Starting phenix.real_space_refine on Tue Jul 29 08:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6a95_6997/07_2025/6a95_6997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6a95_6997/07_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_6997/07_2025/6a95_6997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6a95_6997/07_2025/6a95_6997.map" model { file = "/net/cci-nas-00/data/ceres_data/6a95_6997/07_2025/6a95_6997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6a95_6997/07_2025/6a95_6997.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 4, 'ARG:plan': 6} 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: 7.22, per 1000 atoms: 0.66 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: 2.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 3.97 Time building geometry restraints manager: 3.38 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.880 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.063 0.004 TRP A1063 HIS 0.012 0.003 HIS A 222 PHE 0.035 0.003 PHE A 535 TYR 0.039 0.004 TYR A 933 ARG 0.028 0.002 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.06067 ( 5) link_NAG-ASN : angle 11.51733 ( 15) link_BETA1-4 : bond 0.01968 ( 2) link_BETA1-4 : angle 6.42285 ( 6) hydrogen bonds : bond 0.30950 ( 557) hydrogen bonds : angle 9.20108 ( 1590) SS BOND : bond 0.00565 ( 8) SS BOND : angle 1.82012 ( 16) covalent geometry : bond 0.00707 (11291) covalent geometry : angle 1.06064 (15358) *********************** 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 : 1.215 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: 1.2977 time to fit residues: 409.7836 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 : 1.818 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 40 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 overall best weight: 0.1578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 291 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 936 ASN A 966 ASN A1077 HIS A1133 GLN A1183 ASN A1301 ASN A1438 GLN A1517 ASN B 29 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.171440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125319 restraints weight = 12277.071| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.55 r_work: 0.3266 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 11306 Z= 0.143 Angle : 0.697 15.255 15395 Z= 0.352 Chirality : 0.043 0.264 1764 Planarity : 0.005 0.051 1893 Dihedral : 7.385 58.379 1704 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.49 % Favored : 93.29 % Rotamer: Outliers : 3.87 % Allowed : 10.72 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.20), residues: 1356 helix: -1.34 (0.16), residues: 831 sheet: -2.41 (0.76), residues: 31 loop : -2.45 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 624 HIS 0.005 0.001 HIS A 222 PHE 0.015 0.001 PHE A 410 TYR 0.016 0.001 TYR A1240 ARG 0.007 0.001 ARG B 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 5) link_NAG-ASN : angle 5.43690 ( 15) link_BETA1-4 : bond 0.00654 ( 2) link_BETA1-4 : angle 3.90948 ( 6) hydrogen bonds : bond 0.06597 ( 557) hydrogen bonds : angle 4.63287 ( 1590) SS BOND : bond 0.00507 ( 8) SS BOND : angle 2.34651 ( 16) covalent geometry : bond 0.00282 (11291) covalent geometry : angle 0.66765 (15358) *********************** 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 243 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.6948 (m-10) cc_final: 0.6722 (m-80) REVERT: A 214 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7939 (mt) REVERT: A 219 ASP cc_start: 0.2653 (OUTLIER) cc_final: 0.2326 (m-30) REVERT: A 259 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8241 (mptt) REVERT: A 374 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 424 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7907 (mtpp) REVERT: A 598 LEU cc_start: 0.7990 (mm) cc_final: 0.7701 (mm) REVERT: A 860 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7845 (mptp) REVERT: A 914 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 1137 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.8261 (tmt90) REVERT: A 1144 MET cc_start: 0.8005 (mtm) cc_final: 0.7664 (mpp) REVERT: A 1147 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7758 (mtmm) REVERT: A 1226 HIS cc_start: 0.6811 (p-80) cc_final: 0.6592 (p-80) REVERT: A 1230 LYS cc_start: 0.7090 (mptp) cc_final: 0.6613 (mmpt) REVERT: A 1369 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7646 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7715 (m-30) cc_final: 0.7428 (m-30) REVERT: A 1443 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: A 1486 HIS cc_start: 0.7049 (m-70) cc_final: 0.6735 (m-70) REVERT: B 15 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7721 (mmmt) REVERT: B 28 LYS cc_start: 0.7674 (mttt) cc_final: 0.7409 (mttp) REVERT: B 34 LYS cc_start: 0.8319 (ptpp) cc_final: 0.8095 (ptpt) REVERT: B 50 SER cc_start: 0.8899 (m) cc_final: 0.8618 (p) outliers start: 44 outliers final: 10 residues processed: 227 average time/residue: 1.4186 time to fit residues: 352.9590 Evaluate side-chains 194 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 423 VAL Chi-restraints excluded: chain A residue 568 LEU 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 1156 THR 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 A residue 1453 LEU 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 61 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 GLN A 936 ASN A1133 GLN A1227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122784 restraints weight = 12253.451| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.80 r_work: 0.3168 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11306 Z= 0.144 Angle : 0.724 19.587 15395 Z= 0.362 Chirality : 0.044 0.275 1764 Planarity : 0.004 0.039 1893 Dihedral : 7.042 59.707 1702 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.42 % Favored : 93.36 % Rotamer: Outliers : 4.31 % Allowed : 12.83 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1356 helix: -0.04 (0.18), residues: 836 sheet: -2.40 (0.78), residues: 31 loop : -2.23 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 624 HIS 0.006 0.001 HIS A 392 PHE 0.014 0.002 PHE A1488 TYR 0.023 0.002 TYR A 933 ARG 0.013 0.001 ARG B 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 4.53921 ( 15) link_BETA1-4 : bond 0.00346 ( 2) link_BETA1-4 : angle 3.98365 ( 6) hydrogen bonds : bond 0.05543 ( 557) hydrogen bonds : angle 4.21343 ( 1590) SS BOND : bond 0.00756 ( 8) SS BOND : angle 4.67946 ( 16) covalent geometry : bond 0.00324 (11291) covalent geometry : angle 0.68982 (15358) *********************** 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 231 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 219 ASP cc_start: 0.2583 (OUTLIER) cc_final: 0.2271 (m-30) REVERT: A 259 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8178 (mptt) REVERT: A 374 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7974 (mp) REVERT: A 424 LYS cc_start: 0.8255 (mmtp) cc_final: 0.7834 (mtpp) REVERT: A 598 LEU cc_start: 0.7939 (mm) cc_final: 0.7627 (mm) REVERT: A 855 ASN cc_start: 0.7402 (t0) cc_final: 0.7012 (t0) REVERT: A 860 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7885 (mtpp) REVERT: A 914 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7968 (t80) REVERT: A 1025 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (mmt) REVERT: A 1033 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 1144 MET cc_start: 0.7859 (mtp) cc_final: 0.7658 (mpp) REVERT: A 1147 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7703 (mtmm) REVERT: A 1177 MET cc_start: 0.8543 (tpt) cc_final: 0.8260 (tpt) REVERT: A 1211 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 1226 HIS cc_start: 0.6780 (p-80) cc_final: 0.6555 (p-80) REVERT: A 1369 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7575 (mtp-110) REVERT: A 1431 ASP cc_start: 0.7940 (m-30) cc_final: 0.7612 (m-30) REVERT: A 1443 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: A 1486 HIS cc_start: 0.6987 (m-70) cc_final: 0.6721 (m-70) REVERT: B 15 LYS cc_start: 0.8242 (mmtp) cc_final: 0.7830 (mmmt) REVERT: B 28 LYS cc_start: 0.7790 (mttt) cc_final: 0.7568 (mttp) outliers start: 49 outliers final: 22 residues processed: 214 average time/residue: 1.0770 time to fit residues: 251.7216 Evaluate side-chains 201 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 255 ILE Chi-restraints excluded: chain A residue 374 LEU 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 860 LYS Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 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 A residue 1453 LEU 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 91 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 743 ASN A1133 GLN A1517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120177 restraints weight = 12170.833| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.56 r_work: 0.3179 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11306 Z= 0.135 Angle : 0.684 17.582 15395 Z= 0.343 Chirality : 0.043 0.272 1764 Planarity : 0.004 0.043 1893 Dihedral : 6.755 55.055 1702 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 3.95 % Allowed : 13.97 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1356 helix: 0.50 (0.18), residues: 839 sheet: -2.25 (0.82), residues: 31 loop : -2.10 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.013 0.001 PHE A1102 TYR 0.023 0.002 TYR A 933 ARG 0.007 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 5) link_NAG-ASN : angle 4.11027 ( 15) link_BETA1-4 : bond 0.00821 ( 2) link_BETA1-4 : angle 3.85140 ( 6) hydrogen bonds : bond 0.05036 ( 557) hydrogen bonds : angle 4.05356 ( 1590) SS BOND : bond 0.00194 ( 8) SS BOND : angle 4.54578 ( 16) covalent geometry : bond 0.00301 (11291) covalent geometry : angle 0.65158 (15358) *********************** 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 219 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.8014 (mt) REVERT: A 219 ASP cc_start: 0.2531 (OUTLIER) cc_final: 0.2213 (m-30) REVERT: A 259 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8230 (mptt) REVERT: A 424 LYS cc_start: 0.8199 (mmtp) cc_final: 0.7780 (mtpp) REVERT: A 598 LEU cc_start: 0.7851 (mm) cc_final: 0.7554 (mm) REVERT: A 634 MET cc_start: 0.8060 (mtm) cc_final: 0.7395 (mmt) REVERT: A 855 ASN cc_start: 0.7247 (t0) cc_final: 0.6840 (t0) REVERT: A 914 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7977 (t80) REVERT: A 1025 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7769 (mmt) REVERT: A 1033 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 1147 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7653 (mtmm) REVERT: A 1177 MET cc_start: 0.8461 (tpt) cc_final: 0.8091 (tpt) REVERT: A 1211 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 1225 ARG cc_start: 0.7708 (mtm180) cc_final: 0.7502 (mtm180) REVERT: A 1226 HIS cc_start: 0.6784 (p-80) cc_final: 0.6542 (p-80) REVERT: A 1286 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7626 (ptp90) REVERT: A 1431 ASP cc_start: 0.7889 (m-30) cc_final: 0.7556 (m-30) REVERT: A 1443 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 1486 HIS cc_start: 0.7006 (m-70) cc_final: 0.6733 (m-70) REVERT: B 14 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7388 (mtpp) REVERT: B 15 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7788 (mmmt) REVERT: B 28 LYS cc_start: 0.7889 (mttt) cc_final: 0.7627 (mttp) REVERT: B 31 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7996 (pp) outliers start: 45 outliers final: 25 residues processed: 202 average time/residue: 1.0446 time to fit residues: 231.2359 Evaluate side-chains 201 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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 872 LEU Chi-restraints excluded: chain A residue 906 ILE 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 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 1218 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 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 128 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.166910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121205 restraints weight = 12256.867| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.81 r_work: 0.3166 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11306 Z= 0.135 Angle : 0.674 16.754 15395 Z= 0.338 Chirality : 0.043 0.269 1764 Planarity : 0.004 0.043 1893 Dihedral : 6.413 56.050 1702 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.14 % Rotamer: Outliers : 4.13 % Allowed : 14.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1356 helix: 0.81 (0.18), residues: 840 sheet: -2.02 (0.84), residues: 31 loop : -2.00 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.004 0.001 HIS A 392 PHE 0.011 0.001 PHE A1488 TYR 0.022 0.002 TYR A 933 ARG 0.009 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 5) link_NAG-ASN : angle 3.89743 ( 15) link_BETA1-4 : bond 0.00496 ( 2) link_BETA1-4 : angle 3.87098 ( 6) hydrogen bonds : bond 0.04874 ( 557) hydrogen bonds : angle 3.97438 ( 1590) SS BOND : bond 0.00153 ( 8) SS BOND : angle 4.54393 ( 16) covalent geometry : bond 0.00306 (11291) covalent geometry : angle 0.64250 (15358) *********************** 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 224 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 136 THR cc_start: 0.8273 (m) cc_final: 0.8017 (m) REVERT: A 216 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7437 (tp) REVERT: A 219 ASP cc_start: 0.2683 (OUTLIER) cc_final: 0.2386 (m-30) REVERT: A 259 LYS cc_start: 0.8769 (ttpp) cc_final: 0.8128 (mmtp) REVERT: A 424 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7687 (mtpp) REVERT: A 598 LEU cc_start: 0.7824 (mm) cc_final: 0.7503 (mm) REVERT: A 631 MET cc_start: 0.8322 (mtp) cc_final: 0.7637 (mmm) REVERT: A 634 MET cc_start: 0.7864 (mtm) cc_final: 0.7166 (mmt) REVERT: A 855 ASN cc_start: 0.7176 (t0) cc_final: 0.6770 (t0) REVERT: A 914 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 1025 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7855 (mmt) REVERT: A 1033 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 1142 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8114 (mtt180) REVERT: A 1147 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7667 (mtmm) REVERT: A 1177 MET cc_start: 0.8448 (tpt) cc_final: 0.8048 (tpt) REVERT: A 1211 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 1226 HIS cc_start: 0.6733 (p-80) cc_final: 0.6492 (p-80) REVERT: A 1285 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.7916 (mmt) REVERT: A 1286 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7610 (ptp90) REVERT: A 1431 ASP cc_start: 0.8021 (m-30) cc_final: 0.7704 (m-30) REVERT: A 1443 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 1486 HIS cc_start: 0.7024 (m-70) cc_final: 0.6741 (m-70) REVERT: B 15 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7781 (mmmt) REVERT: B 28 LYS cc_start: 0.7854 (mttt) cc_final: 0.7568 (mttp) REVERT: B 31 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8013 (pp) outliers start: 47 outliers final: 23 residues processed: 203 average time/residue: 1.0859 time to fit residues: 240.8492 Evaluate side-chains 201 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 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 872 LEU 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 1025 MET Chi-restraints excluded: chain A residue 1052 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 1218 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 81 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.165573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117814 restraints weight = 12282.407| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.58 r_work: 0.3164 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11306 Z= 0.158 Angle : 0.699 17.261 15395 Z= 0.351 Chirality : 0.044 0.263 1764 Planarity : 0.004 0.044 1893 Dihedral : 6.196 56.067 1702 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.71 % Favored : 92.99 % Rotamer: Outliers : 4.31 % Allowed : 14.41 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1356 helix: 0.91 (0.18), residues: 842 sheet: -2.06 (0.83), residues: 31 loop : -1.84 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.005 0.001 HIS A 392 PHE 0.013 0.002 PHE A 586 TYR 0.024 0.002 TYR A 933 ARG 0.011 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 3.83235 ( 15) link_BETA1-4 : bond 0.00430 ( 2) link_BETA1-4 : angle 3.83450 ( 6) hydrogen bonds : bond 0.05136 ( 557) hydrogen bonds : angle 3.99004 ( 1590) SS BOND : bond 0.00214 ( 8) SS BOND : angle 4.61561 ( 16) covalent geometry : bond 0.00370 (11291) covalent geometry : angle 0.66882 (15358) *********************** 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 223 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8218 (m) cc_final: 0.7962 (m) REVERT: A 216 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 219 ASP cc_start: 0.2491 (OUTLIER) cc_final: 0.2205 (m-30) REVERT: A 259 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8163 (mmtp) REVERT: A 424 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7682 (mtpp) REVERT: A 598 LEU cc_start: 0.7872 (mm) cc_final: 0.7589 (mm) REVERT: A 634 MET cc_start: 0.7870 (mtm) cc_final: 0.7192 (mmt) REVERT: A 855 ASN cc_start: 0.7250 (t0) cc_final: 0.6812 (t0) REVERT: A 914 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 1025 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7830 (mmt) REVERT: A 1033 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 1142 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8185 (mtt180) REVERT: A 1147 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7617 (mtmm) REVERT: A 1165 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: A 1177 MET cc_start: 0.8414 (tpt) cc_final: 0.8052 (tpt) REVERT: A 1226 HIS cc_start: 0.6828 (p-80) cc_final: 0.6590 (p-80) REVERT: A 1285 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.7907 (mmt) REVERT: A 1431 ASP cc_start: 0.7987 (m-30) cc_final: 0.7693 (m-30) REVERT: A 1486 HIS cc_start: 0.7042 (m-70) cc_final: 0.6822 (m-70) REVERT: B 8 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6048 (tt0) REVERT: B 14 LYS cc_start: 0.7613 (mmmm) cc_final: 0.7385 (mttp) REVERT: B 15 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7823 (mmmt) REVERT: B 31 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8031 (pp) outliers start: 49 outliers final: 25 residues processed: 201 average time/residue: 1.3129 time to fit residues: 288.2534 Evaluate side-chains 200 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 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 595 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 872 LEU 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 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 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 1.9990 chunk 114 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.166458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118992 restraints weight = 12486.904| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.58 r_work: 0.3178 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11306 Z= 0.132 Angle : 0.671 17.978 15395 Z= 0.334 Chirality : 0.043 0.264 1764 Planarity : 0.004 0.045 1893 Dihedral : 6.018 55.765 1701 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 3.43 % Allowed : 15.55 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1356 helix: 1.10 (0.18), residues: 845 sheet: -2.35 (1.07), residues: 20 loop : -1.85 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.011 0.001 PHE A1095 TYR 0.020 0.001 TYR A 933 ARG 0.012 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 5) link_NAG-ASN : angle 3.57556 ( 15) link_BETA1-4 : bond 0.00447 ( 2) link_BETA1-4 : angle 3.56843 ( 6) hydrogen bonds : bond 0.04712 ( 557) hydrogen bonds : angle 3.92714 ( 1590) SS BOND : bond 0.00102 ( 8) SS BOND : angle 4.38133 ( 16) covalent geometry : bond 0.00299 (11291) covalent geometry : angle 0.64338 (15358) *********************** 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 221 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8155 (m) cc_final: 0.7896 (m) REVERT: A 219 ASP cc_start: 0.2600 (OUTLIER) cc_final: 0.2304 (m-30) REVERT: A 259 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8114 (mmtp) REVERT: A 424 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7577 (mtpp) REVERT: A 598 LEU cc_start: 0.7856 (mm) cc_final: 0.7565 (mm) REVERT: A 634 MET cc_start: 0.7829 (mtm) cc_final: 0.7134 (mmt) REVERT: A 662 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 855 ASN cc_start: 0.7187 (t0) cc_final: 0.6761 (t0) REVERT: A 914 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 969 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: A 1025 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7824 (mmt) REVERT: A 1033 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 1142 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8124 (mtt180) REVERT: A 1147 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7551 (mtmm) REVERT: A 1165 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: A 1226 HIS cc_start: 0.6790 (p-80) cc_final: 0.6578 (p-80) REVERT: A 1285 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7885 (mmt) REVERT: A 1286 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7751 (ptp90) REVERT: A 1431 ASP cc_start: 0.7974 (m-30) cc_final: 0.7709 (m-30) REVERT: A 1486 HIS cc_start: 0.7058 (m-70) cc_final: 0.6778 (m-70) REVERT: B 8 GLU cc_start: 0.6417 (tm-30) cc_final: 0.6051 (tt0) REVERT: B 14 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7373 (mttp) REVERT: B 15 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7789 (mmmt) REVERT: B 31 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8012 (pp) outliers start: 39 outliers final: 21 residues processed: 201 average time/residue: 1.4163 time to fit residues: 311.1093 Evaluate side-chains 202 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE 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 595 ILE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 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 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.166352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118953 restraints weight = 12266.605| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.55 r_work: 0.3180 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11306 Z= 0.131 Angle : 0.666 16.480 15395 Z= 0.333 Chirality : 0.043 0.262 1764 Planarity : 0.004 0.053 1893 Dihedral : 5.942 56.125 1701 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.78 % Favored : 92.99 % Rotamer: Outliers : 3.69 % Allowed : 15.47 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1356 helix: 1.22 (0.18), residues: 842 sheet: -2.41 (1.08), residues: 20 loop : -1.73 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.011 0.001 PHE A1095 TYR 0.017 0.002 TYR A 933 ARG 0.012 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 5) link_NAG-ASN : angle 3.37669 ( 15) link_BETA1-4 : bond 0.00425 ( 2) link_BETA1-4 : angle 3.52240 ( 6) hydrogen bonds : bond 0.04687 ( 557) hydrogen bonds : angle 3.91373 ( 1590) SS BOND : bond 0.00097 ( 8) SS BOND : angle 4.37979 ( 16) covalent geometry : bond 0.00296 (11291) covalent geometry : angle 0.63947 (15358) *********************** 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 222 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8136 (m) cc_final: 0.7904 (m) REVERT: A 216 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7494 (tp) REVERT: A 219 ASP cc_start: 0.2559 (OUTLIER) cc_final: 0.2247 (m-30) REVERT: A 259 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8112 (mmtp) REVERT: A 424 LYS cc_start: 0.7961 (mmtp) cc_final: 0.7591 (mtpp) REVERT: A 598 LEU cc_start: 0.7882 (mm) cc_final: 0.7599 (mm) REVERT: A 634 MET cc_start: 0.7930 (mtm) cc_final: 0.7231 (mmt) REVERT: A 855 ASN cc_start: 0.7103 (t0) cc_final: 0.6697 (t0) REVERT: A 914 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 953 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 969 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: A 1025 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7807 (mmt) REVERT: A 1033 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 1147 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7541 (mtmm) REVERT: A 1165 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 1177 MET cc_start: 0.8409 (tpt) cc_final: 0.8042 (tpt) REVERT: A 1226 HIS cc_start: 0.6769 (p-80) cc_final: 0.6553 (p-80) REVERT: A 1285 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7890 (mmt) REVERT: A 1286 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7683 (ptp90) REVERT: A 1431 ASP cc_start: 0.7971 (m-30) cc_final: 0.7705 (m-30) REVERT: A 1486 HIS cc_start: 0.7067 (m-70) cc_final: 0.6808 (m-70) REVERT: B 14 LYS cc_start: 0.7605 (mmmm) cc_final: 0.7385 (mttp) REVERT: B 15 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7784 (mmmt) REVERT: B 31 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7993 (pp) outliers start: 42 outliers final: 22 residues processed: 206 average time/residue: 1.0768 time to fit residues: 242.3542 Evaluate side-chains 205 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 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 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 4 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 104 optimal weight: 0.0020 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.166286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118985 restraints weight = 12265.568| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.54 r_work: 0.3178 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3590 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= 0.132 Angle : 0.665 16.631 15395 Z= 0.332 Chirality : 0.043 0.262 1764 Planarity : 0.004 0.057 1893 Dihedral : 5.944 56.477 1701 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 3.25 % Allowed : 15.99 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1356 helix: 1.16 (0.18), residues: 859 sheet: -2.39 (1.07), residues: 20 loop : -1.92 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.011 0.001 PHE A1095 TYR 0.018 0.001 TYR A1228 ARG 0.013 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 5) link_NAG-ASN : angle 3.27392 ( 15) link_BETA1-4 : bond 0.00394 ( 2) link_BETA1-4 : angle 3.49269 ( 6) hydrogen bonds : bond 0.04658 ( 557) hydrogen bonds : angle 3.91877 ( 1590) SS BOND : bond 0.00084 ( 8) SS BOND : angle 4.32255 ( 16) covalent geometry : bond 0.00300 (11291) covalent geometry : angle 0.63953 (15358) *********************** 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 214 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8117 (m) cc_final: 0.7874 (m) REVERT: A 216 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7492 (tp) REVERT: A 219 ASP cc_start: 0.2670 (OUTLIER) cc_final: 0.2351 (m-30) REVERT: A 259 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8108 (mmtp) REVERT: A 424 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7576 (mtpp) REVERT: A 598 LEU cc_start: 0.7868 (mm) cc_final: 0.7583 (mm) REVERT: A 634 MET cc_start: 0.7915 (mtm) cc_final: 0.7250 (mmt) REVERT: A 855 ASN cc_start: 0.7071 (t0) cc_final: 0.6704 (t0) REVERT: A 914 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8096 (t80) REVERT: A 953 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8633 (mp) REVERT: A 969 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: A 1025 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7809 (mmt) REVERT: A 1033 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 1147 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7545 (mtmm) REVERT: A 1165 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: A 1226 HIS cc_start: 0.6746 (p-80) cc_final: 0.6532 (p-80) REVERT: A 1277 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7490 (mtm-85) REVERT: A 1285 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7887 (mmt) REVERT: A 1286 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7772 (ptp90) REVERT: A 1431 ASP cc_start: 0.8009 (m-30) cc_final: 0.7722 (m-30) REVERT: A 1486 HIS cc_start: 0.7088 (m-70) cc_final: 0.6827 (m-70) REVERT: B 14 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7347 (mttp) REVERT: B 15 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7771 (mmmt) REVERT: B 27 GLN cc_start: 0.7930 (mp10) cc_final: 0.7639 (mm110) REVERT: B 31 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7997 (pp) outliers start: 37 outliers final: 24 residues processed: 198 average time/residue: 1.0717 time to fit residues: 232.4088 Evaluate side-chains 207 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 914 PHE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1015 ASN Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1130 SER Chi-restraints excluded: chain A residue 1165 ASP Chi-restraints excluded: chain A residue 1173 GLU Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 1 optimal weight: 30.0000 chunk 132 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117465 restraints weight = 12211.792| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.77 r_work: 0.3042 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11306 Z= 0.209 Angle : 0.762 18.530 15395 Z= 0.382 Chirality : 0.047 0.271 1764 Planarity : 0.004 0.058 1893 Dihedral : 6.191 58.619 1701 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.70 % Rotamer: Outliers : 2.90 % Allowed : 16.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1356 helix: 0.96 (0.18), residues: 855 sheet: -2.00 (0.81), residues: 31 loop : -1.91 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 624 HIS 0.006 0.001 HIS A 153 PHE 0.016 0.002 PHE A1115 TYR 0.021 0.002 TYR A 933 ARG 0.014 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 5) link_NAG-ASN : angle 3.67224 ( 15) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 3.73775 ( 6) hydrogen bonds : bond 0.05692 ( 557) hydrogen bonds : angle 4.08141 ( 1590) SS BOND : bond 0.00317 ( 8) SS BOND : angle 4.77293 ( 16) covalent geometry : bond 0.00504 (11291) covalent geometry : angle 0.73469 (15358) ********************** 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: 33 poor density : 182 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 THR cc_start: 0.8127 (m) cc_final: 0.7838 (m) REVERT: A 259 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8102 (mmtp) REVERT: A 424 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7652 (mtpp) REVERT: A 582 SER cc_start: 0.7950 (m) cc_final: 0.7718 (p) REVERT: A 598 LEU cc_start: 0.7876 (mm) cc_final: 0.7587 (mm) REVERT: A 631 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: A 634 MET cc_start: 0.7992 (mtm) cc_final: 0.7377 (mmt) REVERT: A 855 ASN cc_start: 0.7621 (t0) cc_final: 0.7272 (t0) REVERT: A 914 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8180 (t80) REVERT: A 915 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7365 (mttp) REVERT: A 1025 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7870 (mmt) REVERT: A 1147 LYS cc_start: 0.8003 (mtmm) cc_final: 0.7563 (mtmm) REVERT: A 1165 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: A 1177 MET cc_start: 0.8522 (tpt) cc_final: 0.8163 (tpt) REVERT: A 1226 HIS cc_start: 0.6763 (p-80) cc_final: 0.6546 (p-80) REVERT: A 1277 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7562 (mtm-85) REVERT: A 1285 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7941 (mmt) REVERT: A 1431 ASP cc_start: 0.8049 (m-30) cc_final: 0.7779 (m-30) REVERT: A 1486 HIS cc_start: 0.7074 (m-70) cc_final: 0.6810 (m-70) REVERT: B 8 GLU cc_start: 0.6458 (tm-30) cc_final: 0.6038 (tt0) REVERT: B 15 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7749 (mmmt) REVERT: B 31 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8023 (pp) outliers start: 33 outliers final: 22 residues processed: 202 average time/residue: 1.0674 time to fit residues: 235.4346 Evaluate side-chains 206 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 631 MET Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 878 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 1108 VAL 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 1285 MET Chi-restraints excluded: chain A residue 1398 THR Chi-restraints excluded: chain A residue 1401 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 52 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 96 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.166002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120776 restraints weight = 12262.937| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.78 r_work: 0.3157 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11306 Z= 0.127 Angle : 0.672 17.808 15395 Z= 0.336 Chirality : 0.043 0.266 1764 Planarity : 0.004 0.062 1893 Dihedral : 6.009 56.384 1701 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 2.55 % Allowed : 17.31 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1356 helix: 1.20 (0.18), residues: 856 sheet: -2.43 (1.07), residues: 20 loop : -1.86 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS A 153 PHE 0.012 0.001 PHE A1488 TYR 0.018 0.001 TYR A1228 ARG 0.014 0.001 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 5) link_NAG-ASN : angle 3.29247 ( 15) link_BETA1-4 : bond 0.00298 ( 2) link_BETA1-4 : angle 3.42076 ( 6) hydrogen bonds : bond 0.04690 ( 557) hydrogen bonds : angle 3.92798 ( 1590) SS BOND : bond 0.00359 ( 8) SS BOND : angle 4.48095 ( 16) covalent geometry : bond 0.00285 (11291) covalent geometry : angle 0.64581 (15358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11441.86 seconds wall clock time: 203 minutes 58.41 seconds (12238.41 seconds total)