Starting phenix.real_space_refine on Wed Jun 18 18:00:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we7_37473/06_2025/8we7_37473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we7_37473/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8we7_37473/06_2025/8we7_37473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we7_37473/06_2025/8we7_37473.map" model { file = "/net/cci-nas-00/data/ceres_data/8we7_37473/06_2025/8we7_37473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we7_37473/06_2025/8we7_37473.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.56, per 1000 atoms: 0.60 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: 5.08 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.58 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: 10.59 Time building geometry restraints manager: 6.13 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.700 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (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 TRP 0.019 0.001 TRP A 336 HIS 0.004 0.001 HIS C 94 PHE 0.036 0.001 PHE D 780 TYR 0.039 0.001 TYR A1503 ARG 0.006 0.000 ARG A1383 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 8) link_NAG-ASN : angle 4.38882 ( 24) link_BETA1-4 : bond 0.01125 ( 8) link_BETA1-4 : angle 3.62195 ( 24) hydrogen bonds : bond 0.21273 ( 842) hydrogen bonds : angle 7.42663 ( 2454) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.96188 ( 28) covalent geometry : bond 0.00370 (21465) covalent geometry : angle 0.74734 (29084) *********************** 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 : 2.295 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: 0.3323 time to fit residues: 162.4282 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 : 2.293 ------------------------------------------------------------------------------- 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 217 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 931 HIS D 111 HIS D 374 ASN D 718 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133064 restraints weight = 30493.082| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.95 r_work: 0.3386 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 21495 Z= 0.226 Angle : 0.753 13.855 29160 Z= 0.378 Chirality : 0.046 0.328 3328 Planarity : 0.006 0.106 3666 Dihedral : 9.508 102.327 3276 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.74 % Allowed : 10.51 % Favored : 88.75 % Rotamer: Outliers : 4.29 % Allowed : 26.59 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2551 helix: -0.48 (0.15), residues: 1124 sheet: -1.80 (0.35), residues: 209 loop : -2.69 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 634 HIS 0.005 0.001 HIS C 348 PHE 0.038 0.002 PHE D 780 TYR 0.026 0.002 TYR D 161 ARG 0.004 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 8) link_NAG-ASN : angle 4.51432 ( 24) link_BETA1-4 : bond 0.01120 ( 8) link_BETA1-4 : angle 3.14393 ( 24) hydrogen bonds : bond 0.04919 ( 842) hydrogen bonds : angle 5.21799 ( 2454) SS BOND : bond 0.00324 ( 14) SS BOND : angle 1.24021 ( 28) covalent geometry : bond 0.00536 (21465) covalent geometry : angle 0.73638 (29084) *********************** 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 385 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 287 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4296 (OUTLIER) cc_final: 0.3747 (m-10) REVERT: A 353 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7965 (ttp) REVERT: A 380 TRP cc_start: 0.8389 (p-90) cc_final: 0.8136 (p-90) REVERT: A 437 TYR cc_start: 0.4642 (m-10) cc_final: 0.4423 (m-10) REVERT: A 590 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.6425 (mtm-85) REVERT: A 958 TYR cc_start: 0.7509 (m-80) cc_final: 0.7203 (m-80) REVERT: A 1125 MET cc_start: 0.8165 (mmm) cc_final: 0.7850 (mtp) REVERT: A 1382 MET cc_start: 0.7669 (mmt) cc_final: 0.7355 (mmp) REVERT: A 1513 PHE cc_start: 0.8389 (t80) cc_final: 0.8072 (t80) REVERT: A 1605 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3280 (tpt) REVERT: D 181 ASN cc_start: 0.8600 (m-40) cc_final: 0.8242 (m110) REVERT: D 246 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8680 (tt0) REVERT: D 259 ASP cc_start: 0.8731 (t0) cc_final: 0.8514 (t0) REVERT: D 599 TYR cc_start: 0.8612 (m-80) cc_final: 0.7886 (m-80) REVERT: D 757 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7915 (tp30) REVERT: D 1035 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7793 (mm-30) REVERT: C 177 MET cc_start: 0.4268 (mmm) cc_final: 0.3336 (tpp) REVERT: C 197 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5409 (mm-40) REVERT: C 320 MET cc_start: 0.7785 (mpp) cc_final: 0.7271 (mpp) REVERT: B 5 ILE cc_start: 0.0538 (OUTLIER) cc_final: 0.0121 (pt) outliers start: 98 outliers final: 51 residues processed: 358 average time/residue: 0.3166 time to fit residues: 181.4635 Evaluate side-chains 327 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 TRP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 564 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 691 ASN Chi-restraints excluded: chain A residue 729 VAL 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 970 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1172 ILE 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 1537 LEU Chi-restraints excluded: chain A residue 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 100 LEU 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 463 THR 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 757 GLU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS 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 167 HIS 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 222 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 232 optimal weight: 40.0000 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN C 49 GLN C 275 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 = 0.4264 r_free = 0.4264 target = 0.192372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136907 restraints weight = 31079.427| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.33 r_work: 0.3439 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 21495 Z= 0.210 Angle : 0.708 13.184 29160 Z= 0.356 Chirality : 0.044 0.304 3328 Planarity : 0.005 0.106 3666 Dihedral : 8.583 97.317 3268 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.19 % Favored : 89.14 % Rotamer: Outliers : 4.50 % Allowed : 26.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2551 helix: -0.45 (0.15), residues: 1140 sheet: -1.84 (0.35), residues: 208 loop : -2.65 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 634 HIS 0.007 0.001 HIS C 314 PHE 0.026 0.002 PHE D 780 TYR 0.020 0.002 TYR D 161 ARG 0.003 0.000 ARG C 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 8) link_NAG-ASN : angle 4.28377 ( 24) link_BETA1-4 : bond 0.01066 ( 8) link_BETA1-4 : angle 3.34407 ( 24) hydrogen bonds : bond 0.04576 ( 842) hydrogen bonds : angle 5.00592 ( 2454) SS BOND : bond 0.00387 ( 14) SS BOND : angle 1.15546 ( 28) covalent geometry : bond 0.00496 (21465) covalent geometry : angle 0.69104 (29084) *********************** 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 386 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 283 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TRP cc_start: 0.4259 (OUTLIER) cc_final: 0.3685 (m-10) REVERT: A 128 ILE cc_start: 0.7958 (mm) cc_final: 0.7565 (mt) REVERT: A 325 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6000 (mm-40) REVERT: A 353 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: A 590 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6533 (mtm-85) REVERT: A 963 ILE cc_start: 0.6663 (tp) cc_final: 0.6373 (mm) REVERT: A 1084 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: A 1125 MET cc_start: 0.8195 (mmm) cc_final: 0.7953 (mtp) REVERT: A 1382 MET cc_start: 0.7700 (mmt) cc_final: 0.7344 (mmp) REVERT: A 1513 PHE cc_start: 0.8427 (t80) cc_final: 0.8198 (t80) REVERT: A 1605 MET cc_start: 0.3783 (OUTLIER) cc_final: 0.3222 (tpt) REVERT: D 246 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: D 259 ASP cc_start: 0.8691 (t0) cc_final: 0.8483 (t0) REVERT: D 396 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8543 (mtt-85) REVERT: D 599 TYR cc_start: 0.8589 (m-80) cc_final: 0.7873 (m-80) REVERT: D 1035 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7744 (mm-30) REVERT: C 177 MET cc_start: 0.4118 (mmm) cc_final: 0.3418 (mmm) REVERT: C 320 MET cc_start: 0.7848 (mpp) cc_final: 0.7313 (mpp) REVERT: B 5 ILE cc_start: 0.0632 (OUTLIER) cc_final: 0.0198 (pt) outliers start: 103 outliers final: 63 residues processed: 357 average time/residue: 0.3026 time to fit residues: 174.0083 Evaluate side-chains 331 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 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 353 MET Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 529 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 666 SER Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 729 VAL 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 1046 ILE Chi-restraints excluded: chain A residue 1054 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 1284 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1309 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 1588 CYS Chi-restraints excluded: chain A residue 1605 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 192 VAL 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 331 THR 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 661 ILE 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 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 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 204 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 241 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 229 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A1630 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 = 0.4281 r_free = 0.4281 target = 0.194914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140146 restraints weight = 31313.850| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.14 r_work: 0.3485 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21495 Z= 0.125 Angle : 0.649 12.535 29160 Z= 0.324 Chirality : 0.042 0.296 3328 Planarity : 0.005 0.105 3666 Dihedral : 7.873 92.193 3268 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.45 % Favored : 89.96 % Rotamer: Outliers : 4.20 % Allowed : 27.50 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2551 helix: -0.19 (0.15), residues: 1148 sheet: -1.65 (0.32), residues: 239 loop : -2.59 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.003 0.001 HIS C 348 PHE 0.029 0.001 PHE D 780 TYR 0.017 0.001 TYR D 161 ARG 0.010 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 8) link_NAG-ASN : angle 3.88221 ( 24) link_BETA1-4 : bond 0.00987 ( 8) link_BETA1-4 : angle 3.26319 ( 24) hydrogen bonds : bond 0.03708 ( 842) hydrogen bonds : angle 4.67436 ( 2454) SS BOND : bond 0.00267 ( 14) SS BOND : angle 0.85838 ( 28) covalent geometry : bond 0.00281 (21465) covalent geometry : angle 0.63231 (29084) *********************** 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 408 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 312 time to evaluate : 2.423 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: 0.4376 (OUTLIER) cc_final: 0.3882 (m-10) REVERT: A 528 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: A 548 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7742 (mt0) REVERT: A 771 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5622 (mp0) REVERT: A 963 ILE cc_start: 0.6614 (tp) cc_final: 0.6336 (mm) REVERT: A 1191 GLU cc_start: 0.7034 (pp20) cc_final: 0.6787 (tp30) REVERT: A 1256 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8789 (tt) REVERT: A 1382 MET cc_start: 0.7620 (mmt) cc_final: 0.7383 (mmp) REVERT: A 1513 PHE cc_start: 0.8483 (t80) cc_final: 0.8254 (t80) REVERT: A 1516 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8099 (mp) REVERT: A 1605 MET cc_start: 0.3798 (OUTLIER) cc_final: 0.3256 (tpt) REVERT: D 599 TYR cc_start: 0.8510 (m-80) cc_final: 0.7853 (m-80) REVERT: D 714 GLU cc_start: 0.8828 (tp30) cc_final: 0.8500 (tp30) REVERT: D 852 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (tt) REVERT: D 1010 ASN cc_start: 0.8507 (m-40) cc_final: 0.8307 (t0) REVERT: C 177 MET cc_start: 0.4534 (mmm) cc_final: 0.3883 (mmm) REVERT: C 209 ASP cc_start: 0.3636 (t0) cc_final: 0.2701 (m-30) REVERT: B 5 ILE cc_start: 0.0754 (OUTLIER) cc_final: 0.0277 (pt) outliers start: 96 outliers final: 54 residues processed: 375 average time/residue: 0.3142 time to fit residues: 187.7228 Evaluate side-chains 340 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 362 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 GLN 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 777 LYS 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 1150 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1256 LEU 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 1441 ILE 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 1605 MET Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 100 LEU 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 648 LEU Chi-restraints excluded: chain D residue 667 CYS Chi-restraints excluded: chain D residue 675 ASN 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 852 ILE 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 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 204 LEU 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 Chi-restraints excluded: chain B residue 53 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 108 optimal weight: 0.0270 chunk 53 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 chunk 211 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN A 755 ASN A 931 HIS C 47 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 = 0.4308 r_free = 0.4308 target = 0.194629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141106 restraints weight = 30568.024| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.97 r_work: 0.3435 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1853 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= 0.119 Angle : 0.642 12.049 29160 Z= 0.320 Chirality : 0.042 0.311 3328 Planarity : 0.005 0.104 3666 Dihedral : 7.461 85.896 3266 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.21 % Favored : 90.20 % Rotamer: Outliers : 4.33 % Allowed : 27.59 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2551 helix: -0.03 (0.15), residues: 1146 sheet: -1.57 (0.32), residues: 239 loop : -2.52 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.005 0.001 HIS C 314 PHE 0.030 0.001 PHE D 780 TYR 0.020 0.001 TYR D 629 ARG 0.005 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 8) link_NAG-ASN : angle 3.65640 ( 24) link_BETA1-4 : bond 0.01050 ( 8) link_BETA1-4 : angle 3.31836 ( 24) hydrogen bonds : bond 0.03538 ( 842) hydrogen bonds : angle 4.52819 ( 2454) SS BOND : bond 0.00213 ( 14) SS BOND : angle 0.85438 ( 28) covalent geometry : bond 0.00268 (21465) covalent geometry : angle 0.62619 (29084) *********************** 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 391 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 292 time to evaluate : 2.194 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: symmetry clash REVERT: A 123 TRP cc_start: 0.4358 (OUTLIER) cc_final: 0.3911 (m-10) REVERT: A 128 ILE cc_start: 0.7884 (mm) cc_final: 0.7493 (mt) REVERT: A 325 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6072 (mm-40) REVERT: A 526 PHE cc_start: 0.5198 (t80) cc_final: 0.4818 (t80) REVERT: A 528 TRP cc_start: 0.6588 (OUTLIER) cc_final: 0.6377 (m-10) REVERT: A 762 LEU cc_start: 0.5158 (OUTLIER) cc_final: 0.4794 (tp) REVERT: A 963 ILE cc_start: 0.6591 (tp) cc_final: 0.6335 (mm) REVERT: A 1084 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 1125 MET cc_start: 0.7780 (mtp) cc_final: 0.7569 (mtp) REVERT: A 1191 GLU cc_start: 0.7163 (pp20) cc_final: 0.6773 (tp30) REVERT: A 1382 MET cc_start: 0.7564 (mmt) cc_final: 0.7299 (mmp) REVERT: A 1441 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.7824 (tt) REVERT: A 1509 MET cc_start: 0.7589 (mtm) cc_final: 0.7210 (mtp) REVERT: A 1513 PHE cc_start: 0.8405 (t80) cc_final: 0.8142 (t80) REVERT: A 1516 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 1605 MET cc_start: 0.3973 (OUTLIER) cc_final: 0.3350 (tpt) REVERT: D 506 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8246 (mt) REVERT: D 599 TYR cc_start: 0.8539 (m-80) cc_final: 0.7801 (m-80) REVERT: D 714 GLU cc_start: 0.8968 (tp30) cc_final: 0.8759 (tm-30) REVERT: D 1010 ASN cc_start: 0.8530 (m-40) cc_final: 0.8267 (t0) REVERT: D 1035 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7875 (mm-30) REVERT: C 209 ASP cc_start: 0.3477 (t0) cc_final: 0.2576 (m-30) REVERT: C 347 GLU cc_start: 0.8025 (tp30) cc_final: 0.7764 (mt-10) REVERT: B 5 ILE cc_start: 0.0536 (OUTLIER) cc_final: 0.0108 (pt) outliers start: 99 outliers final: 62 residues processed: 363 average time/residue: 0.3064 time to fit residues: 178.9649 Evaluate side-chains 348 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 276 time to evaluate : 2.169 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 509 TRP Chi-restraints excluded: chain A residue 528 TRP Chi-restraints excluded: chain A residue 536 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 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 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1441 ILE 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 37 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 100 LEU 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 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 623 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 888 ASN 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 42 ARG Chi-restraints excluded: chain C residue 47 GLN 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 265 GLN 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 27 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 A 931 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.190679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133047 restraints weight = 30453.563| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.90 r_work: 0.3400 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21495 Z= 0.178 Angle : 0.674 12.099 29160 Z= 0.334 Chirality : 0.043 0.321 3328 Planarity : 0.005 0.077 3666 Dihedral : 7.434 79.259 3266 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.72 % Favored : 89.73 % Rotamer: Outliers : 4.94 % Allowed : 26.63 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2551 helix: -0.09 (0.15), residues: 1159 sheet: -1.73 (0.33), residues: 214 loop : -2.46 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1549 HIS 0.005 0.001 HIS C 314 PHE 0.032 0.001 PHE D 780 TYR 0.018 0.002 TYR A1529 ARG 0.008 0.000 ARG D 873 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 8) link_NAG-ASN : angle 3.66793 ( 24) link_BETA1-4 : bond 0.00977 ( 8) link_BETA1-4 : angle 3.45787 ( 24) hydrogen bonds : bond 0.03768 ( 842) hydrogen bonds : angle 4.59459 ( 2454) SS BOND : bond 0.00634 ( 14) SS BOND : angle 1.33908 ( 28) covalent geometry : bond 0.00420 (21465) covalent geometry : angle 0.65796 (29084) *********************** 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 402 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 289 time to evaluate : 2.430 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: 0.4443 (OUTLIER) cc_final: 0.3959 (m-10) REVERT: A 325 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.5886 (mm-40) REVERT: A 548 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: A 561 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7149 (mmtm) REVERT: A 771 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.5500 (mp0) REVERT: A 963 ILE cc_start: 0.6643 (tp) cc_final: 0.6371 (mm) REVERT: A 1084 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: A 1151 ASP cc_start: 0.8154 (m-30) cc_final: 0.7473 (t0) REVERT: A 1309 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 1441 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 1509 MET cc_start: 0.7744 (mtm) cc_final: 0.7358 (mtp) REVERT: A 1513 PHE cc_start: 0.8542 (t80) cc_final: 0.8310 (t80) REVERT: A 1516 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8102 (mp) REVERT: A 1605 MET cc_start: 0.3979 (OUTLIER) cc_final: 0.3361 (tpt) REVERT: D 396 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8350 (mtt-85) REVERT: D 599 TYR cc_start: 0.8542 (m-80) cc_final: 0.7807 (m-80) REVERT: D 1010 ASN cc_start: 0.8550 (m-40) cc_final: 0.8331 (t0) REVERT: C 209 ASP cc_start: 0.3468 (t0) cc_final: 0.2590 (m-30) REVERT: C 320 MET cc_start: 0.7863 (mpp) cc_final: 0.7578 (mmm) REVERT: C 347 GLU cc_start: 0.8094 (tp30) cc_final: 0.7765 (mt-10) REVERT: B 5 ILE cc_start: 0.0622 (OUTLIER) cc_final: 0.0178 (pt) outliers start: 113 outliers final: 75 residues processed: 369 average time/residue: 0.3075 time to fit residues: 180.9011 Evaluate side-chains 354 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain A residue 362 MET 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 536 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 561 LYS 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 680 ASP 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 1035 LEU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1054 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 1309 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1441 ILE 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 59 ASP Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 661 ILE 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 768 LEU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 782 LYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 888 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 205 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN A 931 HIS C 47 GLN ** 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 = 0.4301 r_free = 0.4301 target = 0.194009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139925 restraints weight = 30557.676| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.07 r_work: 0.3440 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21495 Z= 0.123 Angle : 0.656 11.801 29160 Z= 0.324 Chirality : 0.042 0.312 3328 Planarity : 0.004 0.078 3666 Dihedral : 7.076 71.466 3266 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.78 % Favored : 90.67 % Rotamer: Outliers : 4.11 % Allowed : 27.50 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2551 helix: 0.06 (0.15), residues: 1157 sheet: -1.57 (0.32), residues: 226 loop : -2.44 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 185 HIS 0.004 0.001 HIS C 314 PHE 0.031 0.001 PHE D 780 TYR 0.014 0.001 TYR D 629 ARG 0.007 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00687 ( 8) link_NAG-ASN : angle 3.53798 ( 24) link_BETA1-4 : bond 0.00942 ( 8) link_BETA1-4 : angle 3.45523 ( 24) hydrogen bonds : bond 0.03449 ( 842) hydrogen bonds : angle 4.44971 ( 2454) SS BOND : bond 0.00369 ( 14) SS BOND : angle 1.40006 ( 28) covalent geometry : bond 0.00279 (21465) covalent geometry : angle 0.63967 (29084) *********************** 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 383 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 289 time to evaluate : 2.451 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: 0.4509 (OUTLIER) cc_final: 0.3998 (m-10) REVERT: A 128 ILE cc_start: 0.7954 (mm) cc_final: 0.7518 (mt) REVERT: A 325 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.5861 (mm-40) REVERT: A 561 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7083 (mmtm) REVERT: A 577 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5905 (p) REVERT: A 707 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8169 (m-30) REVERT: A 771 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: A 1125 MET cc_start: 0.7824 (mtp) cc_final: 0.7582 (mtp) REVERT: A 1151 ASP cc_start: 0.8147 (m-30) cc_final: 0.7462 (t0) REVERT: A 1206 GLN cc_start: 0.6843 (mp10) cc_final: 0.6450 (mp10) REVERT: A 1379 PHE cc_start: 0.5686 (m-80) cc_final: 0.5318 (m-80) REVERT: A 1441 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.7971 (tt) REVERT: A 1509 MET cc_start: 0.7672 (mtm) cc_final: 0.7295 (mtp) REVERT: A 1513 PHE cc_start: 0.8482 (t80) cc_final: 0.8225 (t80) REVERT: A 1516 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8081 (mp) REVERT: A 1605 MET cc_start: 0.3947 (OUTLIER) cc_final: 0.3366 (tpt) REVERT: D 396 ARG cc_start: 0.8676 (mtt-85) cc_final: 0.8348 (mtt-85) REVERT: D 506 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8358 (mt) REVERT: D 599 TYR cc_start: 0.8500 (m-80) cc_final: 0.7839 (m-80) REVERT: D 671 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8304 (tptt) REVERT: D 852 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (tt) REVERT: D 1010 ASN cc_start: 0.8516 (m-40) cc_final: 0.8261 (t0) REVERT: C 47 GLN cc_start: 0.4204 (OUTLIER) cc_final: 0.3708 (tt0) REVERT: C 209 ASP cc_start: 0.3258 (t0) cc_final: 0.2398 (m-30) REVERT: C 347 GLU cc_start: 0.8006 (tp30) cc_final: 0.7689 (mt-10) REVERT: B 5 ILE cc_start: 0.0740 (OUTLIER) cc_final: 0.0234 (pt) outliers start: 94 outliers final: 61 residues processed: 358 average time/residue: 0.3865 time to fit residues: 224.6750 Evaluate side-chains 340 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 2.837 ------------------------------------------------------------------------------- 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 360 ILE 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 536 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 577 SER 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 680 ASP Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 771 GLU 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 1441 ILE 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 100 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 331 THR 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 805 LYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 888 ASN 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 47 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 7 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 234 optimal weight: 5.9990 chunk 225 optimal weight: 40.0000 chunk 250 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 ASN ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** 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 = 0.4297 r_free = 0.4297 target = 0.193712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139041 restraints weight = 30800.827| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.25 r_work: 0.3439 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2215 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= 0.132 Angle : 0.661 11.642 29160 Z= 0.326 Chirality : 0.042 0.316 3328 Planarity : 0.004 0.077 3666 Dihedral : 6.911 65.335 3266 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.09 % Favored : 90.40 % Rotamer: Outliers : 3.85 % Allowed : 27.63 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2551 helix: 0.13 (0.15), residues: 1154 sheet: -1.51 (0.33), residues: 224 loop : -2.41 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 195 HIS 0.004 0.001 HIS C 314 PHE 0.029 0.001 PHE D 780 TYR 0.019 0.001 TYR A1298 ARG 0.007 0.000 ARG D 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 8) link_NAG-ASN : angle 3.49905 ( 24) link_BETA1-4 : bond 0.00952 ( 8) link_BETA1-4 : angle 3.49630 ( 24) hydrogen bonds : bond 0.03501 ( 842) hydrogen bonds : angle 4.44552 ( 2454) SS BOND : bond 0.00307 ( 14) SS BOND : angle 1.45717 ( 28) covalent geometry : bond 0.00304 (21465) covalent geometry : angle 0.64528 (29084) *********************** 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: 88 poor density : 273 time to evaluate : 2.109 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: 0.4525 (OUTLIER) cc_final: 0.4025 (m-10) REVERT: A 128 ILE cc_start: 0.7977 (mm) cc_final: 0.7543 (mt) REVERT: A 325 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.5911 (mm-40) REVERT: A 561 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7121 (mmtm) REVERT: A 577 SER cc_start: 0.6462 (OUTLIER) cc_final: 0.5994 (p) REVERT: A 707 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: A 1125 MET cc_start: 0.7828 (mtp) cc_final: 0.7616 (mtp) REVERT: A 1151 ASP cc_start: 0.8156 (m-30) cc_final: 0.7479 (t0) REVERT: A 1206 GLN cc_start: 0.6839 (mp10) cc_final: 0.6455 (mp10) REVERT: A 1441 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 1509 MET cc_start: 0.7695 (mtm) cc_final: 0.7312 (mtp) REVERT: A 1513 PHE cc_start: 0.8497 (t80) cc_final: 0.8245 (t80) REVERT: A 1516 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 1605 MET cc_start: 0.3856 (OUTLIER) cc_final: 0.3419 (tpt) REVERT: D 396 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8427 (mtt-85) REVERT: D 495 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7619 (tm-30) REVERT: D 499 ARG cc_start: 0.8988 (ttm-80) cc_final: 0.8460 (mtm-85) REVERT: D 506 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8284 (mt) REVERT: D 599 TYR cc_start: 0.8535 (m-80) cc_final: 0.7780 (m-80) REVERT: D 671 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8317 (tptt) REVERT: D 852 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8367 (tt) REVERT: D 861 MET cc_start: 0.7251 (mmm) cc_final: 0.7008 (mmt) REVERT: D 1010 ASN cc_start: 0.8510 (m-40) cc_final: 0.8258 (t0) REVERT: C 47 GLN cc_start: 0.4134 (OUTLIER) cc_final: 0.3863 (tt0) REVERT: C 209 ASP cc_start: 0.3497 (t0) cc_final: 0.2709 (m-30) REVERT: C 320 MET cc_start: 0.6629 (mmm) cc_final: 0.5987 (mpp) REVERT: C 343 GLU cc_start: 0.8488 (pt0) cc_final: 0.7290 (mm-30) REVERT: C 347 GLU cc_start: 0.8011 (tp30) cc_final: 0.7680 (mt-10) REVERT: B 5 ILE cc_start: 0.0757 (OUTLIER) cc_final: 0.0241 (pt) outliers start: 88 outliers final: 65 residues processed: 340 average time/residue: 0.2968 time to fit residues: 161.3349 Evaluate side-chains 343 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 266 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 509 TRP 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 577 SER 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 707 ASP Chi-restraints excluded: chain A residue 729 VAL 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 1441 ILE 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 A residue 1614 VAL Chi-restraints excluded: chain D residue 70 VAL 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 331 THR 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 805 LYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 888 ASN 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 47 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 49 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 ASN C 47 GLN ** 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 = 0.4287 r_free = 0.4287 target = 0.192698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138878 restraints weight = 30549.224| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.90 r_work: 0.3418 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21495 Z= 0.165 Angle : 0.684 14.871 29160 Z= 0.336 Chirality : 0.043 0.322 3328 Planarity : 0.005 0.077 3666 Dihedral : 6.862 61.981 3266 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.60 % Favored : 89.89 % Rotamer: Outliers : 3.94 % Allowed : 27.68 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2551 helix: 0.16 (0.16), residues: 1141 sheet: -1.61 (0.33), residues: 212 loop : -2.40 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1549 HIS 0.004 0.001 HIS C 314 PHE 0.031 0.001 PHE D 780 TYR 0.012 0.001 TYR D 512 ARG 0.006 0.000 ARG D 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 3.51701 ( 24) link_BETA1-4 : bond 0.00942 ( 8) link_BETA1-4 : angle 3.54266 ( 24) hydrogen bonds : bond 0.03678 ( 842) hydrogen bonds : angle 4.51212 ( 2454) SS BOND : bond 0.00319 ( 14) SS BOND : angle 1.48734 ( 28) covalent geometry : bond 0.00391 (21465) covalent geometry : angle 0.66772 (29084) *********************** 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 357 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 267 time to evaluate : 2.377 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: 0.4528 (OUTLIER) cc_final: 0.4022 (m-10) REVERT: A 325 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.5946 (mm-40) REVERT: A 561 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7044 (mmtm) REVERT: A 577 SER cc_start: 0.6439 (OUTLIER) cc_final: 0.5957 (p) REVERT: A 707 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: A 1151 ASP cc_start: 0.8218 (m-30) cc_final: 0.7545 (t0) REVERT: A 1206 GLN cc_start: 0.6883 (mp10) cc_final: 0.6487 (mp10) REVERT: A 1441 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.7956 (tt) REVERT: A 1509 MET cc_start: 0.7660 (mtm) cc_final: 0.7292 (mtp) REVERT: A 1513 PHE cc_start: 0.8472 (t80) cc_final: 0.8226 (t80) REVERT: A 1516 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 1605 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3434 (tpt) REVERT: D 396 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8463 (mtt-85) REVERT: D 506 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8229 (mt) REVERT: D 599 TYR cc_start: 0.8564 (m-80) cc_final: 0.7837 (m-80) REVERT: D 671 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8359 (tptt) REVERT: D 1010 ASN cc_start: 0.8509 (m-40) cc_final: 0.8251 (t0) REVERT: C 47 GLN cc_start: 0.3784 (OUTLIER) cc_final: 0.3416 (tt0) REVERT: C 209 ASP cc_start: 0.3528 (t0) cc_final: 0.2915 (m-30) REVERT: C 265 GLN cc_start: 0.4891 (OUTLIER) cc_final: 0.4244 (mt0) REVERT: C 320 MET cc_start: 0.6557 (mmm) cc_final: 0.5966 (mpp) REVERT: C 343 GLU cc_start: 0.8477 (pt0) cc_final: 0.7291 (mm-30) REVERT: C 347 GLU cc_start: 0.8013 (tp30) cc_final: 0.7671 (mt-10) REVERT: B 5 ILE cc_start: 0.0746 (OUTLIER) cc_final: 0.0239 (pt) outliers start: 90 outliers final: 70 residues processed: 334 average time/residue: 0.3210 time to fit residues: 171.6981 Evaluate side-chains 343 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 261 time to evaluate : 2.295 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain A residue 362 MET 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 536 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 577 SER 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 707 ASP Chi-restraints excluded: chain A residue 729 VAL 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 1305 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1441 ILE 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 A residue 1614 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 331 THR 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 613 ASN 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 805 LYS Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 888 ASN 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 47 GLN 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 196 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 C residue 315 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 131 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 157 optimal weight: 0.0070 chunk 235 optimal weight: 0.8980 chunk 236 optimal weight: 0.0980 chunk 215 optimal weight: 6.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 398 ASN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** 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 = 0.4315 r_free = 0.4315 target = 0.195430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140533 restraints weight = 30619.525| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.02 r_work: 0.3463 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 21495 Z= 0.116 Angle : 0.659 12.682 29160 Z= 0.323 Chirality : 0.042 0.310 3328 Planarity : 0.004 0.078 3666 Dihedral : 6.524 59.489 3266 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.71 % Rotamer: Outliers : 3.19 % Allowed : 28.55 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2551 helix: 0.27 (0.16), residues: 1156 sheet: -1.45 (0.34), residues: 208 loop : -2.32 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.004 0.001 HIS C 314 PHE 0.026 0.001 PHE A 175 TYR 0.024 0.001 TYR A1298 ARG 0.006 0.000 ARG D 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 8) link_NAG-ASN : angle 3.44124 ( 24) link_BETA1-4 : bond 0.00886 ( 8) link_BETA1-4 : angle 3.46259 ( 24) hydrogen bonds : bond 0.03390 ( 842) hydrogen bonds : angle 4.38453 ( 2454) SS BOND : bond 0.00278 ( 14) SS BOND : angle 1.26658 ( 28) covalent geometry : bond 0.00259 (21465) covalent geometry : angle 0.64374 (29084) ********************** 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 361 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 2.440 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: symmetry clash REVERT: A 128 ILE cc_start: 0.7917 (mm) cc_final: 0.7484 (mt) REVERT: A 195 TRP cc_start: 0.7445 (m100) cc_final: 0.6997 (m100) REVERT: A 325 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.5905 (mm-40) REVERT: A 561 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7046 (mmtm) REVERT: A 577 SER cc_start: 0.6383 (OUTLIER) cc_final: 0.5908 (p) REVERT: A 707 ASP cc_start: 0.8523 (m-30) cc_final: 0.8193 (m-30) REVERT: A 1125 MET cc_start: 0.7822 (mtp) cc_final: 0.7532 (mtp) REVERT: A 1151 ASP cc_start: 0.8155 (m-30) cc_final: 0.7490 (t0) REVERT: A 1206 GLN cc_start: 0.6849 (mp10) cc_final: 0.6494 (mp10) REVERT: A 1441 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8022 (tt) REVERT: A 1509 MET cc_start: 0.7671 (mtm) cc_final: 0.7291 (mtp) REVERT: A 1513 PHE cc_start: 0.8473 (t80) cc_final: 0.8202 (t80) REVERT: A 1516 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 1605 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.3753 (tpt) REVERT: D 396 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8408 (mtt-85) REVERT: D 499 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8509 (mtm-85) REVERT: D 506 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (mt) REVERT: D 599 TYR cc_start: 0.8477 (m-80) cc_final: 0.7753 (m-80) REVERT: D 671 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8336 (tptt) REVERT: D 852 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8376 (tt) REVERT: D 1010 ASN cc_start: 0.8449 (m-40) cc_final: 0.8202 (t0) REVERT: C 47 GLN cc_start: 0.3967 (OUTLIER) cc_final: 0.3512 (tt0) REVERT: C 209 ASP cc_start: 0.3300 (t0) cc_final: 0.2562 (m-30) REVERT: C 343 GLU cc_start: 0.8320 (pt0) cc_final: 0.7208 (mm-30) REVERT: C 347 GLU cc_start: 0.7988 (tp30) cc_final: 0.7685 (mt-10) REVERT: B 5 ILE cc_start: 0.0728 (OUTLIER) cc_final: 0.0233 (pt) outliers start: 73 outliers final: 53 residues processed: 344 average time/residue: 0.3180 time to fit residues: 176.3706 Evaluate side-chains 338 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 509 TRP 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 577 SER Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 729 VAL 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 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1441 ILE 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 A residue 1614 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 538 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 805 LYS Chi-restraints excluded: chain D residue 852 ILE 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 47 GLN 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 196 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 C residue 322 TYR 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 60 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 184 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 GLN A 398 ASN ** A 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 GLN ** 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 = 0.4293 r_free = 0.4293 target = 0.194015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140293 restraints weight = 30578.324| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.10 r_work: 0.3438 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21495 Z= 0.124 Angle : 0.660 11.871 29160 Z= 0.322 Chirality : 0.042 0.316 3328 Planarity : 0.004 0.077 3666 Dihedral : 6.376 58.585 3266 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.09 % Favored : 90.51 % Rotamer: Outliers : 3.19 % Allowed : 28.86 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2551 helix: 0.36 (0.16), residues: 1146 sheet: -1.43 (0.34), residues: 208 loop : -2.33 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.004 0.001 HIS C 314 PHE 0.025 0.001 PHE D 780 TYR 0.012 0.001 TYR A1529 ARG 0.007 0.000 ARG D 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 8) link_NAG-ASN : angle 3.39047 ( 24) link_BETA1-4 : bond 0.00921 ( 8) link_BETA1-4 : angle 3.43774 ( 24) hydrogen bonds : bond 0.03364 ( 842) hydrogen bonds : angle 4.36049 ( 2454) SS BOND : bond 0.00277 ( 14) SS BOND : angle 1.34173 ( 28) covalent geometry : bond 0.00284 (21465) covalent geometry : angle 0.64500 (29084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19984.60 seconds wall clock time: 346 minutes 54.33 seconds (20814.33 seconds total)