Starting phenix.real_space_refine on Sun Aug 24 17:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we7_37473/08_2025/8we7_37473.map" } resolution = 3.2 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= 0.002 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 114 5.16 5 C 13548 2.51 5 N 3488 2.21 5 O 3862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21014 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1251, 10101 Classifications: {'peptide': 1251} Link IDs: {'PTRANS': 39, 'TRANS': 1211} 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: {'PTRANS': 19, 'TRANS': 304} Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 56} Chain: "E" 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: "F" 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: "G" 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: "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: "I" 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {' CA': 1, 'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 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: 3.49, per 1000 atoms: 0.17 Number of scatterers: 21014 At special positions: 0 Unit cell: (168.214, 177.126, 188.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 114 16.00 O 3862 8.00 N 3488 7.00 C 13548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " 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=2.03 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 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 58 " 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 E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " NAG G 3 " " NAG G 3 " - " NAG G 4 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2304 " - " ASN A1436 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 184 " " NAG F 1 " - " ASN D 348 " " NAG G 1 " - " ASN D 468 " " NAG H 1 " - " ASN D 613 " " NAG I 1 " - " ASN D 895 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 704.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 20 sheets defined 50.5% alpha, 8.0% 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 123 through 144 Processing helix chain 'A' and resid 147 through 151 removed outlier: 4.073A pdb=" N ASP A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 151 " --> pdb=" O PRO A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 153 through 182 removed outlier: 3.558A pdb=" N GLU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 217 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 251 through 266 removed outlier: 5.104A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 removed outlier: 4.350A pdb=" N VAL A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.510A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 375 " --> pdb=" O TRP A 371 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.684A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 417 removed outlier: 3.572A pdb=" N LEU A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 447 removed outlier: 3.764A pdb=" N LYS A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.630A pdb=" N ALA A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 543 removed outlier: 3.627A pdb=" N PHE A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 579 removed outlier: 4.154A pdb=" N ASN A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.209A pdb=" N SER A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.903A pdb=" N LYS A 609 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 624 through 630 removed outlier: 3.707A pdb=" N PHE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 630 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 647 removed outlier: 3.653A pdb=" N LEU A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 673 Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 707 through 719 removed outlier: 3.714A pdb=" N VAL A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 712 " --> pdb=" O TRP A 708 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 728 removed outlier: 3.644A pdb=" N LEU A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 725 through 728' Processing helix chain 'A' and resid 729 through 767 removed outlier: 3.956A pdb=" N PHE A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 752 " --> pdb=" O PHE A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 775 removed outlier: 4.153A pdb=" N GLU A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 783 removed outlier: 3.528A pdb=" N ARG A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 removed outlier: 4.138A pdb=" N PHE A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 953 Processing helix chain 'A' and resid 958 through 973 removed outlier: 3.684A pdb=" N SER A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1004 removed outlier: 3.922A pdb=" N ILE A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 992 " --> pdb=" O TYR A 988 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A1000 " --> pdb=" O VAL A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1019 through 1022 Processing helix chain 'A' and resid 1023 through 1028 removed outlier: 3.586A pdb=" N ARG A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A1028 " --> pdb=" O ARG A1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1023 through 1028' Processing helix chain 'A' and resid 1034 through 1069 removed outlier: 5.277A pdb=" N ASN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE A1052 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A1069 " --> pdb=" O CYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1133 Processing helix chain 'A' and resid 1136 through 1145 removed outlier: 3.531A pdb=" N LEU A1140 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1173 removed outlier: 4.179A pdb=" N PHE A1166 " --> pdb=" O ILE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1192 removed outlier: 3.666A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1197 removed outlier: 3.651A pdb=" N TYR A1197 " --> pdb=" O GLU A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1215 Processing helix chain 'A' and resid 1227 through 1237 Processing helix chain 'A' and resid 1240 through 1257 removed outlier: 3.629A pdb=" N LEU A1244 " --> pdb=" O TYR A1240 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1249 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A1252 " --> pdb=" O LEU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1298 removed outlier: 3.699A pdb=" N ILE A1269 " --> pdb=" O CYS A1265 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A1291 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A1292 " --> pdb=" O LEU A1288 " (cutoff:3.500A) Proline residue: A1295 - end of helix Processing helix chain 'A' and resid 1301 through 1322 removed outlier: 4.066A pdb=" N ILE A1316 " --> pdb=" O ILE A1312 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1377 Processing helix chain 'A' and resid 1379 through 1390 removed outlier: 3.611A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1408 Processing helix chain 'A' and resid 1411 through 1430 removed outlier: 4.111A pdb=" N ILE A1415 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N MET A1417 " --> pdb=" O LEU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1462 Processing helix chain 'A' and resid 1465 through 1473 Processing helix chain 'A' and resid 1499 through 1526 removed outlier: 3.943A pdb=" N TYR A1508 " --> pdb=" O PHE A1504 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1526 " --> pdb=" O VAL A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1531 Processing helix chain 'A' and resid 1538 through 1551 removed outlier: 3.507A pdb=" N LEU A1542 " --> pdb=" O GLY A1538 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 removed outlier: 4.355A pdb=" N THR A1567 " --> pdb=" O LEU A1563 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A1570 " --> pdb=" O VAL A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1594 Processing helix chain 'A' and resid 1605 through 1618 Processing helix chain 'A' and resid 1625 through 1633 Processing helix chain 'A' and resid 1645 through 1649 removed outlier: 3.550A pdb=" N LEU A1648 " --> pdb=" O SER A1645 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1649 " --> pdb=" O MET A1646 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1645 through 1649' Processing helix chain 'D' and resid 28 through 53 removed outlier: 4.568A pdb=" N THR D 32 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 64 removed outlier: 4.105A pdb=" N ASP D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 3.781A pdb=" N LEU D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 3.665A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 3.768A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 241 through 249 removed outlier: 4.134A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 removed outlier: 3.618A pdb=" N VAL D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.547A pdb=" N LYS D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.636A pdb=" N LEU D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 371 through 376 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.746A pdb=" N GLN D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.823A pdb=" N VAL D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 436 Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.729A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 removed outlier: 3.578A pdb=" N GLU D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 644 Processing helix chain 'D' and resid 675 through 688 removed outlier: 3.596A pdb=" N PHE D 679 " --> pdb=" O ASN D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 717 removed outlier: 4.247A pdb=" N VAL D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 723 removed outlier: 4.384A pdb=" N GLN D 723 " --> pdb=" O TYR D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.791A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 770 removed outlier: 3.717A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 770 " --> pdb=" O ARG D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 827 removed outlier: 3.777A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 827 " --> pdb=" O GLU D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 889 removed outlier: 3.740A pdb=" N MET D 883 " --> pdb=" O ASP D 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1024 Processing helix chain 'D' and resid 1042 through 1047 Processing helix chain 'C' and resid 39 through 53 removed outlier: 3.914A pdb=" N GLU C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU C 53 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 128 removed outlier: 4.072A pdb=" N GLU C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 removed outlier: 4.300A pdb=" N GLN C 133 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C 134 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 3.694A pdb=" N MET C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS C 198 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 removed outlier: 4.025A pdb=" N HIS C 206 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.548A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.842A pdb=" N ARG C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 314 removed outlier: 4.449A pdb=" N LYS C 313 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.940A pdb=" N TYR C 322 " --> pdb=" O GLN C 318 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP C 323 " --> pdb=" O MET C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 359 removed outlier: 4.147A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 298 removed outlier: 3.925A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 333 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1076 through 1078 Processing sheet with id=AA3, first strand: chain 'A' and resid 1092 through 1096 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 122 through 123 removed outlier: 6.160A pdb=" N VAL D 122 " --> pdb=" O GLN D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.304A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 125 through 126 removed outlier: 6.304A pdb=" N TYR D 125 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 486 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.502A pdb=" N ILE D 159 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.512A pdb=" N VAL D 308 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.281A pdb=" N ILE D 256 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE D 294 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL D 258 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE D 358 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE D 387 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 360 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 389 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR D 362 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL D 384 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.587A pdb=" N ALA D 514 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 515 " --> pdb=" O SER D 618 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 588 through 593 removed outlier: 3.506A pdb=" N ARG D 605 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 601 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 658 through 659 removed outlier: 4.446A pdb=" N VAL D 743 " --> pdb=" O TYR D 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 732 through 735 removed outlier: 3.528A pdb=" N PHE D 733 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 774 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 859 through 861 removed outlier: 6.812A pdb=" N LEU D 859 " --> pdb=" O ASP D 854 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASP D 854 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET D 861 " --> pdb=" O ILE D 852 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 892 through 894 Processing sheet with id=AB8, first strand: chain 'D' and resid 897 through 904 removed outlier: 4.613A pdb=" N GLN D 901 " --> pdb=" O CYS D 974 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N CYS D 974 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL D 903 " --> pdb=" O GLN D 972 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN D 972 " --> pdb=" O VAL D 903 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AC1, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.550A pdb=" N VAL C 335 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 34 through 37 856 hydrogen bonds defined for protein. 2454 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: 2.89 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3418 1.31 - 1.44: 5742 1.44 - 1.57: 12133 1.57 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 21465 Sorted by residual: bond pdb=" CA TYR A 527 " pdb=" C TYR A 527 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.24e-02 6.50e+03 4.28e+01 bond pdb=" CA GLU D 182 " pdb=" C GLU D 182 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" C1 NAG G 3 " pdb=" O5 NAG G 3 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C THR D 212 " pdb=" O THR D 212 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.33e-02 5.65e+03 1.38e+01 bond pdb=" CA ARG C 178 " pdb=" C ARG C 178 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.26e-02 6.30e+03 1.18e+01 ... (remaining 21460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 28368 2.10 - 4.20: 598 4.20 - 6.31: 89 6.31 - 8.41: 22 8.41 - 10.51: 7 Bond angle restraints: 29084 Sorted by residual: angle pdb=" C ARG C 178 " pdb=" N PRO C 179 " pdb=" CA PRO C 179 " ideal model delta sigma weight residual 119.78 112.22 7.56 1.03e+00 9.43e-01 5.38e+01 angle pdb=" N ASN A 904 " pdb=" CA ASN A 904 " pdb=" C ASN A 904 " ideal model delta sigma weight residual 111.40 103.31 8.09 1.22e+00 6.72e-01 4.40e+01 angle pdb=" N SER A 636 " pdb=" CA SER A 636 " pdb=" C SER A 636 " ideal model delta sigma weight residual 114.62 107.19 7.43 1.14e+00 7.69e-01 4.25e+01 angle pdb=" C TYR A 527 " pdb=" CA TYR A 527 " pdb=" CB TYR A 527 " ideal model delta sigma weight residual 110.96 100.92 10.04 1.54e+00 4.22e-01 4.25e+01 angle pdb=" N ARG A 626 " pdb=" CA ARG A 626 " pdb=" C ARG A 626 " ideal model delta sigma weight residual 111.36 104.88 6.48 1.09e+00 8.42e-01 3.53e+01 ... (remaining 29079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 11829 24.48 - 48.97: 1158 48.97 - 73.45: 165 73.45 - 97.93: 43 97.93 - 122.42: 10 Dihedral angle restraints: 13205 sinusoidal: 5644 harmonic: 7561 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 -177.66 -89.34 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 17 " pdb=" SG CYS B 17 " pdb=" SG CYS B 39 " pdb=" CB CYS B 39 " ideal model delta sinusoidal sigma weight residual -86.00 -19.15 -66.85 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS D 404 " pdb=" SG CYS D 404 " pdb=" SG CYS D1071 " pdb=" CB CYS D1071 " ideal model delta sinusoidal sigma weight residual 93.00 153.88 -60.88 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 13202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2780 0.056 - 0.112: 488 0.112 - 0.168: 52 0.168 - 0.224: 2 0.224 - 0.280: 6 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN D 348 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 613 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 895 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3325 not shown) Planarity restraints: 3674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 78 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO C 79 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 921 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 922 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 922 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 922 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 744 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO D 745 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 745 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 745 " 0.047 5.00e-02 4.00e+02 ... (remaining 3671 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1755 2.74 - 3.28: 21697 3.28 - 3.82: 33768 3.82 - 4.36: 40581 4.36 - 4.90: 68191 Nonbonded interactions: 165992 Sorted by model distance: nonbonded pdb=" O ASN A1012 " pdb=" N VAL A1014 " model vdw 2.198 3.120 nonbonded pdb=" OG SER D 388 " pdb=" NH1 ARG D 396 " model vdw 2.215 3.120 nonbonded pdb=" O LEU D 506 " pdb=" OH TYR D 759 " model vdw 2.216 3.040 nonbonded pdb=" O ALA C 55 " pdb=" N HIS C 57 " model vdw 2.217 3.120 nonbonded pdb=" NH1 ARG D 884 " pdb=" O ARG D1029 " model vdw 2.218 3.120 ... (remaining 165987 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 'F' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.083 21495 Z= 0.202 Angle : 0.765 11.515 29160 Z= 0.426 Chirality : 0.044 0.280 3328 Planarity : 0.006 0.113 3666 Dihedral : 18.919 122.416 8269 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 1.02 % Allowed : 9.92 % Favored : 89.06 % Rotamer: Outliers : 0.74 % Allowed : 29.47 % Favored : 69.79 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -2.42 (0.16), residues: 2551 helix: -0.53 (0.16), residues: 1109 sheet: -1.91 (0.33), residues: 231 loop : -2.63 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1383 TYR 0.039 0.001 TYR A1503 PHE 0.036 0.001 PHE D 780 TRP 0.019 0.001 TRP A 336 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00370 (21465) covalent geometry : angle 0.74734 (29084) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.96188 ( 28) hydrogen bonds : bond 0.21273 ( 842) hydrogen bonds : angle 7.42663 ( 2454) link_BETA1-4 : bond 0.01125 ( 8) link_BETA1-4 : angle 3.62195 ( 24) link_NAG-ASN : bond 0.00931 ( 8) link_NAG-ASN : angle 4.38882 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 300 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TRP cc_start: 0.7469 (m100) cc_final: 0.7182 (m100) REVERT: A 1119 ASP cc_start: 0.8285 (m-30) cc_final: 0.7859 (m-30) REVERT: A 1191 GLU cc_start: 0.6456 (pp20) cc_final: 0.6206 (tp30) REVERT: A 1382 MET cc_start: 0.7137 (mmt) cc_final: 0.6889 (mmp) REVERT: A 1499 PHE cc_start: 0.8273 (t80) cc_final: 0.8000 (t80) REVERT: D 182 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: D 259 ASP cc_start: 0.8938 (t0) cc_final: 0.8629 (t0) REVERT: C 230 ASN cc_start: 0.5102 (OUTLIER) cc_final: 0.4666 (m110) REVERT: C 320 MET cc_start: 0.7554 (mpp) cc_final: 0.7329 (mpp) outliers start: 17 outliers final: 5 residues processed: 311 average time/residue: 0.1205 time to fit residues: 59.1567 Evaluate side-chains 282 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 275 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 304 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 429 GLN A 646 ASN A 746 ASN A 755 ASN A 931 HIS D 111 HIS D 374 ASN D 718 ASN C 275 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.194695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140022 restraints weight = 30465.985| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.76 r_work: 0.3467 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21495 Z= 0.138 Angle : 0.689 13.383 29160 Z= 0.346 Chirality : 0.043 0.291 3328 Planarity : 0.005 0.106 3666 Dihedral : 9.386 106.970 3276 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.78 % Allowed : 9.60 % Favored : 89.61 % Rotamer: Outliers : 3.45 % Allowed : 26.15 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -2.27 (0.16), residues: 2551 helix: -0.39 (0.15), residues: 1142 sheet: -1.71 (0.33), residues: 235 loop : -2.63 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 620 TYR 0.023 0.001 TYR C 356 PHE 0.031 0.001 PHE D 780 TRP 0.016 0.001 TRP A 634 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00298 (21465) covalent geometry : angle 0.67288 (29084) SS BOND : bond 0.00222 ( 14) SS BOND : angle 0.97104 ( 28) hydrogen bonds : bond 0.04578 ( 842) hydrogen bonds : angle 5.07153 ( 2454) link_BETA1-4 : bond 0.00823 ( 8) link_BETA1-4 : angle 2.88609 ( 24) link_NAG-ASN : bond 0.00898 ( 8) link_NAG-ASN : angle 4.28582 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ARG cc_start: 0.6627 (mtm-85) cc_final: 0.6334 (mtm-85) REVERT: A 958 TYR cc_start: 0.7456 (m-80) cc_final: 0.7170 (m-80) REVERT: A 963 ILE cc_start: 0.6582 (tp) cc_final: 0.6303 (mm) REVERT: A 1002 ILE cc_start: 0.6918 (mt) cc_final: 0.6631 (tp) REVERT: A 1119 ASP cc_start: 0.8422 (m-30) cc_final: 0.8109 (m-30) REVERT: A 1125 MET cc_start: 0.8142 (mmm) cc_final: 0.7764 (mtp) REVERT: A 1379 PHE cc_start: 0.5213 (m-80) cc_final: 0.4944 (m-80) REVERT: A 1382 MET cc_start: 0.7491 (mmt) cc_final: 0.7254 (mmp) REVERT: A 1532 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6950 (ttt180) REVERT: A 1605 MET cc_start: 0.3772 (OUTLIER) cc_final: 0.3273 (tpt) REVERT: D 181 ASN cc_start: 0.8374 (m-40) cc_final: 0.8004 (m110) REVERT: D 246 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8565 (tt0) REVERT: D 374 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8700 (m-40) REVERT: D 396 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8434 (mtt-85) REVERT: D 599 TYR cc_start: 0.8540 (m-80) cc_final: 0.7813 (m-80) REVERT: D 782 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7382 (mtpp) REVERT: D 1035 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7740 (mm-30) REVERT: C 177 MET cc_start: 0.4243 (mmm) cc_final: 0.3245 (tpp) REVERT: C 197 GLN cc_start: 0.5591 (OUTLIER) cc_final: 0.5350 (mm-40) REVERT: C 320 MET cc_start: 0.7749 (mpp) cc_final: 0.7232 (mpp) REVERT: B 5 ILE cc_start: 0.0429 (OUTLIER) cc_final: 0.0023 (pt) outliers start: 79 outliers final: 35 residues processed: 370 average time/residue: 0.1202 time to fit residues: 71.2958 Evaluate side-chains 318 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1532 ARG Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 198 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 145 optimal weight: 0.0980 chunk 163 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 931 HIS D1062 ASN C 49 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.195702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140569 restraints weight = 31153.025| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.55 r_work: 0.3488 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21495 Z= 0.129 Angle : 0.654 13.290 29160 Z= 0.327 Chirality : 0.042 0.275 3328 Planarity : 0.005 0.106 3666 Dihedral : 8.267 103.361 3268 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.06 % Favored : 90.24 % Rotamer: Outliers : 3.54 % Allowed : 26.93 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -2.07 (0.16), residues: 2551 helix: -0.22 (0.15), residues: 1138 sheet: -1.59 (0.34), residues: 228 loop : -2.54 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 396 TYR 0.018 0.001 TYR C 356 PHE 0.020 0.001 PHE A 208 TRP 0.012 0.001 TRP A 634 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00293 (21465) covalent geometry : angle 0.63769 (29084) SS BOND : bond 0.00575 ( 14) SS BOND : angle 1.07851 ( 28) hydrogen bonds : bond 0.04039 ( 842) hydrogen bonds : angle 4.78196 ( 2454) link_BETA1-4 : bond 0.01034 ( 8) link_BETA1-4 : angle 3.06836 ( 24) link_NAG-ASN : bond 0.00800 ( 8) link_NAG-ASN : angle 4.05326 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 307 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4487 (OUTLIER) cc_final: 0.3699 (m-10) REVERT: A 528 TRP cc_start: 0.6652 (t60) cc_final: 0.6308 (m-10) REVERT: A 590 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6453 (mtm-85) REVERT: A 771 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5677 (mp0) REVERT: A 963 ILE cc_start: 0.6629 (tp) cc_final: 0.6368 (mm) REVERT: A 1002 ILE cc_start: 0.6926 (mt) cc_final: 0.6647 (tp) REVERT: A 1125 MET cc_start: 0.8130 (mmm) cc_final: 0.7848 (mtp) REVERT: A 1191 GLU cc_start: 0.6973 (pp20) cc_final: 0.6767 (tp30) REVERT: A 1286 MET cc_start: 0.7680 (mmm) cc_final: 0.7321 (mmt) REVERT: A 1379 PHE cc_start: 0.5451 (m-80) cc_final: 0.5165 (m-80) REVERT: A 1382 MET cc_start: 0.7509 (mmt) cc_final: 0.7288 (mmp) REVERT: A 1513 PHE cc_start: 0.8353 (t80) cc_final: 0.8103 (t80) REVERT: A 1605 MET cc_start: 0.3732 (OUTLIER) cc_final: 0.3253 (ttt) REVERT: D 181 ASN cc_start: 0.8402 (m-40) cc_final: 0.7991 (m110) REVERT: D 246 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: D 396 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8335 (mtt-85) REVERT: D 599 TYR cc_start: 0.8471 (m-80) cc_final: 0.7690 (m-80) REVERT: D 671 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8049 (mmmt) REVERT: D 714 GLU cc_start: 0.8847 (tp30) cc_final: 0.8540 (tp30) REVERT: D 1035 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7769 (mm-30) REVERT: C 177 MET cc_start: 0.4236 (mmm) cc_final: 0.3079 (tpt) REVERT: C 209 ASP cc_start: 0.3663 (t0) cc_final: 0.2844 (m-30) REVERT: C 320 MET cc_start: 0.7781 (mpp) cc_final: 0.7255 (mpp) REVERT: C 347 GLU cc_start: 0.8051 (tp30) cc_final: 0.7736 (mt-10) REVERT: B 5 ILE cc_start: 0.0469 (OUTLIER) cc_final: 0.0067 (pt) outliers start: 81 outliers final: 48 residues processed: 365 average time/residue: 0.1258 time to fit residues: 73.5146 Evaluate side-chains 323 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1266 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 814 ILE Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 322 TYR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 178 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 225 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 755 ASN A1630 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.194913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142940 restraints weight = 31318.232| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.21 r_work: 0.3471 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21495 Z= 0.139 Angle : 0.649 12.956 29160 Z= 0.324 Chirality : 0.042 0.295 3328 Planarity : 0.005 0.105 3666 Dihedral : 7.817 99.154 3268 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.29 % Favored : 90.16 % Rotamer: Outliers : 4.02 % Allowed : 26.45 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.96 (0.16), residues: 2551 helix: -0.08 (0.16), residues: 1139 sheet: -1.56 (0.33), residues: 228 loop : -2.53 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 620 TYR 0.017 0.001 TYR D 161 PHE 0.021 0.001 PHE A 208 TRP 0.010 0.001 TRP A 634 HIS 0.005 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00324 (21465) covalent geometry : angle 0.63242 (29084) SS BOND : bond 0.00196 ( 14) SS BOND : angle 1.38264 ( 28) hydrogen bonds : bond 0.03752 ( 842) hydrogen bonds : angle 4.61152 ( 2454) link_BETA1-4 : bond 0.01044 ( 8) link_BETA1-4 : angle 3.16418 ( 24) link_NAG-ASN : bond 0.00684 ( 8) link_NAG-ASN : angle 3.84584 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 299 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4473 (OUTLIER) cc_final: 0.3877 (m-10) REVERT: A 128 ILE cc_start: 0.7982 (mm) cc_final: 0.7577 (mt) REVERT: A 325 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6045 (mm-40) REVERT: A 528 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.6379 (m-10) REVERT: A 590 ARG cc_start: 0.6732 (mtm-85) cc_final: 0.6478 (mtm-85) REVERT: A 771 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5573 (mp0) REVERT: A 963 ILE cc_start: 0.6644 (tp) cc_final: 0.6388 (mm) REVERT: A 1084 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7073 (pt0) REVERT: A 1102 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (t70) REVERT: A 1125 MET cc_start: 0.8177 (mmm) cc_final: 0.7910 (mtp) REVERT: A 1191 GLU cc_start: 0.7151 (pp20) cc_final: 0.6885 (tp30) REVERT: A 1382 MET cc_start: 0.7611 (mmt) cc_final: 0.7390 (mmp) REVERT: A 1516 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 1605 MET cc_start: 0.3707 (OUTLIER) cc_final: 0.3213 (tpt) REVERT: D 181 ASN cc_start: 0.8459 (m-40) cc_final: 0.8100 (m-40) REVERT: D 246 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: D 396 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8366 (mtt-85) REVERT: D 599 TYR cc_start: 0.8450 (m-80) cc_final: 0.7715 (m-80) REVERT: C 177 MET cc_start: 0.4538 (mmm) cc_final: 0.3871 (mmm) REVERT: C 209 ASP cc_start: 0.3457 (t0) cc_final: 0.2613 (m-30) REVERT: C 347 GLU cc_start: 0.8085 (tp30) cc_final: 0.7756 (mt-10) REVERT: B 5 ILE cc_start: 0.0583 (OUTLIER) cc_final: 0.0131 (pt) outliers start: 92 outliers final: 49 residues processed: 366 average time/residue: 0.1211 time to fit residues: 70.8855 Evaluate side-chains 343 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1102 ASP Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 190 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 177 optimal weight: 0.4980 chunk 230 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 28 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.195232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144289 restraints weight = 31183.742| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.37 r_work: 0.3472 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21495 Z= 0.125 Angle : 0.643 12.546 29160 Z= 0.317 Chirality : 0.042 0.300 3328 Planarity : 0.005 0.104 3666 Dihedral : 7.470 95.240 3266 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.90 % Favored : 90.55 % Rotamer: Outliers : 4.11 % Allowed : 26.89 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.80 (0.16), residues: 2551 helix: 0.10 (0.16), residues: 1134 sheet: -1.54 (0.33), residues: 228 loop : -2.48 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 499 TYR 0.022 0.001 TYR A1529 PHE 0.022 0.001 PHE A 208 TRP 0.009 0.001 TRP D 185 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00287 (21465) covalent geometry : angle 0.62699 (29084) SS BOND : bond 0.00448 ( 14) SS BOND : angle 1.31206 ( 28) hydrogen bonds : bond 0.03522 ( 842) hydrogen bonds : angle 4.47539 ( 2454) link_BETA1-4 : bond 0.00946 ( 8) link_BETA1-4 : angle 3.17151 ( 24) link_NAG-ASN : bond 0.00697 ( 8) link_NAG-ASN : angle 3.65058 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 306 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4361 (OUTLIER) cc_final: 0.3767 (m-10) REVERT: A 325 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.5985 (mm-40) REVERT: A 762 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4932 (tp) REVERT: A 771 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: A 963 ILE cc_start: 0.6794 (tp) cc_final: 0.6526 (mm) REVERT: A 1191 GLU cc_start: 0.7037 (pp20) cc_final: 0.6791 (tp30) REVERT: A 1206 GLN cc_start: 0.6789 (mp10) cc_final: 0.6418 (mp10) REVERT: A 1382 MET cc_start: 0.7596 (mmt) cc_final: 0.7395 (mmp) REVERT: A 1516 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 1605 MET cc_start: 0.3717 (OUTLIER) cc_final: 0.3232 (tpt) REVERT: D 161 TYR cc_start: 0.8160 (m-10) cc_final: 0.7950 (m-80) REVERT: D 246 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: D 396 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8233 (mtt-85) REVERT: D 506 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8193 (mt) REVERT: D 599 TYR cc_start: 0.8467 (m-80) cc_final: 0.7756 (m-80) REVERT: D 1010 ASN cc_start: 0.8476 (m-40) cc_final: 0.8269 (t0) REVERT: C 200 LEU cc_start: 0.6670 (mt) cc_final: 0.6253 (tp) REVERT: C 209 ASP cc_start: 0.3114 (t0) cc_final: 0.2391 (m-30) REVERT: C 320 MET cc_start: 0.7971 (mpp) cc_final: 0.7472 (mpp) REVERT: C 347 GLU cc_start: 0.8086 (tp30) cc_final: 0.7770 (mt-10) REVERT: B 5 ILE cc_start: 0.0633 (OUTLIER) cc_final: 0.0166 (pt) outliers start: 94 outliers final: 64 residues processed: 375 average time/residue: 0.1201 time to fit residues: 72.5550 Evaluate side-chains 352 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 888 ASN Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 16 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 140 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN D1062 ASN ** C 340 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 = 0.4290 r_free = 0.4290 target = 0.195443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142999 restraints weight = 31065.314| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.09 r_work: 0.3497 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21495 Z= 0.124 Angle : 0.642 12.214 29160 Z= 0.316 Chirality : 0.042 0.308 3328 Planarity : 0.004 0.077 3666 Dihedral : 7.177 90.078 3266 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.02 % Favored : 90.44 % Rotamer: Outliers : 3.76 % Allowed : 27.20 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.72 (0.16), residues: 2551 helix: 0.18 (0.16), residues: 1136 sheet: -1.49 (0.33), residues: 228 loop : -2.45 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 246 TYR 0.019 0.001 TYR D 629 PHE 0.024 0.001 PHE A 208 TRP 0.010 0.001 TRP D 185 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00282 (21465) covalent geometry : angle 0.62697 (29084) SS BOND : bond 0.00313 ( 14) SS BOND : angle 1.37769 ( 28) hydrogen bonds : bond 0.03408 ( 842) hydrogen bonds : angle 4.40162 ( 2454) link_BETA1-4 : bond 0.00956 ( 8) link_BETA1-4 : angle 3.23638 ( 24) link_NAG-ASN : bond 0.00677 ( 8) link_NAG-ASN : angle 3.52011 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 292 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4375 (OUTLIER) cc_final: 0.3790 (m-10) REVERT: A 128 ILE cc_start: 0.7940 (mm) cc_final: 0.7511 (mt) REVERT: A 325 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.5975 (mm-40) REVERT: A 536 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 762 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.4910 (tp) REVERT: A 771 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5498 (mp0) REVERT: A 963 ILE cc_start: 0.6767 (tp) cc_final: 0.6510 (mm) REVERT: A 1125 MET cc_start: 0.7757 (mtp) cc_final: 0.7550 (mtp) REVERT: A 1206 GLN cc_start: 0.6772 (mp10) cc_final: 0.6411 (mp10) REVERT: A 1516 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 1605 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3406 (ttt) REVERT: D 396 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8251 (mtt-85) REVERT: D 599 TYR cc_start: 0.8420 (m-80) cc_final: 0.7717 (m-80) REVERT: D 671 LYS cc_start: 0.8565 (mmmt) cc_final: 0.8352 (mmmt) REVERT: D 875 PHE cc_start: 0.8988 (t80) cc_final: 0.8746 (t80) REVERT: D 1010 ASN cc_start: 0.8420 (m-40) cc_final: 0.8186 (t0) REVERT: C 209 ASP cc_start: 0.3103 (t0) cc_final: 0.2503 (m-30) REVERT: C 265 GLN cc_start: 0.4972 (OUTLIER) cc_final: 0.4287 (mt0) REVERT: C 320 MET cc_start: 0.7933 (mpp) cc_final: 0.7369 (mpp) REVERT: C 347 GLU cc_start: 0.8033 (tp30) cc_final: 0.7721 (mt-10) REVERT: B 5 ILE cc_start: 0.0655 (OUTLIER) cc_final: 0.0200 (pt) outliers start: 86 outliers final: 60 residues processed: 354 average time/residue: 0.1216 time to fit residues: 69.5819 Evaluate side-chains 342 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 125 optimal weight: 0.1980 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN A 931 HIS ** C 340 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 = 0.4304 r_free = 0.4304 target = 0.194734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.141107 restraints weight = 30635.356| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.79 r_work: 0.3478 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21495 Z= 0.113 Angle : 0.633 11.934 29160 Z= 0.311 Chirality : 0.042 0.306 3328 Planarity : 0.004 0.078 3666 Dihedral : 6.841 84.265 3266 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.43 % Favored : 91.02 % Rotamer: Outliers : 3.67 % Allowed : 27.46 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.58 (0.16), residues: 2551 helix: 0.28 (0.16), residues: 1142 sheet: -1.35 (0.34), residues: 222 loop : -2.39 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 511 TYR 0.015 0.001 TYR D 629 PHE 0.022 0.001 PHE C 201 TRP 0.019 0.001 TRP A 509 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00250 (21465) covalent geometry : angle 0.61837 (29084) SS BOND : bond 0.00277 ( 14) SS BOND : angle 1.25091 ( 28) hydrogen bonds : bond 0.03231 ( 842) hydrogen bonds : angle 4.33401 ( 2454) link_BETA1-4 : bond 0.00972 ( 8) link_BETA1-4 : angle 3.26185 ( 24) link_NAG-ASN : bond 0.00721 ( 8) link_NAG-ASN : angle 3.41483 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4345 (OUTLIER) cc_final: 0.3872 (m-10) REVERT: A 128 ILE cc_start: 0.7873 (mm) cc_final: 0.7436 (mt) REVERT: A 195 TRP cc_start: 0.7596 (m100) cc_final: 0.7310 (m100) REVERT: A 325 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.5870 (mm-40) REVERT: A 536 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7176 (mp) REVERT: A 561 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7058 (mmtm) REVERT: A 762 LEU cc_start: 0.5229 (OUTLIER) cc_final: 0.4812 (tp) REVERT: A 771 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5441 (mp0) REVERT: A 963 ILE cc_start: 0.6774 (tp) cc_final: 0.6528 (mm) REVERT: A 1084 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6833 (pt0) REVERT: A 1206 GLN cc_start: 0.6800 (mp10) cc_final: 0.6428 (mp10) REVERT: A 1516 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 1605 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.3408 (ttt) REVERT: D 396 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8226 (mtt-85) REVERT: D 506 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8082 (mt) REVERT: D 599 TYR cc_start: 0.8455 (m-80) cc_final: 0.7681 (m-80) REVERT: D 768 LEU cc_start: 0.8653 (mt) cc_final: 0.7961 (mt) REVERT: D 1010 ASN cc_start: 0.8453 (m-40) cc_final: 0.8183 (t0) REVERT: C 200 LEU cc_start: 0.6648 (mt) cc_final: 0.6281 (tp) REVERT: C 209 ASP cc_start: 0.3127 (t0) cc_final: 0.2461 (m-30) REVERT: C 265 GLN cc_start: 0.4746 (OUTLIER) cc_final: 0.4108 (mt0) REVERT: C 320 MET cc_start: 0.7874 (mpp) cc_final: 0.7567 (mmm) REVERT: C 343 GLU cc_start: 0.8373 (pt0) cc_final: 0.7241 (mm-30) REVERT: C 347 GLU cc_start: 0.8008 (tp30) cc_final: 0.7693 (mt-10) REVERT: B 5 ILE cc_start: 0.0493 (OUTLIER) cc_final: 0.0074 (pt) outliers start: 84 outliers final: 56 residues processed: 356 average time/residue: 0.1206 time to fit residues: 69.6000 Evaluate side-chains 339 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 270 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1277 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1449 THR Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 48 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN D 311 ASN D 314 ASN D1062 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.194378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139576 restraints weight = 31114.747| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.23 r_work: 0.3456 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21495 Z= 0.166 Angle : 0.675 11.925 29160 Z= 0.332 Chirality : 0.043 0.325 3328 Planarity : 0.004 0.076 3666 Dihedral : 6.769 75.815 3266 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.53 % Favored : 89.96 % Rotamer: Outliers : 3.67 % Allowed : 27.46 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.62 (0.16), residues: 2551 helix: 0.21 (0.16), residues: 1158 sheet: -1.49 (0.33), residues: 228 loop : -2.36 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.015 0.001 TYR D 629 PHE 0.019 0.001 PHE A1545 TRP 0.014 0.001 TRP A 509 HIS 0.004 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00395 (21465) covalent geometry : angle 0.66023 (29084) SS BOND : bond 0.00306 ( 14) SS BOND : angle 1.42055 ( 28) hydrogen bonds : bond 0.03586 ( 842) hydrogen bonds : angle 4.45335 ( 2454) link_BETA1-4 : bond 0.01008 ( 8) link_BETA1-4 : angle 3.44100 ( 24) link_NAG-ASN : bond 0.00555 ( 8) link_NAG-ASN : angle 3.42942 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 277 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4323 (OUTLIER) cc_final: 0.3824 (m-10) REVERT: A 195 TRP cc_start: 0.7636 (m100) cc_final: 0.7320 (m100) REVERT: A 325 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.5930 (mm-40) REVERT: A 762 LEU cc_start: 0.5329 (OUTLIER) cc_final: 0.4936 (tp) REVERT: A 963 ILE cc_start: 0.6621 (tp) cc_final: 0.6362 (mm) REVERT: A 1084 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: A 1151 ASP cc_start: 0.8104 (m-30) cc_final: 0.7491 (t0) REVERT: A 1206 GLN cc_start: 0.6790 (mp10) cc_final: 0.6424 (mp10) REVERT: A 1516 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 1529 TYR cc_start: 0.8431 (t80) cc_final: 0.8166 (t80) REVERT: A 1605 MET cc_start: 0.3814 (OUTLIER) cc_final: 0.3403 (ttt) REVERT: D 43 ASP cc_start: 0.8387 (p0) cc_final: 0.8135 (p0) REVERT: D 246 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: D 396 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8355 (mtt-85) REVERT: D 506 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8145 (mt) REVERT: D 599 TYR cc_start: 0.8456 (m-80) cc_final: 0.7758 (m-80) REVERT: D 671 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8309 (tptt) REVERT: D 1010 ASN cc_start: 0.8439 (m-40) cc_final: 0.8206 (t0) REVERT: C 200 LEU cc_start: 0.6593 (mt) cc_final: 0.6187 (tp) REVERT: C 209 ASP cc_start: 0.3076 (t0) cc_final: 0.2471 (m-30) REVERT: C 265 GLN cc_start: 0.4937 (OUTLIER) cc_final: 0.4286 (mt0) REVERT: C 320 MET cc_start: 0.7878 (mpp) cc_final: 0.7390 (mpp) REVERT: C 343 GLU cc_start: 0.8432 (pt0) cc_final: 0.7410 (mm-30) REVERT: B 5 ILE cc_start: 0.0677 (OUTLIER) cc_final: 0.0223 (pt) outliers start: 84 outliers final: 56 residues processed: 338 average time/residue: 0.1217 time to fit residues: 66.4972 Evaluate side-chains 334 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 267 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1084 GLN Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1172 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 123 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN D 311 ASN ** C 340 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 = 0.4325 r_free = 0.4325 target = 0.194920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140083 restraints weight = 30472.905| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.81 r_work: 0.3486 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21495 Z= 0.132 Angle : 0.654 11.874 29160 Z= 0.321 Chirality : 0.042 0.315 3328 Planarity : 0.004 0.077 3666 Dihedral : 6.551 68.887 3266 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.98 % Favored : 90.51 % Rotamer: Outliers : 3.54 % Allowed : 27.63 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.52 (0.16), residues: 2551 helix: 0.34 (0.16), residues: 1143 sheet: -1.39 (0.33), residues: 224 loop : -2.35 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 499 TYR 0.014 0.001 TYR D 629 PHE 0.023 0.001 PHE D 780 TRP 0.014 0.001 TRP A 509 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00306 (21465) covalent geometry : angle 0.63901 (29084) SS BOND : bond 0.00289 ( 14) SS BOND : angle 1.27797 ( 28) hydrogen bonds : bond 0.03368 ( 842) hydrogen bonds : angle 4.37205 ( 2454) link_BETA1-4 : bond 0.00949 ( 8) link_BETA1-4 : angle 3.45337 ( 24) link_NAG-ASN : bond 0.00657 ( 8) link_NAG-ASN : angle 3.38882 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4352 (OUTLIER) cc_final: 0.3871 (m-10) REVERT: A 128 ILE cc_start: 0.7863 (mm) cc_final: 0.7417 (mt) REVERT: A 325 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.5849 (mm-40) REVERT: A 561 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7039 (mmtm) REVERT: A 762 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4753 (tp) REVERT: A 963 ILE cc_start: 0.6682 (tp) cc_final: 0.6435 (mm) REVERT: A 1151 ASP cc_start: 0.8143 (m-30) cc_final: 0.7434 (t0) REVERT: A 1206 GLN cc_start: 0.6820 (mp10) cc_final: 0.6458 (mp10) REVERT: A 1516 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 1529 TYR cc_start: 0.8389 (t80) cc_final: 0.8184 (t80) REVERT: A 1605 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3532 (ttt) REVERT: D 158 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (pm20) REVERT: D 396 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8292 (mtt-85) REVERT: D 499 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8271 (mtm-85) REVERT: D 506 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8113 (mt) REVERT: D 599 TYR cc_start: 0.8492 (m-80) cc_final: 0.7723 (m-80) REVERT: D 671 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8384 (tptt) REVERT: D 1010 ASN cc_start: 0.8445 (m-40) cc_final: 0.8181 (t0) REVERT: C 209 ASP cc_start: 0.3119 (t0) cc_final: 0.2530 (m-30) REVERT: C 265 GLN cc_start: 0.4718 (OUTLIER) cc_final: 0.4101 (mt0) REVERT: C 320 MET cc_start: 0.7851 (mpp) cc_final: 0.7424 (mpp) REVERT: C 343 GLU cc_start: 0.8376 (pt0) cc_final: 0.7316 (mm-30) REVERT: C 347 GLU cc_start: 0.8005 (tp30) cc_final: 0.7652 (mt-10) REVERT: B 5 ILE cc_start: 0.0570 (OUTLIER) cc_final: 0.0144 (pt) outliers start: 81 outliers final: 62 residues processed: 344 average time/residue: 0.1210 time to fit residues: 67.2662 Evaluate side-chains 343 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 278 GLU Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 109 optimal weight: 30.0000 chunk 182 optimal weight: 0.8980 chunk 145 optimal weight: 0.0070 chunk 191 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1062 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.196423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143081 restraints weight = 30666.888| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.75 r_work: 0.3514 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 21495 Z= 0.121 Angle : 0.654 11.967 29160 Z= 0.319 Chirality : 0.042 0.315 3328 Planarity : 0.004 0.077 3666 Dihedral : 6.297 60.407 3266 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.02 % Favored : 90.51 % Rotamer: Outliers : 2.97 % Allowed : 28.38 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.43 (0.16), residues: 2551 helix: 0.41 (0.16), residues: 1143 sheet: -1.33 (0.34), residues: 222 loop : -2.29 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1383 TYR 0.014 0.001 TYR D 629 PHE 0.031 0.001 PHE D 780 TRP 0.012 0.001 TRP A 195 HIS 0.003 0.000 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00282 (21465) covalent geometry : angle 0.63838 (29084) SS BOND : bond 0.00275 ( 14) SS BOND : angle 1.25127 ( 28) hydrogen bonds : bond 0.03234 ( 842) hydrogen bonds : angle 4.32966 ( 2454) link_BETA1-4 : bond 0.00944 ( 8) link_BETA1-4 : angle 3.46167 ( 24) link_NAG-ASN : bond 0.00657 ( 8) link_NAG-ASN : angle 3.35834 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 287 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4466 (OUTLIER) cc_final: 0.3959 (m-10) REVERT: A 128 ILE cc_start: 0.7882 (mm) cc_final: 0.7426 (mt) REVERT: A 195 TRP cc_start: 0.7588 (m100) cc_final: 0.7360 (m100) REVERT: A 325 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.5837 (mm-40) REVERT: A 707 ASP cc_start: 0.8446 (m-30) cc_final: 0.8109 (m-30) REVERT: A 762 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4709 (tp) REVERT: A 1151 ASP cc_start: 0.8127 (m-30) cc_final: 0.7440 (t0) REVERT: A 1206 GLN cc_start: 0.6809 (mp10) cc_final: 0.6464 (mp10) REVERT: A 1516 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.7988 (mp) REVERT: A 1605 MET cc_start: 0.3875 (OUTLIER) cc_final: 0.3520 (ttt) REVERT: D 396 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8286 (mtt-85) REVERT: D 499 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8325 (mtm-85) REVERT: D 506 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (mt) REVERT: D 599 TYR cc_start: 0.8452 (m-80) cc_final: 0.7751 (m-80) REVERT: D 671 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8370 (tptt) REVERT: D 1010 ASN cc_start: 0.8397 (m-40) cc_final: 0.8138 (t0) REVERT: C 200 LEU cc_start: 0.6652 (mt) cc_final: 0.6228 (tp) REVERT: C 209 ASP cc_start: 0.3053 (t0) cc_final: 0.2480 (m-30) REVERT: C 265 GLN cc_start: 0.4671 (OUTLIER) cc_final: 0.4049 (mt0) REVERT: C 320 MET cc_start: 0.7867 (mpp) cc_final: 0.7447 (mpp) REVERT: C 343 GLU cc_start: 0.8316 (pt0) cc_final: 0.7316 (mm-30) REVERT: C 347 GLU cc_start: 0.8033 (tp30) cc_final: 0.7689 (mt-10) REVERT: B 5 ILE cc_start: 0.0680 (OUTLIER) cc_final: 0.0187 (pt) outliers start: 68 outliers final: 54 residues processed: 334 average time/residue: 0.1260 time to fit residues: 67.1357 Evaluate side-chains 335 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 272 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 720 TRP Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 812 VAL Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 1017 MET Chi-restraints excluded: chain D residue 1028 THR Chi-restraints excluded: chain D residue 1065 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 167 HIS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 253 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 198 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 226 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.193671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139099 restraints weight = 30689.837| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.88 r_work: 0.3468 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 21495 Z= 0.164 Angle : 0.682 11.812 29160 Z= 0.333 Chirality : 0.043 0.327 3328 Planarity : 0.004 0.076 3666 Dihedral : 6.363 59.798 3266 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.41 % Favored : 90.12 % Rotamer: Outliers : 3.02 % Allowed : 28.29 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 aren not related in a simple way. whole: -1.51 (0.16), residues: 2551 helix: 0.33 (0.16), residues: 1154 sheet: -1.34 (0.34), residues: 224 loop : -2.36 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 873 TYR 0.019 0.001 TYR D 64 PHE 0.032 0.001 PHE D 780 TRP 0.014 0.001 TRP A 509 HIS 0.004 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00389 (21465) covalent geometry : angle 0.66681 (29084) SS BOND : bond 0.00331 ( 14) SS BOND : angle 1.36405 ( 28) hydrogen bonds : bond 0.03555 ( 842) hydrogen bonds : angle 4.40430 ( 2454) link_BETA1-4 : bond 0.00934 ( 8) link_BETA1-4 : angle 3.49155 ( 24) link_NAG-ASN : bond 0.00535 ( 8) link_NAG-ASN : angle 3.40570 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7684.20 seconds wall clock time: 131 minutes 10.91 seconds (7870.91 seconds total)