Starting phenix.real_space_refine on Tue Nov 18 04:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a95_6997/11_2025/6a95_6997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a95_6997/11_2025/6a95_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_6997/11_2025/6a95_6997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a95_6997/11_2025/6a95_6997.map" model { file = "/net/cci-nas-00/data/ceres_data/6a95_6997/11_2025/6a95_6997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a95_6997/11_2025/6a95_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.75, per 1000 atoms: 0.25 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: 0.92 Conformation dependent library (CDL) restraints added in 565.5 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: 0.42 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: 1.77 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: 6247 15.29 - 30.59: 354 30.59 - 45.88: 83 45.88 - 61.17: 22 61.17 - 76.47: 7 Dihedral angle restraints: 6713 sinusoidal: 2704 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 6710 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 11.040 76.466 4103 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 covalent geometry : bond 0.00707 (11291) covalent geometry : angle 1.06064 (15358) SS BOND : bond 0.00565 ( 8) SS BOND : angle 1.82012 ( 16) hydrogen bonds : bond 0.30950 ( 557) hydrogen bonds : angle 9.20108 ( 1590) link_BETA1-4 : bond 0.01968 ( 2) link_BETA1-4 : angle 6.42285 ( 6) link_NAG-ASN : bond 0.06067 ( 5) link_NAG-ASN : angle 11.51733 ( 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 : 0.421 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: 0.5978 time to fit residues: 188.0248 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 : 0.378 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 222 HIS 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122550 restraints weight = 12272.837| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.54 r_work: 0.3219 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11306 Z= 0.151 Angle : 0.721 15.604 15395 Z= 0.365 Chirality : 0.044 0.292 1764 Planarity : 0.006 0.048 1893 Dihedral : 7.432 58.918 1704 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.42 % Favored : 93.36 % Rotamer: Outliers : 4.75 % Allowed : 10.11 % 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: -2.83 (0.20), residues: 1356 helix: -1.43 (0.15), residues: 839 sheet: -2.38 (0.79), residues: 31 loop : -2.44 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 233 TYR 0.019 0.002 TYR A 933 PHE 0.016 0.002 PHE A 410 TRP 0.028 0.002 TRP A 624 HIS 0.006 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00329 (11291) covalent geometry : angle 0.69345 (15358) SS BOND : bond 0.01221 ( 8) SS BOND : angle 2.36114 ( 16) hydrogen bonds : bond 0.06621 ( 557) hydrogen bonds : angle 4.57631 ( 1590) link_BETA1-4 : bond 0.00910 ( 2) link_BETA1-4 : angle 3.98647 ( 6) link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 5.35712 ( 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 249 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (mt) REVERT: A 219 ASP cc_start: 0.2633 (OUTLIER) cc_final: 0.2339 (m-30) REVERT: A 259 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8243 (mptt) REVERT: A 374 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7667 (mp) REVERT: A 424 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7881 (mtpp) REVERT: A 425 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7854 (ttp-170) REVERT: A 598 LEU cc_start: 0.7985 (mm) cc_final: 0.7678 (mm) REVERT: A 665 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8323 (mmm) REVERT: A 671 MET cc_start: 0.8816 (ttp) cc_final: 0.8553 (ttm) REVERT: A 860 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7907 (mptp) REVERT: A 914 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 977 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8287 (mm-30) REVERT: A 1136 TYR cc_start: 0.8259 (m-10) cc_final: 0.8057 (m-10) REVERT: A 1137 ARG cc_start: 0.8498 (ttt-90) cc_final: 0.8275 (tmt90) REVERT: A 1144 MET cc_start: 0.7942 (mtm) cc_final: 0.7666 (mpp) REVERT: A 1147 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7759 (mtmm) REVERT: A 1177 MET cc_start: 0.8373 (tpt) cc_final: 0.8164 (tpt) REVERT: A 1190 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: A 1226 HIS cc_start: 0.6875 (p-80) cc_final: 0.6655 (p-80) REVERT: A 1230 LYS cc_start: 0.7193 (mptp) cc_final: 0.6711 (mmpt) REVERT: A 1369 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7668 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7803 (m-30) cc_final: 0.7471 (m-30) REVERT: A 1443 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 1486 HIS cc_start: 0.7001 (m-70) cc_final: 0.6706 (m-70) REVERT: B 15 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7698 (mmmt) REVERT: B 17 ASP cc_start: 0.8062 (t0) cc_final: 0.7859 (m-30) REVERT: B 28 LYS cc_start: 0.7741 (mttt) cc_final: 0.7454 (mttp) REVERT: B 34 LYS cc_start: 0.8349 (ptpp) cc_final: 0.8105 (ptpt) REVERT: B 50 SER cc_start: 0.8872 (m) cc_final: 0.8614 (p) outliers start: 54 outliers final: 14 residues processed: 230 average time/residue: 0.5253 time to fit residues: 131.8123 Evaluate side-chains 197 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 567 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 860 LYS 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 52 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 128 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3885 r_free = 0.3885 target = 0.166868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.122720 restraints weight = 12306.810| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.80 r_work: 0.3154 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11306 Z= 0.157 Angle : 0.731 18.702 15395 Z= 0.366 Chirality : 0.044 0.280 1764 Planarity : 0.004 0.039 1893 Dihedral : 7.061 55.184 1704 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.78 % Favored : 92.99 % Rotamer: Outliers : 4.92 % Allowed : 11.95 % Favored : 83.13 % 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: -1.39 (0.22), residues: 1356 helix: -0.09 (0.17), residues: 837 sheet: -2.32 (0.79), residues: 31 loop : -2.24 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 41 TYR 0.028 0.002 TYR A 933 PHE 0.015 0.002 PHE A1488 TRP 0.029 0.002 TRP A 624 HIS 0.007 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00359 (11291) covalent geometry : angle 0.69657 (15358) SS BOND : bond 0.00240 ( 8) SS BOND : angle 4.77535 ( 16) hydrogen bonds : bond 0.05708 ( 557) hydrogen bonds : angle 4.23099 ( 1590) link_BETA1-4 : bond 0.00838 ( 2) link_BETA1-4 : angle 4.00857 ( 6) link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 4.61160 ( 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 242 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.8194 (t80) cc_final: 0.7892 (t80) REVERT: A 219 ASP cc_start: 0.2534 (OUTLIER) cc_final: 0.2221 (m-30) REVERT: A 259 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8183 (mptt) REVERT: A 424 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7856 (mtpp) REVERT: A 425 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7922 (ttp-170) REVERT: A 598 LEU cc_start: 0.7994 (mm) cc_final: 0.7715 (mm) REVERT: A 665 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8427 (mmm) REVERT: A 671 MET cc_start: 0.8904 (ttp) cc_final: 0.8674 (ttm) REVERT: A 855 ASN cc_start: 0.7391 (t0) cc_final: 0.7000 (t0) REVERT: A 914 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7991 (t80) REVERT: A 977 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 1025 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7858 (mmt) REVERT: A 1033 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 1147 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7708 (mtmm) REVERT: A 1177 MET cc_start: 0.8504 (tpt) cc_final: 0.8166 (tpt) REVERT: A 1190 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 1209 PHE cc_start: 0.8247 (m-10) cc_final: 0.7892 (m-80) REVERT: A 1211 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 1226 HIS cc_start: 0.6813 (p-80) cc_final: 0.6572 (p-80) REVERT: A 1274 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: A 1286 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7733 (ptp90) REVERT: A 1369 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7568 (mtp-110) REVERT: A 1429 ASP cc_start: 0.6850 (m-30) cc_final: 0.6584 (m-30) REVERT: A 1431 ASP cc_start: 0.7959 (m-30) cc_final: 0.7658 (m-30) REVERT: A 1443 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 1486 HIS cc_start: 0.7022 (m-70) cc_final: 0.6769 (m-70) REVERT: B 15 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7836 (mmmt) REVERT: B 28 LYS cc_start: 0.7854 (mttt) cc_final: 0.7533 (mttp) outliers start: 56 outliers final: 24 residues processed: 221 average time/residue: 0.5262 time to fit residues: 126.3447 Evaluate side-chains 202 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 1156 THR 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 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 Chi-restraints excluded: chain B residue 52 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: 9.9990 chunk 117 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117293 restraints weight = 12321.397| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.58 r_work: 0.3158 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11306 Z= 0.175 Angle : 0.735 18.958 15395 Z= 0.370 Chirality : 0.045 0.281 1764 Planarity : 0.004 0.044 1893 Dihedral : 6.764 55.209 1704 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.08 % Favored : 92.77 % Rotamer: Outliers : 5.18 % Allowed : 13.01 % Favored : 81.81 % 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: -0.84 (0.23), residues: 1356 helix: 0.36 (0.18), residues: 842 sheet: -2.36 (0.78), residues: 31 loop : -2.05 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 847 TYR 0.028 0.002 TYR A 933 PHE 0.013 0.002 PHE A 687 TRP 0.022 0.002 TRP A 624 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00414 (11291) covalent geometry : angle 0.70188 (15358) SS BOND : bond 0.00265 ( 8) SS BOND : angle 4.77494 ( 16) hydrogen bonds : bond 0.05544 ( 557) hydrogen bonds : angle 4.12168 ( 1590) link_BETA1-4 : bond 0.00564 ( 2) link_BETA1-4 : angle 3.97831 ( 6) link_NAG-ASN : bond 0.00287 ( 5) link_NAG-ASN : angle 4.33975 ( 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 234 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7354 (mttm) REVERT: A 189 PHE cc_start: 0.8214 (t80) cc_final: 0.7855 (t80) REVERT: A 216 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 219 ASP cc_start: 0.2586 (OUTLIER) cc_final: 0.2303 (m-30) REVERT: A 259 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8162 (mmtp) REVERT: A 424 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7832 (mtpp) REVERT: A 598 LEU cc_start: 0.7905 (mm) cc_final: 0.7610 (mm) REVERT: A 634 MET cc_start: 0.7933 (mtm) cc_final: 0.7352 (mmt) REVERT: A 665 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8438 (mmm) REVERT: A 671 MET cc_start: 0.8877 (ttp) cc_final: 0.8661 (ttm) REVERT: A 855 ASN cc_start: 0.7406 (t0) cc_final: 0.7032 (t0) REVERT: A 876 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: A 914 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (t80) REVERT: A 977 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 1025 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7814 (mmt) REVERT: A 1033 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 1102 PHE cc_start: 0.8828 (t80) cc_final: 0.8561 (t80) REVERT: A 1147 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7703 (mtmm) REVERT: A 1177 MET cc_start: 0.8477 (tpt) cc_final: 0.8134 (tpt) REVERT: A 1190 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: A 1211 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 1226 HIS cc_start: 0.6848 (p-80) cc_final: 0.6618 (p-80) REVERT: A 1274 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7686 (mtt-85) REVERT: A 1285 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7899 (mmt) REVERT: A 1429 ASP cc_start: 0.6915 (m-30) cc_final: 0.6510 (m-30) REVERT: A 1431 ASP cc_start: 0.7974 (m-30) cc_final: 0.7651 (m-30) REVERT: A 1443 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 1486 HIS cc_start: 0.6935 (m-70) cc_final: 0.6724 (m-70) REVERT: B 8 GLU cc_start: 0.6439 (tm-30) cc_final: 0.6117 (tt0) REVERT: B 15 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7871 (mmmt) REVERT: B 31 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7931 (pp) outliers start: 59 outliers final: 28 residues processed: 212 average time/residue: 0.5251 time to fit residues: 121.3646 Evaluate side-chains 215 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 596 LEU Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 876 GLU 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 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1274 ARG 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 1443 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS 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: 0.7980 chunk 39 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.117009 restraints weight = 12290.858| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.57 r_work: 0.3152 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11306 Z= 0.167 Angle : 0.720 17.855 15395 Z= 0.362 Chirality : 0.044 0.283 1764 Planarity : 0.004 0.043 1893 Dihedral : 6.513 55.931 1704 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.15 % Favored : 92.63 % Rotamer: Outliers : 5.10 % Allowed : 13.71 % Favored : 81.20 % 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: -0.50 (0.23), residues: 1356 helix: 0.64 (0.18), residues: 843 sheet: -2.10 (0.82), residues: 31 loop : -1.94 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 847 TYR 0.020 0.002 TYR A 933 PHE 0.014 0.002 PHE A 586 TRP 0.021 0.002 TRP A 624 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00393 (11291) covalent geometry : angle 0.68779 (15358) SS BOND : bond 0.00238 ( 8) SS BOND : angle 4.71816 ( 16) hydrogen bonds : bond 0.05370 ( 557) hydrogen bonds : angle 4.06496 ( 1590) link_BETA1-4 : bond 0.00438 ( 2) link_BETA1-4 : angle 3.82079 ( 6) link_NAG-ASN : bond 0.00302 ( 5) link_NAG-ASN : angle 4.17498 ( 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 236 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 183 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7352 (mttp) REVERT: A 189 PHE cc_start: 0.8264 (t80) cc_final: 0.7905 (t80) REVERT: A 216 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7460 (tp) REVERT: A 219 ASP cc_start: 0.2671 (OUTLIER) cc_final: 0.2364 (m-30) REVERT: A 259 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8168 (mmtp) REVERT: A 598 LEU cc_start: 0.7857 (mm) cc_final: 0.7567 (mm) REVERT: A 634 MET cc_start: 0.7868 (mtm) cc_final: 0.7210 (mmt) REVERT: A 662 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8948 (mt) REVERT: A 855 ASN cc_start: 0.7377 (t0) cc_final: 0.6991 (t0) REVERT: A 914 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 977 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 1025 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7842 (mmt) REVERT: A 1102 PHE cc_start: 0.8815 (t80) cc_final: 0.8549 (t80) REVERT: A 1147 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7601 (mtmm) REVERT: A 1177 MET cc_start: 0.8474 (tpt) cc_final: 0.8115 (tpt) REVERT: A 1226 HIS cc_start: 0.6889 (p-80) cc_final: 0.6636 (p-80) REVERT: A 1235 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 1274 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7722 (mtt-85) REVERT: A 1285 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.7931 (mmt) REVERT: A 1428 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: A 1429 ASP cc_start: 0.7046 (m-30) cc_final: 0.6691 (m-30) REVERT: A 1431 ASP cc_start: 0.8025 (m-30) cc_final: 0.7719 (m-30) REVERT: A 1443 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 1447 TYR cc_start: 0.8023 (m-80) cc_final: 0.7812 (m-80) REVERT: A 1486 HIS cc_start: 0.7056 (m-70) cc_final: 0.6798 (m-70) REVERT: B 8 GLU cc_start: 0.6457 (tm-30) cc_final: 0.6081 (tt0) REVERT: B 14 LYS cc_start: 0.7701 (mmmm) cc_final: 0.7456 (mttp) REVERT: B 15 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7833 (mmmt) REVERT: B 17 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7939 (t0) REVERT: B 31 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8024 (pp) outliers start: 58 outliers final: 27 residues processed: 210 average time/residue: 0.5334 time to fit residues: 122.3767 Evaluate side-chains 212 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 662 LEU 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 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 1143 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU 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 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 A residue 1443 GLU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 127 optimal weight: 0.0060 chunk 115 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.166165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120382 restraints weight = 12281.705| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.81 r_work: 0.3151 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11306 Z= 0.130 Angle : 0.662 16.381 15395 Z= 0.332 Chirality : 0.042 0.263 1764 Planarity : 0.004 0.050 1893 Dihedral : 6.305 55.470 1703 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.86 % Favored : 92.92 % Rotamer: Outliers : 4.22 % Allowed : 14.67 % Favored : 81.11 % 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: -0.17 (0.23), residues: 1356 helix: 0.93 (0.18), residues: 841 sheet: -2.36 (1.08), residues: 20 loop : -1.86 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 847 TYR 0.019 0.002 TYR A1228 PHE 0.011 0.001 PHE A1095 TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00293 (11291) covalent geometry : angle 0.63274 (15358) SS BOND : bond 0.00148 ( 8) SS BOND : angle 4.41105 ( 16) hydrogen bonds : bond 0.04757 ( 557) hydrogen bonds : angle 3.93377 ( 1590) link_BETA1-4 : bond 0.00460 ( 2) link_BETA1-4 : angle 3.58054 ( 6) link_NAG-ASN : bond 0.00373 ( 5) link_NAG-ASN : angle 3.68534 ( 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 235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8122 (m) cc_final: 0.7827 (m) REVERT: A 183 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7295 (mttp) REVERT: A 189 PHE cc_start: 0.8297 (t80) cc_final: 0.7945 (t80) REVERT: A 219 ASP cc_start: 0.2583 (OUTLIER) cc_final: 0.2311 (m-30) REVERT: A 259 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8076 (mmtp) REVERT: A 424 LYS cc_start: 0.8163 (mttm) cc_final: 0.7658 (mtpp) REVERT: A 598 LEU cc_start: 0.7846 (mm) cc_final: 0.7576 (mm) REVERT: A 631 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: A 634 MET cc_start: 0.7972 (mtm) cc_final: 0.7314 (mmt) REVERT: A 855 ASN cc_start: 0.7191 (t0) cc_final: 0.6779 (t0) REVERT: A 977 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8355 (mm-30) REVERT: A 1025 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7907 (mmt) REVERT: A 1102 PHE cc_start: 0.8864 (t80) cc_final: 0.8605 (t80) REVERT: A 1142 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8066 (mtt180) REVERT: A 1144 MET cc_start: 0.8063 (tpp) cc_final: 0.6672 (tmm) REVERT: A 1147 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7597 (mtmm) REVERT: A 1190 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: A 1226 HIS cc_start: 0.6843 (p-80) cc_final: 0.6614 (p-80) REVERT: A 1235 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 1285 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7960 (mmt) REVERT: A 1369 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7247 (mtp-110) REVERT: A 1428 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: A 1429 ASP cc_start: 0.7003 (m-30) cc_final: 0.6666 (m-30) REVERT: A 1431 ASP cc_start: 0.8021 (m-30) cc_final: 0.7770 (m-30) REVERT: A 1443 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 1486 HIS cc_start: 0.7075 (m-70) cc_final: 0.6820 (m-70) REVERT: B 8 GLU cc_start: 0.6436 (tm-30) cc_final: 0.6084 (tt0) REVERT: B 14 LYS cc_start: 0.7663 (mmmm) cc_final: 0.7412 (mttp) REVERT: B 15 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7800 (mmmt) REVERT: B 31 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7905 (pp) outliers start: 48 outliers final: 25 residues processed: 216 average time/residue: 0.5480 time to fit residues: 128.9317 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 : 0.416 ------------------------------------------------------------------------------- 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 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 631 MET Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 906 ILE 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 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 1235 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1285 MET 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 A residue 1443 GLU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 21 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116194 restraints weight = 12264.211| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.55 r_work: 0.3138 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11306 Z= 0.181 Angle : 0.734 17.882 15395 Z= 0.366 Chirality : 0.045 0.268 1764 Planarity : 0.004 0.043 1893 Dihedral : 6.338 57.055 1703 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.45 % Favored : 92.33 % Rotamer: Outliers : 4.92 % Allowed : 14.50 % Favored : 80.58 % 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: -0.17 (0.23), residues: 1356 helix: 0.92 (0.18), residues: 841 sheet: -2.41 (1.08), residues: 20 loop : -1.83 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 847 TYR 0.020 0.002 TYR A 933 PHE 0.014 0.002 PHE A 687 TRP 0.019 0.002 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00431 (11291) covalent geometry : angle 0.70535 (15358) SS BOND : bond 0.00256 ( 8) SS BOND : angle 4.63187 ( 16) hydrogen bonds : bond 0.05403 ( 557) hydrogen bonds : angle 4.01907 ( 1590) link_BETA1-4 : bond 0.00500 ( 2) link_BETA1-4 : angle 3.75177 ( 6) link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 3.81817 ( 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 234 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8145 (m) cc_final: 0.7863 (m) REVERT: A 183 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7408 (mttm) REVERT: A 189 PHE cc_start: 0.8299 (t80) cc_final: 0.7927 (t80) REVERT: A 216 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7550 (tp) REVERT: A 219 ASP cc_start: 0.2521 (OUTLIER) cc_final: 0.2205 (m-30) REVERT: A 259 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8134 (mmtp) REVERT: A 424 LYS cc_start: 0.8171 (mttm) cc_final: 0.7680 (mtpp) REVERT: A 598 LEU cc_start: 0.7913 (mm) cc_final: 0.7636 (mm) REVERT: A 631 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: A 634 MET cc_start: 0.7928 (mtm) cc_final: 0.7304 (mmt) REVERT: A 662 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 855 ASN cc_start: 0.7367 (t0) cc_final: 0.7010 (t0) REVERT: A 977 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 1025 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7849 (mmt) REVERT: A 1102 PHE cc_start: 0.8837 (t80) cc_final: 0.8581 (t80) REVERT: A 1142 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8095 (mtt180) REVERT: A 1147 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7625 (mtmm) REVERT: A 1177 MET cc_start: 0.8422 (tpt) cc_final: 0.8130 (tpt) REVERT: A 1226 HIS cc_start: 0.6883 (p-80) cc_final: 0.6645 (p-80) REVERT: A 1235 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 1285 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7883 (mmt) REVERT: A 1428 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: A 1429 ASP cc_start: 0.7283 (m-30) cc_final: 0.6904 (m-30) REVERT: A 1431 ASP cc_start: 0.8051 (m-30) cc_final: 0.7810 (m-30) REVERT: A 1486 HIS cc_start: 0.7093 (m-70) cc_final: 0.6850 (m-70) REVERT: B 8 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6106 (tt0) REVERT: B 15 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7779 (mmmt) REVERT: B 31 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7965 (pp) outliers start: 56 outliers final: 32 residues processed: 212 average time/residue: 0.5135 time to fit residues: 118.8292 Evaluate side-chains 216 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 240 ILE 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 631 MET Chi-restraints excluded: chain A residue 662 LEU 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 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 1173 GLU 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 7 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120275 restraints weight = 12236.950| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.87 r_work: 0.3146 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 11306 Z= 0.127 Angle : 0.663 16.979 15395 Z= 0.331 Chirality : 0.042 0.263 1764 Planarity : 0.004 0.054 1893 Dihedral : 6.210 56.010 1703 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 3.95 % Allowed : 15.73 % Favored : 80.32 % 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 (0.24), residues: 1356 helix: 1.20 (0.18), residues: 839 sheet: -2.42 (1.08), residues: 20 loop : -1.73 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 847 TYR 0.018 0.001 TYR A1228 PHE 0.011 0.001 PHE A1095 TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00307 (11291) covalent geometry : angle 0.63657 (15358) SS BOND : bond 0.00112 ( 8) SS BOND : angle 4.26630 ( 16) hydrogen bonds : bond 0.04610 ( 557) hydrogen bonds : angle 3.89611 ( 1590) link_BETA1-4 : bond 0.00404 ( 2) link_BETA1-4 : angle 3.50885 ( 6) link_NAG-ASN : bond 0.00383 ( 5) link_NAG-ASN : angle 3.47229 ( 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 227 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8121 (m) cc_final: 0.7824 (m) REVERT: A 183 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7265 (mttm) REVERT: A 189 PHE cc_start: 0.8330 (t80) cc_final: 0.7954 (t80) REVERT: A 214 ILE cc_start: 0.8221 (mp) cc_final: 0.8006 (mt) REVERT: A 216 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7426 (tp) REVERT: A 219 ASP cc_start: 0.2608 (OUTLIER) cc_final: 0.2339 (m-30) REVERT: A 259 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8077 (mmtp) REVERT: A 424 LYS cc_start: 0.8146 (mttm) cc_final: 0.7637 (mtpp) REVERT: A 582 SER cc_start: 0.7853 (m) cc_final: 0.7632 (p) REVERT: A 598 LEU cc_start: 0.7842 (mm) cc_final: 0.7558 (mm) REVERT: A 631 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8279 (mtp) REVERT: A 634 MET cc_start: 0.7917 (mtm) cc_final: 0.7304 (mmt) REVERT: A 662 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8898 (mt) REVERT: A 855 ASN cc_start: 0.7141 (t0) cc_final: 0.6726 (t0) REVERT: A 915 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7377 (mttp) REVERT: A 977 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 1025 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7968 (mmp) REVERT: A 1102 PHE cc_start: 0.8862 (t80) cc_final: 0.8596 (t80) REVERT: A 1142 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8076 (mtt180) REVERT: A 1144 MET cc_start: 0.8044 (tpp) cc_final: 0.6692 (tmm) REVERT: A 1147 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7551 (mtmm) REVERT: A 1165 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: A 1235 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 1263 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8306 (tp) REVERT: A 1285 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7951 (mmt) REVERT: A 1286 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7787 (ptp90) REVERT: A 1369 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7174 (mtp-110) REVERT: A 1428 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: A 1429 ASP cc_start: 0.7161 (m-30) cc_final: 0.6790 (m-30) REVERT: A 1431 ASP cc_start: 0.8030 (m-30) cc_final: 0.7783 (m-30) REVERT: A 1486 HIS cc_start: 0.7074 (m-70) cc_final: 0.6811 (m-70) REVERT: B 8 GLU cc_start: 0.6455 (tm-30) cc_final: 0.6058 (tt0) REVERT: B 15 LYS cc_start: 0.8200 (mmtp) cc_final: 0.7779 (mmmt) REVERT: B 31 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7845 (pp) outliers start: 45 outliers final: 26 residues processed: 207 average time/residue: 0.5344 time to fit residues: 120.6836 Evaluate side-chains 212 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 878 ILE 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 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU 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 7 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 0.0270 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN A1439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121097 restraints weight = 12256.584| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.80 r_work: 0.3162 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 11306 Z= 0.122 Angle : 0.651 16.605 15395 Z= 0.325 Chirality : 0.042 0.256 1764 Planarity : 0.004 0.055 1893 Dihedral : 6.103 56.316 1703 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.93 % Favored : 92.92 % Rotamer: Outliers : 3.43 % Allowed : 16.96 % Favored : 79.61 % 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: 0.34 (0.24), residues: 1356 helix: 1.35 (0.18), residues: 839 sheet: -2.38 (1.09), residues: 20 loop : -1.66 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 847 TYR 0.019 0.001 TYR A1228 PHE 0.011 0.001 PHE A1095 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00286 (11291) covalent geometry : angle 0.62572 (15358) SS BOND : bond 0.00082 ( 8) SS BOND : angle 4.23538 ( 16) hydrogen bonds : bond 0.04430 ( 557) hydrogen bonds : angle 3.84193 ( 1590) link_BETA1-4 : bond 0.00368 ( 2) link_BETA1-4 : angle 3.32249 ( 6) link_NAG-ASN : bond 0.00432 ( 5) link_NAG-ASN : angle 3.17715 ( 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 218 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8114 (m) cc_final: 0.7842 (m) REVERT: A 183 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7254 (mttm) REVERT: A 189 PHE cc_start: 0.8328 (t80) cc_final: 0.7991 (t80) REVERT: A 214 ILE cc_start: 0.8192 (mp) cc_final: 0.7986 (mt) REVERT: A 216 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 219 ASP cc_start: 0.2649 (OUTLIER) cc_final: 0.2347 (m-30) REVERT: A 259 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8084 (mmtp) REVERT: A 424 LYS cc_start: 0.8124 (mttm) cc_final: 0.7631 (mtpp) REVERT: A 598 LEU cc_start: 0.7895 (mm) cc_final: 0.7668 (mm) REVERT: A 631 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: A 634 MET cc_start: 0.7966 (mtm) cc_final: 0.7416 (mmt) REVERT: A 662 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8887 (mt) REVERT: A 855 ASN cc_start: 0.6960 (t0) cc_final: 0.6566 (t0) REVERT: A 915 LYS cc_start: 0.8155 (ptmm) cc_final: 0.7402 (mttp) REVERT: A 969 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: A 977 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 1025 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7940 (mmp) REVERT: A 1102 PHE cc_start: 0.8837 (t80) cc_final: 0.8579 (t80) REVERT: A 1142 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8023 (mtt180) REVERT: A 1144 MET cc_start: 0.8049 (tpp) cc_final: 0.6890 (tmm) REVERT: A 1147 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7576 (mtmm) REVERT: A 1177 MET cc_start: 0.8479 (tpt) cc_final: 0.8096 (tpt) REVERT: A 1235 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 1263 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 1277 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7454 (mtm-85) REVERT: A 1285 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7911 (mmt) REVERT: A 1286 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7805 (ptp90) REVERT: A 1369 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7222 (mtp-110) REVERT: A 1429 ASP cc_start: 0.7153 (m-30) cc_final: 0.6840 (m-30) REVERT: A 1431 ASP cc_start: 0.8062 (m-30) cc_final: 0.7782 (m-30) REVERT: A 1486 HIS cc_start: 0.7000 (m-70) cc_final: 0.6776 (m-70) REVERT: B 15 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7759 (mmmt) REVERT: B 31 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7869 (pp) outliers start: 39 outliers final: 23 residues processed: 203 average time/residue: 0.5586 time to fit residues: 123.4153 Evaluate side-chains 205 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 LEU 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 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 878 ILE 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 1173 GLU 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 B residue 7 VAL Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 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: 0.9990 chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 104 optimal weight: 0.0020 chunk 28 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122201 restraints weight = 12400.248| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.84 r_work: 0.3170 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11306 Z= 0.113 Angle : 0.634 16.495 15395 Z= 0.317 Chirality : 0.041 0.254 1764 Planarity : 0.004 0.059 1893 Dihedral : 6.002 56.125 1703 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 3.08 % Allowed : 17.49 % 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: 0.35 (0.24), residues: 1356 helix: 1.36 (0.18), residues: 856 sheet: -2.25 (1.70), residues: 10 loop : -1.80 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 847 TYR 0.020 0.001 TYR A1136 PHE 0.010 0.001 PHE A1095 TRP 0.016 0.001 TRP A 624 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00256 (11291) covalent geometry : angle 0.61041 (15358) SS BOND : bond 0.00084 ( 8) SS BOND : angle 4.06639 ( 16) hydrogen bonds : bond 0.04189 ( 557) hydrogen bonds : angle 3.79782 ( 1590) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 3.18703 ( 6) link_NAG-ASN : bond 0.00466 ( 5) link_NAG-ASN : angle 2.97269 ( 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 215 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8096 (m) cc_final: 0.7870 (m) REVERT: A 189 PHE cc_start: 0.8387 (t80) cc_final: 0.8023 (t80) REVERT: A 211 ILE cc_start: 0.8193 (mp) cc_final: 0.7978 (mp) REVERT: A 214 ILE cc_start: 0.8201 (mp) cc_final: 0.7989 (mt) REVERT: A 216 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 259 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8070 (mmtp) REVERT: A 424 LYS cc_start: 0.8102 (mttm) cc_final: 0.7615 (mtpp) REVERT: A 598 LEU cc_start: 0.7856 (mm) cc_final: 0.7623 (mm) REVERT: A 631 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (mtp) REVERT: A 662 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (mt) REVERT: A 915 LYS cc_start: 0.8162 (ptmm) cc_final: 0.7396 (mttp) REVERT: A 969 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: A 977 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8294 (mm-30) REVERT: A 1025 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7929 (mmp) REVERT: A 1144 MET cc_start: 0.7957 (tpp) cc_final: 0.6631 (tmm) REVERT: A 1147 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7577 (mtmm) REVERT: A 1165 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 1173 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 1177 MET cc_start: 0.8467 (tpt) cc_final: 0.8093 (tpt) REVERT: A 1285 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7944 (mmt) REVERT: A 1286 ARG cc_start: 0.8140 (ttp-170) cc_final: 0.7791 (ptp90) REVERT: A 1369 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7341 (mmm160) REVERT: A 1429 ASP cc_start: 0.7101 (m-30) cc_final: 0.6801 (m-30) REVERT: A 1431 ASP cc_start: 0.8078 (m-30) cc_final: 0.7810 (m-30) REVERT: A 1486 HIS cc_start: 0.6999 (m-70) cc_final: 0.6770 (m-70) REVERT: B 15 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7733 (mmmt) REVERT: B 27 GLN cc_start: 0.7923 (mp10) cc_final: 0.7645 (mm110) REVERT: B 31 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7856 (pp) outliers start: 35 outliers final: 19 residues processed: 203 average time/residue: 0.4955 time to fit residues: 110.2171 Evaluate side-chains 200 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 LEU 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 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 878 ILE 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 1156 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1211 ILE 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 B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 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: 1.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117641 restraints weight = 12242.259| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.56 r_work: 0.3111 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 11306 Z= 0.151 Angle : 0.689 16.556 15395 Z= 0.346 Chirality : 0.043 0.258 1764 Planarity : 0.004 0.056 1893 Dihedral : 6.126 57.670 1703 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 3.16 % Allowed : 17.66 % Favored : 79.17 % 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: 0.19 (0.24), residues: 1356 helix: 1.21 (0.18), residues: 862 sheet: -2.46 (1.09), residues: 20 loop : -1.82 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 847 TYR 0.018 0.002 TYR A1228 PHE 0.014 0.002 PHE A1095 TRP 0.018 0.001 TRP A 624 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00362 (11291) covalent geometry : angle 0.66431 (15358) SS BOND : bond 0.00121 ( 8) SS BOND : angle 4.38629 ( 16) hydrogen bonds : bond 0.04882 ( 557) hydrogen bonds : angle 3.88988 ( 1590) link_BETA1-4 : bond 0.00280 ( 2) link_BETA1-4 : angle 3.31712 ( 6) link_NAG-ASN : bond 0.00441 ( 5) link_NAG-ASN : angle 3.15506 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.51 seconds wall clock time: 90 minutes 43.06 seconds (5443.06 seconds total)