Starting phenix.real_space_refine on Thu Mar 5 09:31:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.map" model { file = "/net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uhf_26513/03_2026/7uhf_26513.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 112 5.16 5 C 13159 2.51 5 N 3352 2.21 5 O 3753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20379 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9900 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 7 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "C" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2575 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" 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: "H" 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: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {' CA': 1, '3PE': 1, 'N90': 1, 'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.22 Number of scatterers: 20379 At special positions: 0 Unit cell: (171.556, 169.328, 183.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 112 16.00 P 1 15.00 O 3753 8.00 N 3352 7.00 C 13159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1055 " distance=2.03 Simple disulfide: pdb=" SG CYS A1421 " - pdb=" SG CYS A1435 " distance=2.03 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.04 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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 B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG D1201 " - " ASN D 92 " " NAG E 1 " - " ASN D 348 " " NAG F 1 " - " ASN D 468 " " NAG G 1 " - " ASN D 613 " " NAG H 1 " - " ASN D 895 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 993.3 milliseconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 17 sheets defined 53.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 155 through 178 removed outlier: 3.802A pdb=" N TYR A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.518A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.833A pdb=" N PHE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 248 through 254 removed outlier: 4.298A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 271 through 293 removed outlier: 3.815A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 362 removed outlier: 3.537A pdb=" N THR A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.709A pdb=" N TYR A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 3.660A pdb=" N PHE A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.772A pdb=" N GLU A 433 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP A 441 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.121A pdb=" N LYS A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.500A pdb=" N VAL A 531 " --> pdb=" O TRP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 557 through 578 removed outlier: 3.505A pdb=" N GLY A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 removed outlier: 3.848A pdb=" N ARG A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.713A pdb=" N SER A 616 " --> pdb=" O PRO A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.787A pdb=" N THR A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 650 through 673 Processing helix chain 'A' and resid 690 through 704 Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.545A pdb=" N VAL A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.525A pdb=" N GLY A 725 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A 726 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 728 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 729 " --> pdb=" O MET A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 722 through 729' Processing helix chain 'A' and resid 730 through 748 removed outlier: 3.584A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 756 removed outlier: 3.948A pdb=" N ASP A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 756 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.780A pdb=" N SER A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 768 removed outlier: 3.672A pdb=" N GLU A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 885 Processing helix chain 'A' and resid 887 through 905 removed outlier: 4.299A pdb=" N ILE A 892 " --> pdb=" O PHE A 888 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 894 " --> pdb=" O ASN A 890 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.891A pdb=" N LEU A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 970 removed outlier: 3.626A pdb=" N MET A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.532A pdb=" N ARG A 984 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 998 removed outlier: 4.083A pdb=" N ARG A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1013 removed outlier: 4.042A pdb=" N LYS A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1017 through 1037 removed outlier: 3.778A pdb=" N THR A1023 " --> pdb=" O MET A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1086 through 1099 Processing helix chain 'A' and resid 1102 through 1112 Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1128 through 1144 removed outlier: 4.172A pdb=" N PHE A1132 " --> pdb=" O ILE A1128 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1152 removed outlier: 3.672A pdb=" N VAL A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1161 Processing helix chain 'A' and resid 1171 through 1181 removed outlier: 4.023A pdb=" N CYS A1175 " --> pdb=" O ASN A1171 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1203 removed outlier: 4.263A pdb=" N LYS A1197 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A1198 " --> pdb=" O TYR A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1223 removed outlier: 3.865A pdb=" N VAL A1213 " --> pdb=" O TYR A1209 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A1218 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1219 " --> pdb=" O ILE A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1260 removed outlier: 3.629A pdb=" N ILE A1257 " --> pdb=" O VAL A1253 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1283 removed outlier: 3.969A pdb=" N SER A1274 " --> pdb=" O ASN A1270 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1275 " --> pdb=" O THR A1271 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.711A pdb=" N PHE A1321 " --> pdb=" O PHE A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1325 removed outlier: 3.516A pdb=" N ARG A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1325' Processing helix chain 'A' and resid 1326 through 1331 Processing helix chain 'A' and resid 1335 through 1350 removed outlier: 3.568A pdb=" N PHE A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A1350 " --> pdb=" O SER A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1373 removed outlier: 3.673A pdb=" N LEU A1355 " --> pdb=" O PRO A1351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A1356 " --> pdb=" O TYR A1352 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A1357 " --> pdb=" O VAL A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1413 Processing helix chain 'A' and resid 1439 through 1454 Processing helix chain 'A' and resid 1478 through 1492 removed outlier: 4.291A pdb=" N LEU A1482 " --> pdb=" O GLY A1478 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1511 Processing helix chain 'A' and resid 1522 through 1534 removed outlier: 4.155A pdb=" N VAL A1526 " --> pdb=" O CYS A1522 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N CYS A1528 " --> pdb=" O HIS A1524 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS A1529 " --> pdb=" O ARG A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1558 removed outlier: 3.522A pdb=" N PHE A1551 " --> pdb=" O ASN A1547 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A1552 " --> pdb=" O ALA A1548 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A1558 " --> pdb=" O VAL A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1576 removed outlier: 4.137A pdb=" N ALA A1569 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A1570 " --> pdb=" O LEU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1588 removed outlier: 4.423A pdb=" N LYS A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 53 removed outlier: 3.520A pdb=" N TRP D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.660A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 110 removed outlier: 3.583A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.580A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.208A pdb=" N VAL D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.945A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 281 removed outlier: 3.697A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 332 through 345 removed outlier: 3.520A pdb=" N GLN D 343 " --> pdb=" O PHE D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.612A pdb=" N PHE D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 377 " --> pdb=" O PHE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.608A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN D 406 " --> pdb=" O MET D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 431 removed outlier: 4.163A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 438 removed outlier: 3.902A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 560 through 565 removed outlier: 3.701A pdb=" N GLU D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 3.631A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.786A pdb=" N GLN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 644 " --> pdb=" O THR D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 removed outlier: 6.021A pdb=" N ASP D 651 " --> pdb=" O LEU D 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 652 through 657 Processing helix chain 'D' and resid 678 through 689 removed outlier: 3.511A pdb=" N ASP D 688 " --> pdb=" O ASN D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 719 removed outlier: 4.046A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.674A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.608A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 Processing helix chain 'D' and resid 874 through 878 Processing helix chain 'D' and resid 879 through 889 removed outlier: 3.524A pdb=" N HIS D 885 " --> pdb=" O SER D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1047 removed outlier: 3.684A pdb=" N MET D1046 " --> pdb=" O ASN D1042 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D1047 " --> pdb=" O PRO D1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1042 through 1047' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.927A pdb=" N GLU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.932A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 190 through 208 removed outlier: 3.626A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 262 removed outlier: 3.721A pdb=" N GLN C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 254 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.743A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.533A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 361 removed outlier: 3.519A pdb=" N ALA C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS C 361 " --> pdb=" O TRP C 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA2, first strand: chain 'A' and resid 1058 through 1062 Processing sheet with id=AA3, first strand: chain 'A' and resid 1499 through 1500 Processing sheet with id=AA4, first strand: chain 'D' and resid 68 through 72 Processing sheet with id=AA5, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.369A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 142 through 144 removed outlier: 6.369A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL D 166 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 490 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AA8, first strand: chain 'D' and resid 298 through 300 removed outlier: 8.400A pdb=" N ALA D 292 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS D 356 " --> pdb=" O ARG D 383 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE D 385 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.267A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR D 617 " --> pdb=" O VAL D 612 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 658 through 661 removed outlier: 4.513A pdb=" N ILE D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 731 " --> pdb=" O LYS D 815 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 800 through 801 Processing sheet with id=AB3, first strand: chain 'D' and resid 859 through 861 removed outlier: 6.733A pdb=" N ILE D 852 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 992 " --> pdb=" O PHE D1003 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 892 through 904 removed outlier: 3.640A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.553A pdb=" N THR C 66 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 93 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 64 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.943A pdb=" N TYR C 70 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE C 87 " --> pdb=" O TYR C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.551A pdb=" N VAL C 292 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 212 through 215 removed outlier: 3.565A pdb=" N VAL C 268 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C 215 " --> pdb=" O VAL C 268 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2619 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: 4.01 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3809 1.33 - 1.45: 5203 1.45 - 1.57: 11621 1.57 - 1.70: 7 1.70 - 1.82: 176 Bond restraints: 20816 Sorted by residual: bond pdb=" C07 N90 A2201 " pdb=" N14 N90 A2201 " ideal model delta sigma weight residual 1.456 1.288 0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C20 N90 A2201 " pdb=" N17 N90 A2201 " ideal model delta sigma weight residual 1.452 1.336 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " ideal model delta sigma weight residual 1.525 1.639 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 1.520 1.412 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C22 N90 A2201 " pdb=" C23 N90 A2201 " ideal model delta sigma weight residual 1.467 1.570 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 20811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 28062 3.77 - 7.55: 104 7.55 - 11.32: 15 11.32 - 15.09: 5 15.09 - 18.86: 1 Bond angle restraints: 28187 Sorted by residual: angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAT Y01 A2204 " ideal model delta sigma weight residual 109.59 128.45 -18.86 3.00e+00 1.11e-01 3.95e+01 angle pdb=" N ILE A1012 " pdb=" CA ILE A1012 " pdb=" C ILE A1012 " ideal model delta sigma weight residual 110.62 116.77 -6.15 1.14e+00 7.69e-01 2.91e+01 angle pdb=" CAD Y01 A2204 " pdb=" CBH Y01 A2204 " pdb=" CAZ Y01 A2204 " ideal model delta sigma weight residual 108.53 93.63 14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C SER A 723 " pdb=" CA SER A 723 " pdb=" CB SER A 723 " ideal model delta sigma weight residual 115.79 109.99 5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" CAK Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBG Y01 A2204 " ideal model delta sigma weight residual 110.32 96.36 13.96 3.00e+00 1.11e-01 2.16e+01 ... (remaining 28182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 11630 22.64 - 45.29: 913 45.29 - 67.93: 146 67.93 - 90.57: 47 90.57 - 113.21: 19 Dihedral angle restraints: 12755 sinusoidal: 5438 harmonic: 7317 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 160.63 -67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CB CYS D 667 " pdb=" SG CYS D 667 " pdb=" SG CYS D 697 " pdb=" CB CYS D 697 " ideal model delta sinusoidal sigma weight residual 93.00 50.21 42.79 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CA ASN D 613 " pdb=" C ASN D 613 " pdb=" N GLY D 614 " pdb=" CA GLY D 614 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 12752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3179 0.127 - 0.255: 28 0.255 - 0.382: 2 0.382 - 0.509: 2 0.509 - 0.636: 1 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 184 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CBG Y01 A2204 " pdb=" CAQ Y01 A2204 " pdb=" CBD Y01 A2204 " pdb=" CBI Y01 A2204 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3209 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2202 " 0.214 2.00e-02 2.50e+03 1.79e-01 3.99e+02 pdb=" C7 NAG A2202 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A2202 " 0.152 2.00e-02 2.50e+03 pdb=" N2 NAG A2202 " -0.296 2.00e-02 2.50e+03 pdb=" O7 NAG A2202 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 675 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASN D 675 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN D 675 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN D 676 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1428 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A1429 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A1429 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1429 " -0.032 5.00e-02 4.00e+02 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 176 2.62 - 3.19: 17833 3.19 - 3.76: 30154 3.76 - 4.33: 41826 4.33 - 4.90: 68440 Nonbonded interactions: 158429 Sorted by model distance: nonbonded pdb=" O3 NAG A2202 " pdb=" O7 NAG A2202 " model vdw 2.053 3.040 nonbonded pdb=" O TRP A 550 " pdb=" CG2 ILE A 554 " model vdw 2.201 3.460 nonbonded pdb=" OE1 GLN A 359 " pdb=" OH TYR A 712 " model vdw 2.204 3.040 nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP D 516 " pdb=" CD PRO D 517 " model vdw 2.233 3.440 ... (remaining 158424 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 'E' selection = chain 'G' selection = chain 'H' } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.960 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 20840 Z= 0.216 Angle : 0.726 18.864 28249 Z= 0.376 Chirality : 0.047 0.636 3212 Planarity : 0.005 0.179 3559 Dihedral : 16.847 113.215 7989 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 2.31 % Allowed : 1.22 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.17), residues: 2472 helix: -0.23 (0.15), residues: 1138 sheet: -0.19 (0.34), residues: 252 loop : -1.27 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.015 0.001 TYR D1068 PHE 0.030 0.001 PHE A 280 TRP 0.022 0.001 TRP A1341 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00426 (20816) covalent geometry : angle 0.70392 (28187) SS BOND : bond 0.00215 ( 10) SS BOND : angle 1.53306 ( 20) hydrogen bonds : bond 0.23193 ( 899) hydrogen bonds : angle 7.58051 ( 2619) link_BETA1-4 : bond 0.00838 ( 8) link_BETA1-4 : angle 3.19272 ( 24) link_NAG-ASN : bond 0.00993 ( 6) link_NAG-ASN : angle 5.96309 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 276 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8098 (tp) REVERT: A 178 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6857 (pt) REVERT: A 363 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7270 (mtp) REVERT: A 395 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.4689 (m-10) REVERT: A 555 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: A 559 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6916 (p0) REVERT: A 765 GLN cc_start: 0.3835 (OUTLIER) cc_final: 0.2744 (mt0) REVERT: A 766 LYS cc_start: 0.4857 (OUTLIER) cc_final: 0.4039 (mtmm) REVERT: A 767 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4264 (tp30) REVERT: A 960 MET cc_start: 0.6772 (mpp) cc_final: 0.6134 (ttp) REVERT: A 1013 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6355 (tpt90) REVERT: A 1156 GLN cc_start: 0.7025 (pp30) cc_final: 0.6562 (tm-30) REVERT: A 1162 GLU cc_start: 0.4868 (OUTLIER) cc_final: 0.3727 (mm-30) REVERT: A 1217 LEU cc_start: 0.8187 (tp) cc_final: 0.7501 (mt) REVERT: A 1237 MET cc_start: 0.7101 (mmp) cc_final: 0.6681 (mmt) REVERT: A 1468 ASP cc_start: 0.4461 (OUTLIER) cc_final: 0.4212 (p0) REVERT: D 149 PHE cc_start: 0.8318 (m-10) cc_final: 0.8004 (m-10) REVERT: D 268 THR cc_start: 0.8932 (t) cc_final: 0.8503 (m) REVERT: C 312 MET cc_start: 0.2578 (ptt) cc_final: 0.1763 (ttm) outliers start: 51 outliers final: 33 residues processed: 314 average time/residue: 0.1251 time to fit residues: 63.8593 Evaluate side-chains 281 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 724 SER Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 766 LYS Chi-restraints excluded: chain A residue 767 GLU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 1012 ILE Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1455 ILE Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 678 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.2980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN A 555 GLN A 740 ASN A1114 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 481 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1004 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.212537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.143827 restraints weight = 26026.523| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.54 r_work: 0.3265 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20840 Z= 0.121 Angle : 0.614 12.351 28249 Z= 0.301 Chirality : 0.044 0.417 3212 Planarity : 0.004 0.055 3559 Dihedral : 11.924 105.682 3273 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 1.81 % Allowed : 7.47 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2472 helix: 0.33 (0.15), residues: 1187 sheet: -0.16 (0.33), residues: 252 loop : -1.30 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 643 TYR 0.014 0.001 TYR D1068 PHE 0.020 0.001 PHE A 280 TRP 0.011 0.001 TRP D 185 HIS 0.003 0.000 HIS D1004 Details of bonding type rmsd covalent geometry : bond 0.00238 (20816) covalent geometry : angle 0.59491 (28187) SS BOND : bond 0.00278 ( 10) SS BOND : angle 1.27626 ( 20) hydrogen bonds : bond 0.05171 ( 899) hydrogen bonds : angle 4.93222 ( 2619) link_BETA1-4 : bond 0.00702 ( 8) link_BETA1-4 : angle 2.73357 ( 24) link_NAG-ASN : bond 0.01053 ( 6) link_NAG-ASN : angle 5.07499 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 248 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6758 (pt) REVERT: A 559 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7133 (p0) REVERT: A 636 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6694 (mt) REVERT: A 765 GLN cc_start: 0.2784 (OUTLIER) cc_final: 0.1880 (mt0) REVERT: A 932 VAL cc_start: 0.7614 (p) cc_final: 0.7371 (t) REVERT: A 960 MET cc_start: 0.7862 (mpp) cc_final: 0.6664 (ttp) REVERT: A 1161 LYS cc_start: 0.4495 (OUTLIER) cc_final: 0.4012 (tptp) REVERT: A 1211 MET cc_start: 0.6021 (tpt) cc_final: 0.5791 (tpt) REVERT: A 1456 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7045 (mp) REVERT: A 1464 MET cc_start: 0.4909 (OUTLIER) cc_final: 0.3911 (tpp) REVERT: D 328 LYS cc_start: 0.8612 (tttp) cc_final: 0.7917 (ttpp) REVERT: D 713 ASN cc_start: 0.7687 (t0) cc_final: 0.7213 (t0) REVERT: D 727 LYS cc_start: 0.6793 (ttpp) cc_final: 0.6400 (ttpp) REVERT: D 863 ASN cc_start: 0.7237 (t0) cc_final: 0.6825 (t0) REVERT: D 899 ASP cc_start: 0.8665 (t0) cc_final: 0.8460 (t70) REVERT: D 1044 CYS cc_start: 0.7901 (m) cc_final: 0.7682 (m) REVERT: C 351 GLU cc_start: 0.1100 (OUTLIER) cc_final: 0.0875 (pm20) outliers start: 40 outliers final: 21 residues processed: 279 average time/residue: 0.1236 time to fit residues: 55.9787 Evaluate side-chains 258 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 202 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 230 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 172 optimal weight: 0.0270 chunk 234 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN A1114 ASN A1218 ASN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.211522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139843 restraints weight = 26106.417| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.78 r_work: 0.3217 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20840 Z= 0.121 Angle : 0.584 11.699 28249 Z= 0.283 Chirality : 0.043 0.418 3212 Planarity : 0.004 0.055 3559 Dihedral : 10.342 104.133 3214 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 2.26 % Allowed : 9.37 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2472 helix: 0.47 (0.15), residues: 1205 sheet: -0.13 (0.32), residues: 248 loop : -1.29 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 334 TYR 0.015 0.001 TYR D1068 PHE 0.018 0.001 PHE A 392 TRP 0.010 0.001 TRP D 185 HIS 0.002 0.001 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00269 (20816) covalent geometry : angle 0.56445 (28187) SS BOND : bond 0.00264 ( 10) SS BOND : angle 1.32693 ( 20) hydrogen bonds : bond 0.04022 ( 899) hydrogen bonds : angle 4.48748 ( 2619) link_BETA1-4 : bond 0.00819 ( 8) link_BETA1-4 : angle 2.92866 ( 24) link_NAG-ASN : bond 0.00832 ( 6) link_NAG-ASN : angle 4.80134 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6825 (pt) REVERT: A 258 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7656 (mm-40) REVERT: A 363 MET cc_start: 0.8977 (mmm) cc_final: 0.8735 (mmt) REVERT: A 408 GLU cc_start: 0.6553 (mm-30) cc_final: 0.5620 (tt0) REVERT: A 636 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 765 GLN cc_start: 0.2864 (OUTLIER) cc_final: 0.1901 (mt0) REVERT: A 891 LEU cc_start: 0.6357 (mm) cc_final: 0.6125 (mm) REVERT: A 929 ILE cc_start: 0.7616 (mt) cc_final: 0.7349 (mt) REVERT: A 932 VAL cc_start: 0.7654 (p) cc_final: 0.7436 (t) REVERT: A 960 MET cc_start: 0.7882 (mpp) cc_final: 0.6672 (ttm) REVERT: A 963 VAL cc_start: 0.6752 (t) cc_final: 0.6428 (p) REVERT: A 1161 LYS cc_start: 0.4526 (OUTLIER) cc_final: 0.4014 (tptp) REVERT: A 1211 MET cc_start: 0.6257 (tpt) cc_final: 0.5940 (tpt) REVERT: A 1456 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 1464 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.3739 (tpp) REVERT: A 1468 ASP cc_start: 0.4054 (OUTLIER) cc_final: 0.3811 (p0) REVERT: D 94 SER cc_start: 0.8974 (t) cc_final: 0.8765 (m) REVERT: D 149 PHE cc_start: 0.8568 (m-10) cc_final: 0.8350 (m-10) REVERT: D 270 LYS cc_start: 0.8923 (tttp) cc_final: 0.8716 (ttpp) REVERT: D 328 LYS cc_start: 0.8643 (tttp) cc_final: 0.8135 (ttpp) REVERT: D 671 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7472 (mmtt) REVERT: D 713 ASN cc_start: 0.7861 (t0) cc_final: 0.7488 (t0) REVERT: D 727 LYS cc_start: 0.6954 (ttpp) cc_final: 0.6523 (ttpp) REVERT: D 1044 CYS cc_start: 0.8008 (m) cc_final: 0.7803 (m) REVERT: C 351 GLU cc_start: 0.1113 (OUTLIER) cc_final: 0.0908 (pm20) outliers start: 50 outliers final: 28 residues processed: 271 average time/residue: 0.1174 time to fit residues: 51.7789 Evaluate side-chains 263 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1114 ASN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 678 GLU Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 351 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 147 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN A1457 ASN A1466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.209976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.138602 restraints weight = 26162.339| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.02 r_work: 0.3245 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20840 Z= 0.130 Angle : 0.578 11.648 28249 Z= 0.281 Chirality : 0.043 0.430 3212 Planarity : 0.004 0.055 3559 Dihedral : 9.797 103.593 3208 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.49 % Allowed : 11.54 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.17), residues: 2472 helix: 0.52 (0.15), residues: 1209 sheet: -0.37 (0.32), residues: 261 loop : -1.29 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1013 TYR 0.016 0.001 TYR D1068 PHE 0.017 0.001 PHE A 280 TRP 0.010 0.001 TRP A1103 HIS 0.003 0.000 HIS D 885 Details of bonding type rmsd covalent geometry : bond 0.00300 (20816) covalent geometry : angle 0.55780 (28187) SS BOND : bond 0.00250 ( 10) SS BOND : angle 1.46792 ( 20) hydrogen bonds : bond 0.03694 ( 899) hydrogen bonds : angle 4.32405 ( 2619) link_BETA1-4 : bond 0.00845 ( 8) link_BETA1-4 : angle 3.01663 ( 24) link_NAG-ASN : bond 0.00757 ( 6) link_NAG-ASN : angle 4.69396 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6755 (pt) REVERT: A 197 TRP cc_start: 0.7842 (m100) cc_final: 0.7582 (m100) REVERT: A 408 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5544 (tt0) REVERT: A 636 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6767 (mt) REVERT: A 765 GLN cc_start: 0.2962 (OUTLIER) cc_final: 0.2000 (mt0) REVERT: A 891 LEU cc_start: 0.6604 (mm) cc_final: 0.6202 (mm) REVERT: A 929 ILE cc_start: 0.7521 (mt) cc_final: 0.7274 (mt) REVERT: A 960 MET cc_start: 0.7849 (mpp) cc_final: 0.6686 (ttt) REVERT: A 963 VAL cc_start: 0.6712 (t) cc_final: 0.6397 (p) REVERT: A 1211 MET cc_start: 0.6221 (tpt) cc_final: 0.6007 (tpt) REVERT: A 1456 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 1464 MET cc_start: 0.4534 (OUTLIER) cc_final: 0.3766 (tpp) REVERT: A 1468 ASP cc_start: 0.4009 (OUTLIER) cc_final: 0.3753 (p0) REVERT: D 94 SER cc_start: 0.8845 (t) cc_final: 0.8638 (m) REVERT: D 328 LYS cc_start: 0.8520 (tttp) cc_final: 0.8008 (ttpp) REVERT: D 713 ASN cc_start: 0.7761 (t0) cc_final: 0.7363 (t0) REVERT: D 727 LYS cc_start: 0.6897 (ttpp) cc_final: 0.6490 (ttpp) REVERT: D 1017 MET cc_start: 0.8182 (ttp) cc_final: 0.7932 (ttp) REVERT: D 1044 CYS cc_start: 0.7656 (m) cc_final: 0.7419 (m) outliers start: 55 outliers final: 28 residues processed: 280 average time/residue: 0.1199 time to fit residues: 54.5426 Evaluate side-chains 261 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 73 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 341 ASN A 359 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 ASN D 885 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.207589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.135717 restraints weight = 25857.279| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.78 r_work: 0.3128 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20840 Z= 0.185 Angle : 0.632 12.368 28249 Z= 0.309 Chirality : 0.046 0.488 3212 Planarity : 0.004 0.055 3559 Dihedral : 9.611 103.659 3205 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 2.67 % Allowed : 12.90 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2472 helix: 0.47 (0.15), residues: 1204 sheet: -0.19 (0.32), residues: 247 loop : -1.35 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 334 TYR 0.018 0.002 TYR D1068 PHE 0.023 0.002 PHE A 392 TRP 0.011 0.001 TRP A1103 HIS 0.004 0.001 HIS D 885 Details of bonding type rmsd covalent geometry : bond 0.00447 (20816) covalent geometry : angle 0.60996 (28187) SS BOND : bond 0.00537 ( 10) SS BOND : angle 2.07202 ( 20) hydrogen bonds : bond 0.03953 ( 899) hydrogen bonds : angle 4.36314 ( 2619) link_BETA1-4 : bond 0.00854 ( 8) link_BETA1-4 : angle 3.28644 ( 24) link_NAG-ASN : bond 0.00576 ( 6) link_NAG-ASN : angle 4.93215 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6710 (pt) REVERT: A 590 PHE cc_start: 0.7197 (t80) cc_final: 0.6938 (t80) REVERT: A 765 GLN cc_start: 0.3115 (OUTLIER) cc_final: 0.2081 (mt0) REVERT: A 891 LEU cc_start: 0.6764 (mm) cc_final: 0.6300 (mm) REVERT: A 929 ILE cc_start: 0.7516 (mt) cc_final: 0.7280 (mt) REVERT: A 937 LYS cc_start: 0.6487 (mtpt) cc_final: 0.5792 (tmtt) REVERT: A 960 MET cc_start: 0.7766 (mpp) cc_final: 0.7558 (mpp) REVERT: A 963 VAL cc_start: 0.6670 (t) cc_final: 0.6363 (p) REVERT: A 1025 LEU cc_start: 0.8359 (mt) cc_final: 0.8037 (mt) REVERT: A 1161 LYS cc_start: 0.4510 (OUTLIER) cc_final: 0.3989 (tptp) REVERT: A 1211 MET cc_start: 0.6422 (tpt) cc_final: 0.6189 (tpt) REVERT: A 1456 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7218 (mp) REVERT: A 1464 MET cc_start: 0.4507 (OUTLIER) cc_final: 0.3743 (tpp) REVERT: A 1468 ASP cc_start: 0.3956 (OUTLIER) cc_final: 0.3711 (p0) REVERT: A 1534 MET cc_start: 0.1908 (mmm) cc_final: 0.1683 (mmm) REVERT: D 328 LYS cc_start: 0.8500 (tttp) cc_final: 0.7971 (ttpp) REVERT: D 591 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8535 (pp) REVERT: D 655 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7057 (tp30) REVERT: D 713 ASN cc_start: 0.7797 (t0) cc_final: 0.7432 (t0) REVERT: D 727 LYS cc_start: 0.7165 (ttpp) cc_final: 0.6727 (ttpp) outliers start: 59 outliers final: 39 residues processed: 280 average time/residue: 0.1241 time to fit residues: 56.4722 Evaluate side-chains 275 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 39 optimal weight: 0.0000 chunk 82 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 222 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 247 optimal weight: 40.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN A1114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.209990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.139092 restraints weight = 25874.881| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.88 r_work: 0.3243 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20840 Z= 0.105 Angle : 0.565 11.432 28249 Z= 0.275 Chirality : 0.043 0.425 3212 Planarity : 0.004 0.053 3559 Dihedral : 9.072 103.138 3204 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.37 % Favored : 95.55 % Rotamer: Outliers : 2.22 % Allowed : 14.39 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2472 helix: 0.70 (0.15), residues: 1199 sheet: -0.23 (0.32), residues: 245 loop : -1.32 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1013 TYR 0.014 0.001 TYR D1068 PHE 0.033 0.001 PHE A1147 TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00232 (20816) covalent geometry : angle 0.54456 (28187) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.60966 ( 20) hydrogen bonds : bond 0.03289 ( 899) hydrogen bonds : angle 4.18904 ( 2619) link_BETA1-4 : bond 0.00839 ( 8) link_BETA1-4 : angle 2.95697 ( 24) link_NAG-ASN : bond 0.00764 ( 6) link_NAG-ASN : angle 4.65633 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6654 (pt) REVERT: A 197 TRP cc_start: 0.7785 (m100) cc_final: 0.7544 (m100) REVERT: A 408 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5488 (tt0) REVERT: A 765 GLN cc_start: 0.3149 (OUTLIER) cc_final: 0.2185 (mt0) REVERT: A 891 LEU cc_start: 0.6663 (mm) cc_final: 0.6173 (mm) REVERT: A 937 LYS cc_start: 0.6439 (mtpt) cc_final: 0.5842 (tmtt) REVERT: A 963 VAL cc_start: 0.6635 (t) cc_final: 0.6331 (p) REVERT: A 1010 VAL cc_start: 0.5418 (p) cc_final: 0.5218 (m) REVERT: A 1161 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3992 (tptp) REVERT: A 1234 ASN cc_start: 0.6832 (t0) cc_final: 0.6619 (t0) REVERT: A 1456 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 1464 MET cc_start: 0.4557 (OUTLIER) cc_final: 0.3802 (tpp) REVERT: D 328 LYS cc_start: 0.8525 (tttp) cc_final: 0.7985 (ttpp) REVERT: D 428 ASP cc_start: 0.8127 (m-30) cc_final: 0.7921 (m-30) REVERT: D 655 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7030 (tp30) REVERT: D 713 ASN cc_start: 0.7697 (t0) cc_final: 0.7335 (t0) REVERT: D 727 LYS cc_start: 0.6996 (ttpp) cc_final: 0.6564 (ttpp) REVERT: D 846 ASP cc_start: 0.7999 (t0) cc_final: 0.7664 (m-30) REVERT: D 1044 CYS cc_start: 0.7639 (m) cc_final: 0.7390 (m) outliers start: 49 outliers final: 31 residues processed: 282 average time/residue: 0.1238 time to fit residues: 56.5206 Evaluate side-chains 267 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 116 optimal weight: 0.0070 chunk 235 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 143 optimal weight: 0.2980 chunk 93 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.210133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138652 restraints weight = 25950.612| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.95 r_work: 0.3266 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20840 Z= 0.106 Angle : 0.561 11.416 28249 Z= 0.271 Chirality : 0.043 0.428 3212 Planarity : 0.004 0.054 3559 Dihedral : 8.765 102.377 3204 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.99 % Allowed : 15.57 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2472 helix: 0.81 (0.15), residues: 1197 sheet: -0.25 (0.32), residues: 246 loop : -1.30 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1013 TYR 0.014 0.001 TYR D1068 PHE 0.033 0.001 PHE A 590 TRP 0.010 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00236 (20816) covalent geometry : angle 0.54183 (28187) SS BOND : bond 0.00197 ( 10) SS BOND : angle 1.49642 ( 20) hydrogen bonds : bond 0.03185 ( 899) hydrogen bonds : angle 4.12827 ( 2619) link_BETA1-4 : bond 0.00852 ( 8) link_BETA1-4 : angle 2.95493 ( 24) link_NAG-ASN : bond 0.00744 ( 6) link_NAG-ASN : angle 4.56543 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 246 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6606 (pt) REVERT: A 197 TRP cc_start: 0.7731 (m100) cc_final: 0.7422 (m100) REVERT: A 408 GLU cc_start: 0.6336 (mm-30) cc_final: 0.5571 (tt0) REVERT: A 411 LYS cc_start: 0.7225 (tmmt) cc_final: 0.6307 (mmmt) REVERT: A 765 GLN cc_start: 0.3421 (OUTLIER) cc_final: 0.2452 (mt0) REVERT: A 891 LEU cc_start: 0.6544 (mm) cc_final: 0.6063 (mm) REVERT: A 937 LYS cc_start: 0.6258 (mtpt) cc_final: 0.5761 (tmtt) REVERT: A 963 VAL cc_start: 0.6660 (t) cc_final: 0.6351 (p) REVERT: A 1013 ARG cc_start: 0.7565 (tpt90) cc_final: 0.7337 (tpt-90) REVERT: A 1161 LYS cc_start: 0.4297 (OUTLIER) cc_final: 0.3812 (tptp) REVERT: A 1234 ASN cc_start: 0.7010 (t0) cc_final: 0.6749 (t0) REVERT: A 1456 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7358 (mp) REVERT: A 1464 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.3863 (tpp) REVERT: D 328 LYS cc_start: 0.8509 (tttp) cc_final: 0.7974 (ttpp) REVERT: D 655 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7009 (tp30) REVERT: D 713 ASN cc_start: 0.7676 (t0) cc_final: 0.7307 (t0) REVERT: D 727 LYS cc_start: 0.7001 (ttpp) cc_final: 0.6560 (ttpp) REVERT: D 846 ASP cc_start: 0.8018 (t0) cc_final: 0.7638 (m-30) REVERT: D 1044 CYS cc_start: 0.7664 (m) cc_final: 0.7414 (m) outliers start: 44 outliers final: 31 residues processed: 279 average time/residue: 0.1245 time to fit residues: 56.6353 Evaluate side-chains 273 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 GLN Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 0.0270 chunk 234 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.207566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138440 restraints weight = 25913.201| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.00 r_work: 0.3180 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20840 Z= 0.178 Angle : 0.627 12.230 28249 Z= 0.304 Chirality : 0.045 0.482 3212 Planarity : 0.004 0.054 3559 Dihedral : 8.780 101.531 3201 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 2.31 % Allowed : 15.34 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2472 helix: 0.67 (0.15), residues: 1207 sheet: -0.29 (0.32), residues: 246 loop : -1.39 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 619 TYR 0.017 0.002 TYR D1068 PHE 0.039 0.002 PHE A 392 TRP 0.011 0.001 TRP A1103 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00432 (20816) covalent geometry : angle 0.60557 (28187) SS BOND : bond 0.00288 ( 10) SS BOND : angle 1.99717 ( 20) hydrogen bonds : bond 0.03663 ( 899) hydrogen bonds : angle 4.23889 ( 2619) link_BETA1-4 : bond 0.00818 ( 8) link_BETA1-4 : angle 3.24595 ( 24) link_NAG-ASN : bond 0.00542 ( 6) link_NAG-ASN : angle 4.82433 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 140 CYS cc_start: 0.8396 (t) cc_final: 0.7741 (m) REVERT: A 178 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6738 (pt) REVERT: A 197 TRP cc_start: 0.7743 (m100) cc_final: 0.7384 (m100) REVERT: A 411 LYS cc_start: 0.7268 (tmmt) cc_final: 0.6420 (mmtt) REVERT: A 765 GLN cc_start: 0.3465 (OUTLIER) cc_final: 0.2434 (mt0) REVERT: A 891 LEU cc_start: 0.6736 (mm) cc_final: 0.6222 (mm) REVERT: A 937 LYS cc_start: 0.6443 (mtpt) cc_final: 0.5887 (tmtt) REVERT: A 963 VAL cc_start: 0.6753 (t) cc_final: 0.6415 (p) REVERT: A 1025 LEU cc_start: 0.8472 (mt) cc_final: 0.8149 (mt) REVERT: A 1161 LYS cc_start: 0.4553 (OUTLIER) cc_final: 0.3984 (tptp) REVERT: A 1234 ASN cc_start: 0.7190 (t0) cc_final: 0.6922 (t0) REVERT: A 1456 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7195 (mp) REVERT: A 1464 MET cc_start: 0.5080 (OUTLIER) cc_final: 0.4147 (tpp) REVERT: A 1468 ASP cc_start: 0.3894 (OUTLIER) cc_final: 0.3679 (p0) REVERT: D 328 LYS cc_start: 0.8627 (tttp) cc_final: 0.8114 (ttpp) REVERT: D 655 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7230 (tp30) REVERT: D 713 ASN cc_start: 0.7763 (t0) cc_final: 0.7527 (t0) REVERT: D 846 ASP cc_start: 0.8207 (t0) cc_final: 0.7810 (t0) outliers start: 51 outliers final: 30 residues processed: 268 average time/residue: 0.1208 time to fit residues: 52.8817 Evaluate side-chains 262 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain A residue 1468 ASP Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain D residue 1021 LYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 136 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 193 optimal weight: 0.3980 chunk 233 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN ** A1079 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.208982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137365 restraints weight = 25767.948| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.85 r_work: 0.3173 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20840 Z= 0.124 Angle : 0.593 11.655 28249 Z= 0.287 Chirality : 0.044 0.445 3212 Planarity : 0.004 0.053 3559 Dihedral : 8.503 101.183 3199 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 1.90 % Allowed : 16.06 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2472 helix: 0.75 (0.15), residues: 1204 sheet: -0.21 (0.32), residues: 241 loop : -1.38 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1013 TYR 0.016 0.001 TYR A 146 PHE 0.042 0.001 PHE A 392 TRP 0.012 0.001 TRP A1103 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00288 (20816) covalent geometry : angle 0.57264 (28187) SS BOND : bond 0.00222 ( 10) SS BOND : angle 1.72402 ( 20) hydrogen bonds : bond 0.03320 ( 899) hydrogen bonds : angle 4.18902 ( 2619) link_BETA1-4 : bond 0.00828 ( 8) link_BETA1-4 : angle 3.05777 ( 24) link_NAG-ASN : bond 0.00633 ( 6) link_NAG-ASN : angle 4.70170 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 140 CYS cc_start: 0.8209 (t) cc_final: 0.7550 (m) REVERT: A 178 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6677 (pt) REVERT: A 197 TRP cc_start: 0.7717 (m100) cc_final: 0.7398 (m100) REVERT: A 334 ARG cc_start: 0.8339 (ptt90) cc_final: 0.8089 (ptt90) REVERT: A 398 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 408 GLU cc_start: 0.6475 (mm-30) cc_final: 0.5601 (tt0) REVERT: A 411 LYS cc_start: 0.7261 (tmmt) cc_final: 0.6457 (mmtt) REVERT: A 765 GLN cc_start: 0.3417 (OUTLIER) cc_final: 0.2412 (mt0) REVERT: A 891 LEU cc_start: 0.6586 (mm) cc_final: 0.6096 (mm) REVERT: A 937 LYS cc_start: 0.6596 (mtpt) cc_final: 0.5979 (tmtt) REVERT: A 963 VAL cc_start: 0.6758 (t) cc_final: 0.6438 (p) REVERT: A 1025 LEU cc_start: 0.8364 (mt) cc_final: 0.8060 (mt) REVERT: A 1161 LYS cc_start: 0.4495 (OUTLIER) cc_final: 0.4000 (tptp) REVERT: A 1234 ASN cc_start: 0.7046 (t0) cc_final: 0.6827 (t0) REVERT: A 1464 MET cc_start: 0.4927 (OUTLIER) cc_final: 0.4077 (tpp) REVERT: D 149 PHE cc_start: 0.8613 (m-10) cc_final: 0.8227 (m-10) REVERT: D 328 LYS cc_start: 0.8481 (tttp) cc_final: 0.7960 (ttpp) REVERT: D 655 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7109 (tp30) REVERT: D 671 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7193 (mmtt) REVERT: D 713 ASN cc_start: 0.7581 (t0) cc_final: 0.7350 (t0) REVERT: D 846 ASP cc_start: 0.8031 (t0) cc_final: 0.7634 (t0) REVERT: C 196 MET cc_start: 0.3354 (ppp) cc_final: 0.2994 (mmm) outliers start: 42 outliers final: 30 residues processed: 263 average time/residue: 0.1210 time to fit residues: 51.6667 Evaluate side-chains 259 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain D residue 822 ILE Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 GLN D 998 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.209059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139337 restraints weight = 26091.801| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.44 r_work: 0.3276 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20840 Z= 0.113 Angle : 0.580 11.445 28249 Z= 0.280 Chirality : 0.043 0.435 3212 Planarity : 0.004 0.053 3559 Dihedral : 8.195 99.923 3199 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 16.24 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.17), residues: 2472 helix: 0.87 (0.15), residues: 1198 sheet: -0.19 (0.33), residues: 241 loop : -1.32 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1013 TYR 0.015 0.001 TYR A 146 PHE 0.039 0.001 PHE A 392 TRP 0.011 0.001 TRP A1103 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00260 (20816) covalent geometry : angle 0.56046 (28187) SS BOND : bond 0.00209 ( 10) SS BOND : angle 1.52973 ( 20) hydrogen bonds : bond 0.03131 ( 899) hydrogen bonds : angle 4.14274 ( 2619) link_BETA1-4 : bond 0.00821 ( 8) link_BETA1-4 : angle 3.02400 ( 24) link_NAG-ASN : bond 0.00670 ( 6) link_NAG-ASN : angle 4.58212 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 140 CYS cc_start: 0.8330 (t) cc_final: 0.7632 (m) REVERT: A 178 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6688 (pt) REVERT: A 197 TRP cc_start: 0.7791 (m100) cc_final: 0.7498 (m100) REVERT: A 334 ARG cc_start: 0.8241 (ptt90) cc_final: 0.7969 (ptt90) REVERT: A 398 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 408 GLU cc_start: 0.6413 (mm-30) cc_final: 0.5691 (tt0) REVERT: A 411 LYS cc_start: 0.7182 (tmmt) cc_final: 0.6428 (mmtt) REVERT: A 765 GLN cc_start: 0.3700 (OUTLIER) cc_final: 0.2519 (mt0) REVERT: A 891 LEU cc_start: 0.6507 (mm) cc_final: 0.6011 (mm) REVERT: A 937 LYS cc_start: 0.6363 (mtpt) cc_final: 0.5828 (tmtt) REVERT: A 963 VAL cc_start: 0.6719 (t) cc_final: 0.6398 (p) REVERT: A 1142 PHE cc_start: 0.8792 (m-10) cc_final: 0.8553 (m-80) REVERT: A 1161 LYS cc_start: 0.4364 (OUTLIER) cc_final: 0.3870 (tptp) REVERT: A 1234 ASN cc_start: 0.6988 (t0) cc_final: 0.6782 (t0) REVERT: A 1464 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4192 (tpp) REVERT: D 149 PHE cc_start: 0.8626 (m-10) cc_final: 0.8228 (m-10) REVERT: D 328 LYS cc_start: 0.8616 (tttp) cc_final: 0.8089 (ttpp) REVERT: D 345 LEU cc_start: 0.7991 (mt) cc_final: 0.7335 (pp) REVERT: D 655 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7280 (tp30) REVERT: D 671 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7181 (mmtt) REVERT: D 713 ASN cc_start: 0.7680 (t0) cc_final: 0.7470 (t0) REVERT: D 846 ASP cc_start: 0.8136 (t0) cc_final: 0.7735 (t0) REVERT: D 1044 CYS cc_start: 0.8121 (m) cc_final: 0.7901 (m) REVERT: C 196 MET cc_start: 0.3045 (ppp) cc_final: 0.2645 (mmm) outliers start: 34 outliers final: 25 residues processed: 254 average time/residue: 0.1258 time to fit residues: 51.4707 Evaluate side-chains 255 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1161 LYS Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1462 VAL Chi-restraints excluded: chain A residue 1463 ILE Chi-restraints excluded: chain A residue 1464 MET Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1467 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 762 SER Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 223 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 754 ASN ** A1114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.210425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138336 restraints weight = 26072.990| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.74 r_work: 0.3235 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20840 Z= 0.108 Angle : 0.573 11.092 28249 Z= 0.277 Chirality : 0.043 0.421 3212 Planarity : 0.004 0.053 3559 Dihedral : 7.990 98.468 3197 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 16.47 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2472 helix: 1.01 (0.15), residues: 1187 sheet: -0.20 (0.33), residues: 241 loop : -1.30 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 499 TYR 0.015 0.001 TYR D 867 PHE 0.041 0.001 PHE A 392 TRP 0.011 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00244 (20816) covalent geometry : angle 0.55409 (28187) SS BOND : bond 0.00199 ( 10) SS BOND : angle 1.44211 ( 20) hydrogen bonds : bond 0.03028 ( 899) hydrogen bonds : angle 4.09764 ( 2619) link_BETA1-4 : bond 0.00802 ( 8) link_BETA1-4 : angle 2.98512 ( 24) link_NAG-ASN : bond 0.00676 ( 6) link_NAG-ASN : angle 4.46489 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6955.22 seconds wall clock time: 118 minutes 53.20 seconds (7133.20 seconds total)