Starting phenix.real_space_refine on Sat Mar 7 05:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.map" model { file = "/net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1a_14236/03_2026/7r1a_14236.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.054 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 Zn 3 6.06 5 S 192 5.16 5 C 24666 2.51 5 N 6336 2.21 5 O 7419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38616 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7818 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 50, 'TRANS': 947} Chain breaks: 9 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: B, C, E, F, H, I Time building chain proxies: 12.30, per 1000 atoms: 0.32 Number of scatterers: 38616 At special positions: 0 Unit cell: (166.311, 160.876, 238.053, 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) Zn 3 29.99 S 192 16.00 O 7419 8.00 N 6336 7.00 C 24666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 717 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 432 " " NAG D 906 " - " ASN D 546 " " NAG D 907 " - " ASN D 103 " " NAG E 902 " - " ASN E 53 " " NAG E 903 " - " ASN E 90 " " NAG E 904 " - " ASN E 322 " " NAG E 905 " - " ASN E 432 " " NAG E 906 " - " ASN E 546 " " NAG E 907 " - " ASN E 103 " " NAG F 902 " - " ASN F 53 " " NAG F 903 " - " ASN F 90 " " NAG F 904 " - " ASN F 322 " " NAG F 905 " - " ASN F 432 " " NAG F 906 " - " ASN F 546 " " NAG F 907 " - " ASN F 103 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN C 331 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 378 " pdb="ZN ZN E 901 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 901 " pdb="ZN ZN F 901 " - pdb=" NE2 HIS F 378 " pdb="ZN ZN F 901 " - pdb=" NE2 HIS F 374 " 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8946 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 60 sheets defined 41.2% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.670A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.007A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 4.377A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.579A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.316A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.485A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.672A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.996A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.831A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.801A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 157 through 173 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.692A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 223' Processing helix chain 'D' and resid 226 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.980A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.106A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 4.130A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.543A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.781A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.960A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.017A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.644A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.571A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.832A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.801A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 157 through 173 Processing helix chain 'E' and resid 176 through 194 Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 223 removed outlier: 3.692A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 223' Processing helix chain 'E' and resid 226 through 249 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.981A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 305 through 319 Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.107A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 4.131A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.543A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.781A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.961A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 4.017A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.644A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.570A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.832A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.801A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 157 through 173 Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 218 through 223 removed outlier: 3.692A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 223' Processing helix chain 'F' and resid 226 through 249 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 280 removed outlier: 3.980A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 305 through 319 Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.107A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 4.131A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.543A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.782A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 404 " --> pdb=" O PHE F 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.961A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 4.017A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.645A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.572A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.669A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.007A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 4.377A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.579A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.316A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.485A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.672A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.996A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.670A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.006A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 4.376A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.579A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.316A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.486A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.673A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.995A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.367A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.583A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.196A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.449A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.574A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.457A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.503A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.503A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1080 through 1082 removed outlier: 3.732A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.004A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.133A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.004A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.133A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.005A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.133A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.367A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.583A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.196A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 136 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.449A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.573A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.457A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.504A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.504A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1080 through 1082 removed outlier: 3.733A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.368A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.584A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.196A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.449A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.574A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.480A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.457A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.503A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.503A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1080 through 1082 removed outlier: 3.733A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG6, first strand: chain 'C' and resid 1094 through 1097 1680 hydrogen bonds defined for protein. 4689 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: 9.14 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12313 1.34 - 1.46: 9805 1.46 - 1.58: 17155 1.58 - 1.70: 0 1.70 - 1.82: 279 Bond restraints: 39552 Sorted by residual: bond pdb=" C1 NAG D 907 " pdb=" O5 NAG D 907 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG F 907 " pdb=" O5 NAG F 907 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 NAG E 907 " pdb=" O5 NAG E 907 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 39547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 52457 1.54 - 3.08: 1113 3.08 - 4.63: 164 4.63 - 6.17: 26 6.17 - 7.71: 9 Bond angle restraints: 53769 Sorted by residual: angle pdb=" N GLY E 147 " pdb=" CA GLY E 147 " pdb=" C GLY E 147 " ideal model delta sigma weight residual 112.79 106.22 6.57 1.20e+00 6.94e-01 3.00e+01 angle pdb=" N GLY F 147 " pdb=" CA GLY F 147 " pdb=" C GLY F 147 " ideal model delta sigma weight residual 112.79 106.24 6.55 1.20e+00 6.94e-01 2.98e+01 angle pdb=" N GLY D 147 " pdb=" CA GLY D 147 " pdb=" C GLY D 147 " ideal model delta sigma weight residual 112.79 106.25 6.54 1.20e+00 6.94e-01 2.97e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 112.83 118.22 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 112.83 118.20 -5.37 1.22e+00 6.72e-01 1.93e+01 ... (remaining 53764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21851 17.93 - 35.86: 1855 35.86 - 53.78: 300 53.78 - 71.71: 78 71.71 - 89.64: 63 Dihedral angle restraints: 24147 sinusoidal: 10260 harmonic: 13887 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.93 -85.07 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.93 -85.07 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.94 -85.06 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 24144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5570 0.081 - 0.162: 490 0.162 - 0.244: 15 0.244 - 0.325: 0 0.325 - 0.406: 6 Chirality restraints: 6081 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 6078 not shown) Planarity restraints: 6927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU D 35 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU D 35 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA D 36 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 35 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU F 35 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU F 35 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA F 36 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 35 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU E 35 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 35 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 36 " 0.019 2.00e-02 2.50e+03 ... (remaining 6924 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 827 2.69 - 3.24: 38200 3.24 - 3.79: 58886 3.79 - 4.35: 75318 4.35 - 4.90: 126531 Nonbonded interactions: 299762 Sorted by model distance: nonbonded pdb=" OD1 ASN E 103 " pdb=" OG SER E 106 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN F 103 " pdb=" OG SER F 106 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN D 103 " pdb=" OG SER D 106 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.167 3.040 ... (remaining 299757 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 43.190 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.054 39660 Z= 0.167 Angle : 0.597 17.232 54027 Z= 0.288 Chirality : 0.044 0.406 6081 Planarity : 0.004 0.045 6876 Dihedral : 14.136 89.639 15057 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4686 helix: 1.83 (0.13), residues: 1707 sheet: -0.58 (0.20), residues: 690 loop : -1.38 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.015 0.001 TYR B1067 PHE 0.014 0.001 PHE A 43 TRP 0.014 0.001 TRP F 459 HIS 0.008 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00359 (39552) covalent geometry : angle 0.54381 (53769) SS BOND : bond 0.00196 ( 48) SS BOND : angle 1.13701 ( 96) hydrogen bonds : bond 0.20444 ( 1653) hydrogen bonds : angle 7.07214 ( 4689) metal coordination : bond 0.00126 ( 6) link_BETA1-4 : bond 0.00369 ( 3) link_BETA1-4 : angle 2.11911 ( 9) link_NAG-ASN : bond 0.00775 ( 51) link_NAG-ASN : angle 4.54557 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.997 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: 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: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8891 (m-80) cc_final: 0.8659 (m-10) REVERT: A 740 MET cc_start: 0.8890 (tpt) cc_final: 0.8678 (tpt) REVERT: A 774 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8407 (mm-40) REVERT: D 332 MET cc_start: 0.6081 (ppp) cc_final: 0.5760 (ppp) REVERT: E 332 MET cc_start: 0.5323 (ppp) cc_final: 0.4664 (ppp) REVERT: E 360 MET cc_start: 0.8893 (mtp) cc_final: 0.8164 (tpt) REVERT: F 332 MET cc_start: 0.6092 (ppp) cc_final: 0.5848 (ppp) REVERT: F 471 ASP cc_start: 0.9430 (t0) cc_final: 0.9225 (p0) REVERT: B 175 PHE cc_start: 0.8419 (m-80) cc_final: 0.8181 (m-80) REVERT: B 740 MET cc_start: 0.8921 (tpt) cc_final: 0.8672 (tpt) REVERT: C 175 PHE cc_start: 0.8496 (m-80) cc_final: 0.8270 (m-80) REVERT: C 740 MET cc_start: 0.8906 (tpt) cc_final: 0.8663 (tpt) REVERT: C 902 MET cc_start: 0.9115 (tpt) cc_final: 0.8659 (tpt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2298 time to fit residues: 88.4272 Evaluate side-chains 159 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 470 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN D 472 GLN E 98 GLN E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.115871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069751 restraints weight = 161047.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067195 restraints weight = 111511.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066852 restraints weight = 111368.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067496 restraints weight = 91646.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067430 restraints weight = 82947.692| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 39660 Z= 0.282 Angle : 0.722 15.398 54027 Z= 0.356 Chirality : 0.045 0.379 6081 Planarity : 0.004 0.041 6876 Dihedral : 7.008 55.783 6231 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.48 % Allowed : 7.35 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4686 helix: 1.73 (0.12), residues: 1653 sheet: -0.64 (0.19), residues: 723 loop : -1.44 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.032 0.001 TYR C1067 PHE 0.024 0.002 PHE E 315 TRP 0.015 0.001 TRP F 271 HIS 0.006 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00640 (39552) covalent geometry : angle 0.68260 (53769) SS BOND : bond 0.00376 ( 48) SS BOND : angle 1.38443 ( 96) hydrogen bonds : bond 0.05223 ( 1653) hydrogen bonds : angle 5.72011 ( 4689) metal coordination : bond 0.00470 ( 6) link_BETA1-4 : bond 0.00531 ( 3) link_BETA1-4 : angle 1.82187 ( 9) link_NAG-ASN : bond 0.00582 ( 51) link_NAG-ASN : angle 4.33010 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.388 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8520 (m-80) cc_final: 0.8314 (m-80) REVERT: A 195 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8023 (tttt) REVERT: D 366 MET cc_start: 0.7480 (tpp) cc_final: 0.7279 (tpp) REVERT: D 383 MET cc_start: 0.9639 (ptp) cc_final: 0.9267 (ppp) REVERT: D 516 TYR cc_start: 0.8025 (t80) cc_final: 0.6930 (m-80) REVERT: E 332 MET cc_start: 0.4907 (ppp) cc_final: 0.4612 (ppp) REVERT: E 360 MET cc_start: 0.8686 (mtp) cc_final: 0.8095 (tpp) REVERT: E 366 MET cc_start: 0.8024 (tpp) cc_final: 0.7336 (mmm) REVERT: E 455 MET cc_start: 0.5799 (ppp) cc_final: 0.5378 (ppp) REVERT: E 516 TYR cc_start: 0.6631 (t80) cc_final: 0.5527 (m-80) REVERT: F 249 MET cc_start: 0.5495 (mtt) cc_final: 0.4845 (mmm) REVERT: F 270 MET cc_start: 0.7787 (ttp) cc_final: 0.7569 (ptm) REVERT: F 332 MET cc_start: 0.6114 (ppp) cc_final: 0.5833 (ppp) REVERT: F 383 MET cc_start: 0.9652 (ptp) cc_final: 0.9412 (ppp) REVERT: F 474 MET cc_start: 0.7789 (mmp) cc_final: 0.6824 (mmm) REVERT: B 175 PHE cc_start: 0.8280 (m-80) cc_final: 0.8003 (m-80) REVERT: B 740 MET cc_start: 0.8861 (tpt) cc_final: 0.8434 (tpp) REVERT: C 175 PHE cc_start: 0.8340 (m-80) cc_final: 0.8025 (m-80) REVERT: C 902 MET cc_start: 0.9092 (tpt) cc_final: 0.8825 (tpt) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.2269 time to fit residues: 65.8719 Evaluate side-chains 159 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 463 optimal weight: 0.6980 chunk 236 optimal weight: 30.0000 chunk 389 optimal weight: 4.9990 chunk 360 optimal weight: 0.6980 chunk 457 optimal weight: 0.8980 chunk 443 optimal weight: 0.0570 chunk 80 optimal weight: 0.5980 chunk 209 optimal weight: 7.9990 chunk 232 optimal weight: 20.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN E 98 GLN E 472 GLN F 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.117582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071614 restraints weight = 161202.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069684 restraints weight = 102637.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069896 restraints weight = 96996.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069740 restraints weight = 91072.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.070057 restraints weight = 77068.109| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39660 Z= 0.119 Angle : 0.597 13.711 54027 Z= 0.291 Chirality : 0.043 0.373 6081 Planarity : 0.004 0.044 6876 Dihedral : 6.293 53.162 6231 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.67 % Allowed : 9.76 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 4686 helix: 1.99 (0.13), residues: 1659 sheet: -0.41 (0.19), residues: 747 loop : -1.27 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.015 0.001 TYR B1067 PHE 0.012 0.001 PHE B 135 TRP 0.017 0.001 TRP E 271 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00253 (39552) covalent geometry : angle 0.55687 (53769) SS BOND : bond 0.00843 ( 48) SS BOND : angle 1.69705 ( 96) hydrogen bonds : bond 0.04440 ( 1653) hydrogen bonds : angle 5.23590 ( 4689) metal coordination : bond 0.00236 ( 6) link_BETA1-4 : bond 0.00803 ( 3) link_BETA1-4 : angle 1.78972 ( 9) link_NAG-ASN : bond 0.00569 ( 51) link_NAG-ASN : angle 3.83145 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.405 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7385 (p) REVERT: D 249 MET cc_start: 0.5531 (mtt) cc_final: 0.5024 (mmm) REVERT: D 270 MET cc_start: 0.8180 (ptm) cc_final: 0.7059 (pmm) REVERT: D 462 MET cc_start: 0.5956 (ptt) cc_final: 0.5192 (mmt) REVERT: D 516 TYR cc_start: 0.8016 (t80) cc_final: 0.7092 (m-80) REVERT: D 557 MET cc_start: 0.8936 (ppp) cc_final: 0.8717 (ppp) REVERT: D 558 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9071 (mt) REVERT: E 270 MET cc_start: 0.6713 (ptt) cc_final: 0.5444 (pmm) REVERT: E 360 MET cc_start: 0.8820 (mtp) cc_final: 0.8531 (tpp) REVERT: E 366 MET cc_start: 0.7954 (tpp) cc_final: 0.7303 (mmm) REVERT: E 455 MET cc_start: 0.5886 (ppp) cc_final: 0.5491 (ppp) REVERT: E 480 MET cc_start: 0.5999 (ptt) cc_final: 0.5557 (ptt) REVERT: F 106 SER cc_start: 0.7297 (OUTLIER) cc_final: 0.7082 (p) REVERT: F 249 MET cc_start: 0.5867 (mtt) cc_final: 0.5151 (mmm) REVERT: F 270 MET cc_start: 0.7402 (ttp) cc_final: 0.7016 (pmm) REVERT: F 332 MET cc_start: 0.6187 (ppp) cc_final: 0.5789 (ppp) REVERT: F 366 MET cc_start: 0.6473 (tpp) cc_final: 0.5812 (mmm) REVERT: F 455 MET cc_start: 0.7284 (ppp) cc_final: 0.6490 (ppp) REVERT: F 462 MET cc_start: 0.5390 (ptt) cc_final: 0.4972 (mmt) REVERT: F 480 MET cc_start: 0.5964 (ptt) cc_final: 0.5471 (ptt) REVERT: F 557 MET cc_start: 0.8758 (ppp) cc_final: 0.8487 (ppp) REVERT: F 558 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9050 (mt) REVERT: B 427 ASP cc_start: 0.9287 (m-30) cc_final: 0.9040 (m-30) REVERT: B 740 MET cc_start: 0.8920 (tpt) cc_final: 0.8436 (tpp) REVERT: C 175 PHE cc_start: 0.8321 (m-80) cc_final: 0.8106 (m-80) outliers start: 28 outliers final: 14 residues processed: 172 average time/residue: 0.2109 time to fit residues: 62.8895 Evaluate side-chains 163 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 431 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 457 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 371 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C 544 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 = 0.4172 r_free = 0.4172 target = 0.115600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069621 restraints weight = 163283.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067253 restraints weight = 104839.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067214 restraints weight = 119812.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.067179 restraints weight = 103329.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067252 restraints weight = 96870.917| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 39660 Z= 0.254 Angle : 0.656 11.543 54027 Z= 0.323 Chirality : 0.044 0.380 6081 Planarity : 0.004 0.041 6876 Dihedral : 6.139 54.126 6231 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.10 % Allowed : 11.27 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4686 helix: 1.69 (0.13), residues: 1677 sheet: -0.55 (0.18), residues: 729 loop : -1.37 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.025 0.001 TYR B1067 PHE 0.025 0.002 PHE A 135 TRP 0.014 0.001 TRP E 271 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00580 (39552) covalent geometry : angle 0.62315 (53769) SS BOND : bond 0.00289 ( 48) SS BOND : angle 1.64364 ( 96) hydrogen bonds : bond 0.04709 ( 1653) hydrogen bonds : angle 5.40660 ( 4689) metal coordination : bond 0.00297 ( 6) link_BETA1-4 : bond 0.00552 ( 3) link_BETA1-4 : angle 1.55946 ( 9) link_NAG-ASN : bond 0.00496 ( 51) link_NAG-ASN : angle 3.67637 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.534 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: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9232 (mm) cc_final: 0.8600 (tp) REVERT: A 725 GLU cc_start: 0.8528 (tt0) cc_final: 0.8267 (tt0) REVERT: D 106 SER cc_start: 0.7551 (OUTLIER) cc_final: 0.7345 (p) REVERT: D 249 MET cc_start: 0.6050 (mtt) cc_final: 0.5004 (mmm) REVERT: D 270 MET cc_start: 0.8030 (ptm) cc_final: 0.7041 (pmm) REVERT: D 366 MET cc_start: 0.7492 (tpp) cc_final: 0.7093 (tpp) REVERT: D 408 MET cc_start: 0.7618 (ptp) cc_final: 0.7209 (ptt) REVERT: D 462 MET cc_start: 0.6198 (ptt) cc_final: 0.5533 (mmt) REVERT: D 474 MET cc_start: 0.8072 (mmp) cc_final: 0.7426 (mmm) REVERT: D 516 TYR cc_start: 0.8148 (t80) cc_final: 0.7332 (m-80) REVERT: E 270 MET cc_start: 0.6865 (ptm) cc_final: 0.5563 (pmm) REVERT: E 360 MET cc_start: 0.8946 (mtp) cc_final: 0.8640 (tpp) REVERT: E 366 MET cc_start: 0.8096 (tpp) cc_final: 0.7518 (mmm) REVERT: E 455 MET cc_start: 0.6013 (ppp) cc_final: 0.5544 (ppp) REVERT: E 516 TYR cc_start: 0.6802 (t80) cc_final: 0.6071 (m-80) REVERT: E 557 MET cc_start: 0.8830 (ppp) cc_final: 0.8546 (ppp) REVERT: E 558 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9137 (mt) REVERT: F 106 SER cc_start: 0.7341 (OUTLIER) cc_final: 0.7138 (p) REVERT: F 249 MET cc_start: 0.6035 (mtt) cc_final: 0.5353 (mmm) REVERT: F 270 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (pmm) REVERT: F 332 MET cc_start: 0.6484 (ppp) cc_final: 0.6236 (ppp) REVERT: F 408 MET cc_start: 0.7573 (ptp) cc_final: 0.7177 (ptt) REVERT: F 462 MET cc_start: 0.5902 (ptt) cc_final: 0.5237 (mmt) REVERT: F 474 MET cc_start: 0.8252 (mmp) cc_final: 0.7668 (mmm) REVERT: F 516 TYR cc_start: 0.8224 (t80) cc_final: 0.7393 (m-80) REVERT: B 434 ILE cc_start: 0.9242 (mm) cc_final: 0.8591 (tp) REVERT: B 740 MET cc_start: 0.9017 (tpt) cc_final: 0.8614 (tpp) REVERT: C 175 PHE cc_start: 0.8575 (m-80) cc_final: 0.8307 (m-80) outliers start: 46 outliers final: 25 residues processed: 172 average time/residue: 0.2064 time to fit residues: 62.1611 Evaluate side-chains 165 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 470 optimal weight: 0.9980 chunk 384 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 208 optimal weight: 0.0570 chunk 346 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 237 optimal weight: 9.9990 chunk 288 optimal weight: 0.5980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.117125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071954 restraints weight = 161527.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069604 restraints weight = 114894.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069852 restraints weight = 109285.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069795 restraints weight = 93348.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.070047 restraints weight = 78495.987| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39660 Z= 0.113 Angle : 0.567 10.775 54027 Z= 0.278 Chirality : 0.043 0.377 6081 Planarity : 0.003 0.054 6876 Dihedral : 5.762 53.073 6231 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.15 % Allowed : 11.92 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.12), residues: 4686 helix: 1.92 (0.13), residues: 1674 sheet: -0.29 (0.18), residues: 729 loop : -1.28 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 983 TYR 0.015 0.001 TYR C1067 PHE 0.012 0.001 PHE C 43 TRP 0.014 0.001 TRP E 271 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00246 (39552) covalent geometry : angle 0.53654 (53769) SS BOND : bond 0.00178 ( 48) SS BOND : angle 1.16860 ( 96) hydrogen bonds : bond 0.04077 ( 1653) hydrogen bonds : angle 5.11689 ( 4689) metal coordination : bond 0.00075 ( 6) link_BETA1-4 : bond 0.00658 ( 3) link_BETA1-4 : angle 1.72037 ( 9) link_NAG-ASN : bond 0.00487 ( 51) link_NAG-ASN : angle 3.39446 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 1.523 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: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9202 (mm) cc_final: 0.8621 (tp) REVERT: A 725 GLU cc_start: 0.7981 (tt0) cc_final: 0.7741 (tt0) REVERT: D 249 MET cc_start: 0.6130 (mtt) cc_final: 0.5481 (mmm) REVERT: D 270 MET cc_start: 0.7937 (ptm) cc_final: 0.6991 (pmm) REVERT: D 408 MET cc_start: 0.7457 (ptp) cc_final: 0.6939 (ptt) REVERT: D 462 MET cc_start: 0.6195 (ptt) cc_final: 0.5525 (mmt) REVERT: D 474 MET cc_start: 0.8201 (mmp) cc_final: 0.7598 (mmm) REVERT: D 516 TYR cc_start: 0.8135 (t80) cc_final: 0.7363 (m-80) REVERT: D 557 MET cc_start: 0.8840 (ppp) cc_final: 0.8594 (ppp) REVERT: D 558 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9034 (mt) REVERT: E 82 MET cc_start: 0.9443 (ptp) cc_final: 0.9028 (ppp) REVERT: E 270 MET cc_start: 0.6699 (ptm) cc_final: 0.5446 (pmm) REVERT: E 332 MET cc_start: 0.5501 (ppp) cc_final: 0.4555 (ppp) REVERT: E 366 MET cc_start: 0.8098 (tpp) cc_final: 0.7361 (mmm) REVERT: E 455 MET cc_start: 0.5889 (ppp) cc_final: 0.5630 (ppp) REVERT: E 516 TYR cc_start: 0.6867 (t80) cc_final: 0.6257 (m-80) REVERT: E 557 MET cc_start: 0.8853 (ppp) cc_final: 0.8611 (ppp) REVERT: E 558 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9110 (mt) REVERT: F 249 MET cc_start: 0.5960 (mtt) cc_final: 0.5262 (mmm) REVERT: F 332 MET cc_start: 0.6329 (ppp) cc_final: 0.6056 (ppp) REVERT: F 376 MET cc_start: 0.8759 (ptp) cc_final: 0.8512 (ptp) REVERT: F 408 MET cc_start: 0.7314 (ptp) cc_final: 0.6984 (ptt) REVERT: F 455 MET cc_start: 0.7352 (ppp) cc_final: 0.6464 (ppp) REVERT: F 462 MET cc_start: 0.6020 (ptt) cc_final: 0.5382 (mmt) REVERT: F 516 TYR cc_start: 0.8175 (t80) cc_final: 0.7390 (m-80) REVERT: F 558 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9052 (mt) REVERT: B 105 ILE cc_start: 0.9379 (tp) cc_final: 0.9154 (mm) REVERT: B 427 ASP cc_start: 0.9272 (m-30) cc_final: 0.9031 (m-30) REVERT: B 434 ILE cc_start: 0.9248 (mm) cc_final: 0.8638 (tp) REVERT: B 740 MET cc_start: 0.8934 (tpt) cc_final: 0.8523 (tpp) REVERT: C 105 ILE cc_start: 0.9348 (tp) cc_final: 0.9079 (mm) REVERT: C 175 PHE cc_start: 0.8430 (m-80) cc_final: 0.8185 (m-80) outliers start: 48 outliers final: 26 residues processed: 181 average time/residue: 0.1964 time to fit residues: 62.5141 Evaluate side-chains 174 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 141 optimal weight: 30.0000 chunk 338 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 433 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 180 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 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 = 0.4176 r_free = 0.4176 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070766 restraints weight = 162729.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067610 restraints weight = 113144.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067790 restraints weight = 86992.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067971 restraints weight = 84578.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067955 restraints weight = 70643.113| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 39660 Z= 0.205 Angle : 0.614 11.148 54027 Z= 0.302 Chirality : 0.043 0.378 6081 Planarity : 0.004 0.054 6876 Dihedral : 5.732 53.723 6231 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.51 % Allowed : 12.54 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.12), residues: 4686 helix: 1.82 (0.13), residues: 1680 sheet: -0.41 (0.18), residues: 729 loop : -1.30 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.022 0.001 TYR C1067 PHE 0.015 0.001 PHE B 43 TRP 0.021 0.001 TRP F 271 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00468 (39552) covalent geometry : angle 0.58498 (53769) SS BOND : bond 0.00249 ( 48) SS BOND : angle 1.28764 ( 96) hydrogen bonds : bond 0.04295 ( 1653) hydrogen bonds : angle 5.23295 ( 4689) metal coordination : bond 0.00055 ( 6) link_BETA1-4 : bond 0.00616 ( 3) link_BETA1-4 : angle 1.69001 ( 9) link_NAG-ASN : bond 0.00432 ( 51) link_NAG-ASN : angle 3.40750 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 1.489 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: symmetry clash REVERT: A 434 ILE cc_start: 0.9236 (mm) cc_final: 0.8652 (tp) REVERT: D 249 MET cc_start: 0.6351 (mtt) cc_final: 0.5722 (mmm) REVERT: D 270 MET cc_start: 0.7999 (ptm) cc_final: 0.7053 (pmm) REVERT: D 332 MET cc_start: 0.6173 (ppp) cc_final: 0.5649 (ppp) REVERT: D 408 MET cc_start: 0.7744 (ptp) cc_final: 0.7481 (ptt) REVERT: D 462 MET cc_start: 0.6338 (ptt) cc_final: 0.5633 (mmt) REVERT: D 558 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9132 (mt) REVERT: E 82 MET cc_start: 0.9455 (ptp) cc_final: 0.9073 (ppp) REVERT: E 152 MET cc_start: 0.1669 (OUTLIER) cc_final: 0.1130 (tmm) REVERT: E 197 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8363 (pp20) REVERT: E 332 MET cc_start: 0.5963 (ppp) cc_final: 0.5008 (ppp) REVERT: E 366 MET cc_start: 0.8120 (tpp) cc_final: 0.7475 (mmm) REVERT: E 558 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9205 (mt) REVERT: F 249 MET cc_start: 0.6182 (mtt) cc_final: 0.5427 (mmm) REVERT: F 270 MET cc_start: 0.7781 (pmm) cc_final: 0.7551 (pmm) REVERT: F 332 MET cc_start: 0.6671 (ppp) cc_final: 0.6318 (ppp) REVERT: F 376 MET cc_start: 0.8830 (ptp) cc_final: 0.8556 (ptp) REVERT: F 408 MET cc_start: 0.7485 (ptp) cc_final: 0.7077 (ptt) REVERT: F 455 MET cc_start: 0.7446 (ppp) cc_final: 0.6678 (ppp) REVERT: F 462 MET cc_start: 0.6072 (ptt) cc_final: 0.5323 (mmt) REVERT: F 516 TYR cc_start: 0.8316 (t80) cc_final: 0.7579 (m-80) REVERT: F 558 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9175 (mt) REVERT: B 105 ILE cc_start: 0.9404 (tp) cc_final: 0.9163 (mm) REVERT: B 434 ILE cc_start: 0.9255 (mm) cc_final: 0.8636 (tp) REVERT: B 740 MET cc_start: 0.8967 (tpt) cc_final: 0.8563 (tpp) REVERT: C 105 ILE cc_start: 0.9393 (tp) cc_final: 0.9120 (mm) REVERT: C 175 PHE cc_start: 0.8594 (m-80) cc_final: 0.8308 (m-80) outliers start: 63 outliers final: 39 residues processed: 194 average time/residue: 0.2023 time to fit residues: 69.1003 Evaluate side-chains 182 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 432 optimal weight: 0.9980 chunk 357 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 367 optimal weight: 1.9990 chunk 386 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 374 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 599 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 544 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 = 0.4181 r_free = 0.4181 target = 0.116167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068999 restraints weight = 161741.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067949 restraints weight = 101222.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067921 restraints weight = 79518.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.067942 restraints weight = 75869.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068499 restraints weight = 63047.109| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39660 Z= 0.166 Angle : 0.591 11.446 54027 Z= 0.289 Chirality : 0.043 0.379 6081 Planarity : 0.004 0.052 6876 Dihedral : 5.617 52.858 6231 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.58 % Allowed : 13.26 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4686 helix: 1.86 (0.13), residues: 1695 sheet: -0.36 (0.18), residues: 729 loop : -1.28 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.020 0.001 TYR C1067 PHE 0.013 0.001 PHE B 43 TRP 0.015 0.001 TRP F 271 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00376 (39552) covalent geometry : angle 0.56266 (53769) SS BOND : bond 0.00201 ( 48) SS BOND : angle 1.19885 ( 96) hydrogen bonds : bond 0.04092 ( 1653) hydrogen bonds : angle 5.14887 ( 4689) metal coordination : bond 0.00032 ( 6) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 1.75535 ( 9) link_NAG-ASN : bond 0.00433 ( 51) link_NAG-ASN : angle 3.30514 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 145 time to evaluate : 1.414 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 90 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8825 (m) REVERT: A 105 ILE cc_start: 0.9260 (tp) cc_final: 0.9007 (mm) REVERT: A 197 ILE cc_start: 0.9599 (mt) cc_final: 0.9124 (tp) REVERT: A 294 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: A 398 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.6540 (m-30) REVERT: A 434 ILE cc_start: 0.9214 (mm) cc_final: 0.8632 (tp) REVERT: D 249 MET cc_start: 0.6340 (mtt) cc_final: 0.5771 (mmm) REVERT: D 270 MET cc_start: 0.7909 (ptm) cc_final: 0.6972 (pmm) REVERT: D 332 MET cc_start: 0.5510 (ppp) cc_final: 0.5006 (ppp) REVERT: D 408 MET cc_start: 0.7951 (ptp) cc_final: 0.6420 (ppp) REVERT: D 462 MET cc_start: 0.6369 (ptt) cc_final: 0.5805 (mmt) REVERT: D 474 MET cc_start: 0.8050 (mmp) cc_final: 0.7419 (mmm) REVERT: D 480 MET cc_start: 0.5602 (ptt) cc_final: 0.4648 (ptt) REVERT: D 516 TYR cc_start: 0.8147 (t80) cc_final: 0.7155 (m-80) REVERT: D 557 MET cc_start: 0.8776 (ppp) cc_final: 0.8463 (ppp) REVERT: D 558 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9090 (mt) REVERT: E 62 MET cc_start: 0.9367 (mtm) cc_final: 0.9071 (mpp) REVERT: E 82 MET cc_start: 0.9460 (ptp) cc_final: 0.9108 (ppp) REVERT: E 152 MET cc_start: 0.1921 (OUTLIER) cc_final: 0.1565 (tmm) REVERT: E 197 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8246 (pp20) REVERT: E 270 MET cc_start: 0.6940 (ptm) cc_final: 0.6733 (ptm) REVERT: E 332 MET cc_start: 0.5745 (ppp) cc_final: 0.4734 (ppp) REVERT: E 366 MET cc_start: 0.8117 (tpp) cc_final: 0.7461 (mmm) REVERT: E 557 MET cc_start: 0.8828 (ppp) cc_final: 0.8518 (ppp) REVERT: E 558 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9134 (mt) REVERT: F 249 MET cc_start: 0.6102 (mtt) cc_final: 0.5322 (mmm) REVERT: F 270 MET cc_start: 0.7748 (pmm) cc_final: 0.7289 (pmm) REVERT: F 332 MET cc_start: 0.6389 (ppp) cc_final: 0.6005 (ppp) REVERT: F 376 MET cc_start: 0.8765 (ptp) cc_final: 0.8489 (ptp) REVERT: F 408 MET cc_start: 0.7424 (ptp) cc_final: 0.7119 (ptt) REVERT: F 455 MET cc_start: 0.7589 (ppp) cc_final: 0.7102 (ppp) REVERT: F 462 MET cc_start: 0.6095 (ptt) cc_final: 0.5264 (mmt) REVERT: F 558 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9103 (mt) REVERT: B 105 ILE cc_start: 0.9395 (tp) cc_final: 0.9168 (mm) REVERT: B 294 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: B 398 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: B 434 ILE cc_start: 0.9251 (mm) cc_final: 0.8641 (tp) REVERT: B 740 MET cc_start: 0.8951 (tpt) cc_final: 0.8549 (tpp) REVERT: C 105 ILE cc_start: 0.9374 (tp) cc_final: 0.9096 (mm) REVERT: C 175 PHE cc_start: 0.8507 (m-80) cc_final: 0.8263 (m-80) REVERT: C 398 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: C 434 ILE cc_start: 0.9262 (mm) cc_final: 0.8699 (tp) outliers start: 66 outliers final: 42 residues processed: 202 average time/residue: 0.1968 time to fit residues: 70.7891 Evaluate side-chains 196 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 177 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 448 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN D 599 ASN E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 188 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 = 0.4173 r_free = 0.4173 target = 0.115681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.070621 restraints weight = 161996.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067893 restraints weight = 110557.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068036 restraints weight = 111180.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067965 restraints weight = 95490.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068416 restraints weight = 81416.953| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 39660 Z= 0.201 Angle : 0.622 11.185 54027 Z= 0.304 Chirality : 0.043 0.385 6081 Planarity : 0.004 0.052 6876 Dihedral : 5.644 53.495 6231 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.72 % Allowed : 13.50 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 4686 helix: 1.79 (0.13), residues: 1695 sheet: -0.45 (0.18), residues: 729 loop : -1.30 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.021 0.001 TYR C1067 PHE 0.015 0.001 PHE B 43 TRP 0.012 0.001 TRP E 459 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00460 (39552) covalent geometry : angle 0.59481 (53769) SS BOND : bond 0.00247 ( 48) SS BOND : angle 1.27547 ( 96) hydrogen bonds : bond 0.04229 ( 1653) hydrogen bonds : angle 5.22322 ( 4689) metal coordination : bond 0.00297 ( 6) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 1.74397 ( 9) link_NAG-ASN : bond 0.00446 ( 51) link_NAG-ASN : angle 3.30731 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 143 time to evaluate : 1.500 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 90 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8862 (m) REVERT: A 105 ILE cc_start: 0.9270 (tp) cc_final: 0.9014 (mm) REVERT: A 398 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: A 434 ILE cc_start: 0.9239 (mm) cc_final: 0.8648 (tp) REVERT: A 725 GLU cc_start: 0.8121 (tt0) cc_final: 0.7514 (pt0) REVERT: D 249 MET cc_start: 0.6437 (mtt) cc_final: 0.6012 (mmt) REVERT: D 270 MET cc_start: 0.7856 (ptm) cc_final: 0.6904 (pmm) REVERT: D 332 MET cc_start: 0.5895 (ppp) cc_final: 0.5344 (ppp) REVERT: D 366 MET cc_start: 0.7359 (tpp) cc_final: 0.7123 (tpp) REVERT: D 408 MET cc_start: 0.7912 (ptp) cc_final: 0.7368 (ptm) REVERT: D 462 MET cc_start: 0.6424 (ptt) cc_final: 0.5866 (mmt) REVERT: D 480 MET cc_start: 0.5708 (ptt) cc_final: 0.4785 (ptt) REVERT: D 516 TYR cc_start: 0.8271 (t80) cc_final: 0.7313 (m-80) REVERT: D 557 MET cc_start: 0.8852 (ppp) cc_final: 0.8557 (ppp) REVERT: D 558 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9129 (mt) REVERT: E 62 MET cc_start: 0.9472 (mtm) cc_final: 0.9192 (mpp) REVERT: E 82 MET cc_start: 0.9480 (ptp) cc_final: 0.9151 (ppp) REVERT: E 152 MET cc_start: 0.1820 (OUTLIER) cc_final: 0.1290 (tmm) REVERT: E 197 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8314 (pp20) REVERT: E 270 MET cc_start: 0.7102 (ptm) cc_final: 0.6022 (ptm) REVERT: E 332 MET cc_start: 0.5858 (ppp) cc_final: 0.4820 (ppp) REVERT: E 366 MET cc_start: 0.8207 (tpp) cc_final: 0.7532 (mmm) REVERT: E 557 MET cc_start: 0.8903 (ppp) cc_final: 0.8610 (ppp) REVERT: E 558 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9246 (mt) REVERT: F 249 MET cc_start: 0.6328 (mtt) cc_final: 0.5541 (mmm) REVERT: F 270 MET cc_start: 0.7643 (pmm) cc_final: 0.7306 (pmm) REVERT: F 332 MET cc_start: 0.6573 (ppp) cc_final: 0.6125 (ppp) REVERT: F 376 MET cc_start: 0.8760 (ptp) cc_final: 0.8480 (ptp) REVERT: F 455 MET cc_start: 0.7649 (ppp) cc_final: 0.7218 (ppp) REVERT: F 462 MET cc_start: 0.6150 (ptt) cc_final: 0.5279 (mmt) REVERT: F 558 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9225 (mt) REVERT: B 105 ILE cc_start: 0.9375 (tp) cc_final: 0.9135 (mm) REVERT: B 294 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: B 398 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: B 434 ILE cc_start: 0.9277 (mm) cc_final: 0.8661 (tp) REVERT: B 740 MET cc_start: 0.8929 (tpt) cc_final: 0.8542 (tpp) REVERT: C 105 ILE cc_start: 0.9377 (tp) cc_final: 0.9090 (mm) REVERT: C 175 PHE cc_start: 0.8617 (m-80) cc_final: 0.8338 (m-80) REVERT: C 398 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: C 434 ILE cc_start: 0.9283 (mm) cc_final: 0.8745 (tp) outliers start: 72 outliers final: 48 residues processed: 203 average time/residue: 0.1904 time to fit residues: 68.9821 Evaluate side-chains 198 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 210 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 429 optimal weight: 2.9990 chunk 407 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 174 optimal weight: 20.0000 chunk 297 optimal weight: 0.7980 chunk 433 optimal weight: 0.5980 chunk 387 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN B 188 ASN C 188 ASN ** C 544 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 = 0.4189 r_free = 0.4189 target = 0.116681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.070494 restraints weight = 160376.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068559 restraints weight = 100459.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069306 restraints weight = 85865.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068810 restraints weight = 86240.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069141 restraints weight = 71604.055| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39660 Z= 0.124 Angle : 0.581 11.086 54027 Z= 0.282 Chirality : 0.043 0.381 6081 Planarity : 0.003 0.054 6876 Dihedral : 5.476 52.914 6231 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.56 % Allowed : 13.85 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 4686 helix: 1.93 (0.13), residues: 1695 sheet: -0.31 (0.18), residues: 735 loop : -1.20 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.015 0.001 TYR B1067 PHE 0.027 0.001 PHE E 315 TRP 0.012 0.001 TRP E 271 HIS 0.010 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00278 (39552) covalent geometry : angle 0.55456 (53769) SS BOND : bond 0.00190 ( 48) SS BOND : angle 1.10449 ( 96) hydrogen bonds : bond 0.03850 ( 1653) hydrogen bonds : angle 5.05777 ( 4689) metal coordination : bond 0.00308 ( 6) link_BETA1-4 : bond 0.00560 ( 3) link_BETA1-4 : angle 1.82863 ( 9) link_NAG-ASN : bond 0.00445 ( 51) link_NAG-ASN : angle 3.16689 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 1.136 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: symmetry clash REVERT: A 90 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8881 (m) REVERT: A 105 ILE cc_start: 0.9211 (tp) cc_final: 0.8966 (mm) REVERT: A 398 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: A 434 ILE cc_start: 0.9203 (mm) cc_final: 0.8650 (tp) REVERT: A 513 LEU cc_start: 0.9723 (mt) cc_final: 0.9459 (pt) REVERT: A 725 GLU cc_start: 0.8545 (tt0) cc_final: 0.7815 (pt0) REVERT: A 754 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9385 (mm) REVERT: D 190 MET cc_start: 0.8983 (ptp) cc_final: 0.8729 (ptp) REVERT: D 249 MET cc_start: 0.6467 (mtt) cc_final: 0.5996 (mmt) REVERT: D 332 MET cc_start: 0.5563 (ppp) cc_final: 0.4955 (ppp) REVERT: D 366 MET cc_start: 0.7390 (tpp) cc_final: 0.7163 (tpp) REVERT: D 408 MET cc_start: 0.7636 (ptp) cc_final: 0.7191 (ptm) REVERT: D 462 MET cc_start: 0.6401 (ptt) cc_final: 0.5850 (mmt) REVERT: D 480 MET cc_start: 0.5510 (ptt) cc_final: 0.4594 (ptt) REVERT: D 516 TYR cc_start: 0.8270 (t80) cc_final: 0.7343 (m-80) REVERT: D 557 MET cc_start: 0.8869 (ppp) cc_final: 0.8558 (ppp) REVERT: D 558 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9101 (mt) REVERT: E 82 MET cc_start: 0.9480 (ptp) cc_final: 0.9156 (ppp) REVERT: E 152 MET cc_start: 0.1941 (OUTLIER) cc_final: 0.1458 (tmm) REVERT: E 197 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: E 270 MET cc_start: 0.6992 (ptm) cc_final: 0.5967 (ptm) REVERT: E 332 MET cc_start: 0.5714 (ppp) cc_final: 0.4677 (ppp) REVERT: E 366 MET cc_start: 0.8149 (tpp) cc_final: 0.7439 (mmm) REVERT: E 408 MET cc_start: 0.8656 (pmm) cc_final: 0.8065 (pmm) REVERT: E 462 MET cc_start: 0.5351 (ptt) cc_final: 0.4743 (mmt) REVERT: E 557 MET cc_start: 0.8909 (ppp) cc_final: 0.8619 (ppp) REVERT: E 558 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9242 (mt) REVERT: F 249 MET cc_start: 0.6240 (mtt) cc_final: 0.5213 (mmm) REVERT: F 270 MET cc_start: 0.7597 (pmm) cc_final: 0.7349 (pmm) REVERT: F 332 MET cc_start: 0.6485 (ppp) cc_final: 0.6032 (ppp) REVERT: F 462 MET cc_start: 0.6081 (ptt) cc_final: 0.5247 (mmt) REVERT: F 557 MET cc_start: 0.8529 (ppp) cc_final: 0.8173 (ppp) REVERT: F 558 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9177 (mt) REVERT: B 90 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8739 (m) REVERT: B 294 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8364 (m-30) REVERT: B 398 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: B 434 ILE cc_start: 0.9256 (mm) cc_final: 0.8674 (tp) REVERT: B 513 LEU cc_start: 0.9764 (mt) cc_final: 0.9503 (pt) REVERT: B 740 MET cc_start: 0.8921 (tpt) cc_final: 0.8540 (tpp) REVERT: C 105 ILE cc_start: 0.9329 (tp) cc_final: 0.9114 (mm) REVERT: C 175 PHE cc_start: 0.8506 (m-80) cc_final: 0.8260 (m-80) REVERT: C 398 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: C 434 ILE cc_start: 0.9251 (mm) cc_final: 0.8708 (tp) REVERT: C 513 LEU cc_start: 0.9764 (mt) cc_final: 0.9514 (pt) outliers start: 65 outliers final: 44 residues processed: 198 average time/residue: 0.2013 time to fit residues: 70.3125 Evaluate side-chains 195 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 133 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 321 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 356 optimal weight: 0.0870 chunk 451 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 277 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.117145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070928 restraints weight = 161682.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.069629 restraints weight = 103695.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.069778 restraints weight = 91447.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069911 restraints weight = 78041.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070018 restraints weight = 70686.367| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39660 Z= 0.111 Angle : 0.571 12.951 54027 Z= 0.278 Chirality : 0.043 0.363 6081 Planarity : 0.003 0.055 6876 Dihedral : 5.352 53.804 6231 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.32 % Allowed : 14.09 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4686 helix: 2.03 (0.13), residues: 1686 sheet: -0.21 (0.18), residues: 735 loop : -1.13 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 983 TYR 0.013 0.001 TYR B1067 PHE 0.016 0.001 PHE E 315 TRP 0.015 0.001 TRP F 477 HIS 0.007 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00245 (39552) covalent geometry : angle 0.54620 (53769) SS BOND : bond 0.00174 ( 48) SS BOND : angle 1.04918 ( 96) hydrogen bonds : bond 0.03637 ( 1653) hydrogen bonds : angle 4.97026 ( 4689) metal coordination : bond 0.00349 ( 6) link_BETA1-4 : bond 0.00195 ( 3) link_BETA1-4 : angle 1.79115 ( 9) link_NAG-ASN : bond 0.00466 ( 51) link_NAG-ASN : angle 3.07573 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 146 time to evaluate : 1.404 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: symmetry clash REVERT: A 105 ILE cc_start: 0.9222 (tp) cc_final: 0.8976 (mm) REVERT: A 434 ILE cc_start: 0.9248 (mm) cc_final: 0.8809 (tp) REVERT: A 513 LEU cc_start: 0.9729 (mt) cc_final: 0.9436 (pt) REVERT: A 725 GLU cc_start: 0.7997 (tt0) cc_final: 0.7617 (pt0) REVERT: A 754 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9394 (mm) REVERT: D 249 MET cc_start: 0.6427 (mtt) cc_final: 0.5863 (mmt) REVERT: D 332 MET cc_start: 0.5571 (ppp) cc_final: 0.4923 (ppp) REVERT: D 366 MET cc_start: 0.7356 (tpp) cc_final: 0.7076 (tpp) REVERT: D 408 MET cc_start: 0.7688 (ptp) cc_final: 0.6298 (ppp) REVERT: D 462 MET cc_start: 0.6397 (ptt) cc_final: 0.5848 (mmt) REVERT: D 480 MET cc_start: 0.5385 (ptt) cc_final: 0.4699 (ptt) REVERT: D 516 TYR cc_start: 0.8230 (t80) cc_final: 0.7326 (m-80) REVERT: D 557 MET cc_start: 0.8827 (ppp) cc_final: 0.8519 (ppp) REVERT: D 558 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9046 (mt) REVERT: E 82 MET cc_start: 0.9482 (ptp) cc_final: 0.9162 (ppp) REVERT: E 152 MET cc_start: 0.1772 (OUTLIER) cc_final: 0.1351 (tmm) REVERT: E 190 MET cc_start: 0.9325 (ppp) cc_final: 0.8977 (pmm) REVERT: E 197 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: E 270 MET cc_start: 0.6992 (ptm) cc_final: 0.5998 (ptm) REVERT: E 323 MET cc_start: 0.8111 (tmm) cc_final: 0.7332 (ppp) REVERT: E 332 MET cc_start: 0.5527 (ppp) cc_final: 0.4463 (ppp) REVERT: E 366 MET cc_start: 0.8199 (tpp) cc_final: 0.7518 (mmm) REVERT: E 408 MET cc_start: 0.8663 (pmm) cc_final: 0.8167 (pmm) REVERT: E 462 MET cc_start: 0.5352 (ptt) cc_final: 0.4734 (mmt) REVERT: E 557 MET cc_start: 0.8926 (ppp) cc_final: 0.8650 (ppp) REVERT: E 558 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9184 (mt) REVERT: F 249 MET cc_start: 0.6205 (mtt) cc_final: 0.5196 (mmm) REVERT: F 270 MET cc_start: 0.7518 (pmm) cc_final: 0.7250 (pmm) REVERT: F 332 MET cc_start: 0.6393 (ppp) cc_final: 0.5934 (ppp) REVERT: F 462 MET cc_start: 0.6142 (ptt) cc_final: 0.5316 (mmt) REVERT: F 557 MET cc_start: 0.8557 (ppp) cc_final: 0.8169 (ppp) REVERT: F 558 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9148 (mt) REVERT: B 90 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8798 (m) REVERT: B 294 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: B 434 ILE cc_start: 0.9308 (mm) cc_final: 0.8743 (tp) REVERT: B 513 LEU cc_start: 0.9766 (mt) cc_final: 0.9535 (pt) REVERT: B 740 MET cc_start: 0.8898 (tpt) cc_final: 0.8499 (tpp) REVERT: C 105 ILE cc_start: 0.9336 (tp) cc_final: 0.9055 (mm) REVERT: C 175 PHE cc_start: 0.8463 (m-80) cc_final: 0.8251 (m-80) REVERT: C 398 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: C 434 ILE cc_start: 0.9247 (mm) cc_final: 0.8756 (tp) REVERT: C 513 LEU cc_start: 0.9764 (mt) cc_final: 0.9513 (pt) outliers start: 55 outliers final: 39 residues processed: 191 average time/residue: 0.1976 time to fit residues: 66.6667 Evaluate side-chains 190 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 60 optimal weight: 0.9990 chunk 239 optimal weight: 30.0000 chunk 454 optimal weight: 0.0370 chunk 88 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 352 optimal weight: 0.3980 chunk 374 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 458 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 470 optimal weight: 0.0670 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN B1088 HIS ** C 544 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 = 0.4202 r_free = 0.4202 target = 0.117426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071856 restraints weight = 162301.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069979 restraints weight = 99974.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070827 restraints weight = 84774.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070528 restraints weight = 80177.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070833 restraints weight = 69833.589| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 39660 Z= 0.101 Angle : 0.569 12.782 54027 Z= 0.277 Chirality : 0.043 0.357 6081 Planarity : 0.003 0.056 6876 Dihedral : 5.257 53.562 6231 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.27 % Allowed : 14.24 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 4686 helix: 2.04 (0.13), residues: 1686 sheet: -0.08 (0.19), residues: 735 loop : -1.09 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.011 0.001 TYR A1067 PHE 0.031 0.001 PHE E 315 TRP 0.017 0.001 TRP B 104 HIS 0.007 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00218 (39552) covalent geometry : angle 0.54541 (53769) SS BOND : bond 0.00167 ( 48) SS BOND : angle 1.00385 ( 96) hydrogen bonds : bond 0.03524 ( 1653) hydrogen bonds : angle 4.94744 ( 4689) metal coordination : bond 0.00009 ( 6) link_BETA1-4 : bond 0.00568 ( 3) link_BETA1-4 : angle 1.83659 ( 9) link_NAG-ASN : bond 0.00470 ( 51) link_NAG-ASN : angle 3.00583 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6908.42 seconds wall clock time: 120 minutes 24.57 seconds (7224.57 seconds total)