 1230 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7746 (pttt) REVERT: A 1235 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 1263 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8294 (tp) REVERT: A 1285 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7785 (mmt) REVERT: A 1428 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: A 1429 ASP cc_start: 0.7041 (m-30) cc_final: 0.6805 (m-30) REVERT: A 1431 ASP cc_start: 0.8028 (m-30) cc_final: 0.7739 (m-30) REVERT: A 1486 HIS cc_start: 0.7068 (m-70) cc_final: 0.6811 (m-70) REVERT: B 14 LYS cc_start: 0.7670 (mmmm) cc_final: 0.7444 (mtpp) REVERT: B 15 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7766 (mmmt) REVERT: B 31 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8001 (pp) outliers start: 41 outliers final: 25 residues processed: 208 average time/residue: 0.5027 time to fit residues: 114.6178 Evaluate side-chains 209 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1130 SER Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 93 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.166634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121029 restraints weight = 12268.046| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.79 r_work: 0.3163 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11306 Z= 0.126 Angle : 0.654 19.298 15395 Z= 0.324 Chirality : 0.042 0.263 1764 Planarity : 0.004 0.057 1893 Dihedral : 5.023 45.595 1556 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 3.51 % Allowed : 16.96 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1356 helix: 1.23 (0.18), residues: 863 sheet: -2.44 (1.08), residues: 20 loop : -1.87 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 847 TYR 0.018 0.001 TYR A1228 PHE 0.019 0.001 PHE A 641 TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11291) covalent geometry : angle 0.63151 / 0.32 (15358) SS BOND : bond 0.00333 / 0.21 ( 8) SS BOND : angle 3.87276 / 1.92 ( 16) hydrogen bonds : bond 0.04475 / 3.29 ( 557) hydrogen bonds : angle 3.79223 / 2.60 ( 1590) link_BETA1-4 : bond 0.00390 / 0.19 ( 2) link_BETA1-4 : angle 3.33769 / 1.90 ( 6) link_NAG-ASN : bond 0.00457 / 0.24 ( 5) link_NAG-ASN : angle 3.15823 / 1.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8097 (m) cc_final: 0.7853 (m) REVERT: A 189 PHE cc_start: 0.8319 (t80) cc_final: 0.7976 (t80) REVERT: A 214 ILE cc_start: 0.8173 (mp) cc_final: 0.7928 (mt) REVERT: A 216 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7521 (tp) REVERT: A 219 ASP cc_start: 0.2695 (OUTLIER) cc_final: 0.2383 (m-30) REVERT: A 259 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8076 (mmtp) REVERT: A 424 LYS cc_start: 0.8043 (mmtp) cc_final: 0.7648 (mtpp) REVERT: A 598 LEU cc_start: 0.7871 (mm) cc_final: 0.7633 (mm) REVERT: A 634 MET cc_start: 0.7178 (mmp) cc_final: 0.6788 (mtp) REVERT: A 855 ASN cc_start: 0.6976 (t0) cc_final: 0.6596 (t0) REVERT: A 969 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: A 977 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8339 (mm-30) REVERT: A 1025 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7914 (mmp) REVERT: A 1033 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7682 (mm-30) REVERT: A 1142 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.8075 (mtt180) REVERT: A 1144 MET cc_start: 0.7971 (tpp) cc_final: 0.6657 (tmm) REVERT: A 1147 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7527 (mtmm) REVERT: A 1177 MET cc_start: 0.8492 (tpt) cc_final: 0.8062 (tpt) REVERT: A 1190 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: A 1235 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 1263 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 1285 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: A 1286 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7757 (ptp90) REVERT: A 1428 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: A 1429 ASP cc_start: 0.7072 (m-30) cc_final: 0.6822 (m-30) REVERT: A 1431 ASP cc_start: 0.8053 (m-30) cc_final: 0.7795 (m-30) REVERT: A 1486 HIS cc_start: 0.7063 (m-70) cc_final: 0.6803 (m-70) REVERT: B 14 LYS cc_start: 0.7640 (mmmm) cc_final: 0.7411 (mtpp) REVERT: B 15 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7751 (mmmt) REVERT: B 31 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.7965 (pp) outliers start: 40 outliers final: 25 residues processed: 203 average time/residue: 0.4721 time to fit residues: 105.2107 Evaluate side-chains 208 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 104 optimal weight: 0.0170 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119677 restraints weight = 12324.090| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.81 r_work: 0.3136 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11306 Z= 0.149 Angle : 0.685 20.176 15395 Z= 0.341 Chirality : 0.043 0.264 1764 Planarity : 0.004 0.059 1893 Dihedral : 5.074 46.032 1556 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 3.51 % Allowed : 17.14 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1356 helix: 1.18 (0.18), residues: 863 sheet: -2.47 (1.09), residues: 20 loop : -1.84 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 847 TYR 0.018 0.002 TYR A 381 PHE 0.021 0.001 PHE A 641 TRP 0.017 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11291) covalent geometry : angle 0.66185 / 0.33 (15358) SS BOND : bond 0.00434 / 0.27 ( 8) SS BOND : angle 4.07788 / 2.05 ( 16) hydrogen bonds : bond 0.04860 / 3.57 ( 557) hydrogen bonds : angle 3.85967 / 2.64 ( 1590) link_BETA1-4 : bond 0.00341 / 0.16 ( 2) link_BETA1-4 : angle 3.36572 / 1.91 ( 6) link_NAG-ASN : bond 0.00417 / 0.22 ( 5) link_NAG-ASN : angle 3.26258 / 2.02 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8096 (m) cc_final: 0.7854 (m) REVERT: A 189 PHE cc_start: 0.8396 (t80) cc_final: 0.8012 (t80) REVERT: A 214 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 216 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 219 ASP cc_start: 0.2621 (OUTLIER) cc_final: 0.2285 (m-30) REVERT: A 259 LYS cc_start: 0.8828 (ttpp) cc_final: 0.8059 (mmtp) REVERT: A 424 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7578 (mtpp) REVERT: A 582 SER cc_start: 0.7912 (m) cc_final: 0.7687 (p) REVERT: A 598 LEU cc_start: 0.7868 (mm) cc_final: 0.7590 (mm) REVERT: A 634 MET cc_start: 0.7161 (mmp) cc_final: 0.6784 (mtp) REVERT: A 855 ASN cc_start: 0.7182 (t0) cc_final: 0.6779 (t0) REVERT: A 915 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7408 (mttp) REVERT: A 969 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 977 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 1025 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7896 (mmt) REVERT: A 1142 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8122 (mtt180) REVERT: A 1144 MET cc_start: 0.8031 (tpp) cc_final: 0.6797 (tmm) REVERT: A 1147 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7552 (mtmm) REVERT: A 1177 MET cc_start: 0.8513 (tpt) cc_final: 0.8070 (tpt) REVERT: A 1190 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 1235 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8115 (mp) REVERT: A 1263 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 1277 ARG cc_start: 0.8067 (ttm170) cc_final: 0.7491 (mtm-85) REVERT: A 1285 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.7960 (mmt) REVERT: A 1286 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7778 (ptp90) REVERT: A 1428 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: A 1429 ASP cc_start: 0.7186 (m-30) cc_final: 0.6789 (m-30) REVERT: A 1431 ASP cc_start: 0.8102 (m-30) cc_final: 0.7838 (m-30) REVERT: A 1486 HIS cc_start: 0.7080 (m-70) cc_final: 0.6825 (m-70) REVERT: B 15 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7782 (mmmt) REVERT: B 31 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.7991 (pp) outliers start: 40 outliers final: 24 residues processed: 207 average time/residue: 0.4815 time to fit residues: 109.3316 Evaluate side-chains 212 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119208 restraints weight = 12205.179| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.78 r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11306 Z= 0.158 Angle : 0.696 20.160 15395 Z= 0.346 Chirality : 0.044 0.269 1764 Planarity : 0.004 0.058 1893 Dihedral : 5.122 46.612 1556 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.15 % Favored : 92.70 % Rotamer: Outliers : 3.25 % Allowed : 17.31 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1356 helix: 1.17 (0.18), residues: 863 sheet: -1.95 (0.84), residues: 31 loop : -1.83 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 847 TYR 0.017 0.002 TYR A 381 PHE 0.022 0.002 PHE A 641 TRP 0.016 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (11291) covalent geometry : angle 0.67266 / 0.34 (15358) SS BOND : bond 0.00425 / 0.26 ( 8) SS BOND : angle 4.12479 / 2.08 ( 16) hydrogen bonds : bond 0.04987 / 3.66 ( 557) hydrogen bonds : angle 3.89305 / 2.66 ( 1590) link_BETA1-4 : bond 0.00311 / 0.15 ( 2) link_BETA1-4 : angle 3.40090 / 1.93 ( 6) link_NAG-ASN : bond 0.00384 / 0.20 ( 5) link_NAG-ASN : angle 3.36285 / 2.07 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.40 seconds wall clock time: 85 minutes 38.32 seconds (5138.32 seconds total)