Starting phenix.real_space_refine on Mon Jul 6 19:57:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r1a_14236/07_2026/7r1a_14236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r1a_14236/07_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_14236/07_2026/7r1a_14236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r1a_14236/07_2026/7r1a_14236.map" model { file = "/net/cci-nas-00/data/ceres_data/7r1a_14236/07_2026/7r1a_14236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r1a_14236/07_2026/7r1a_14236.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r1a_14236/07_2026/7r1a_14236.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r1a_14236/07_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-6108/lib/python3.11/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 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 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 chiralities: 6 Restraints were copied for chains: B, C, E, F, H, I Time building chain proxies: 14.13, per 1000 atoms: 0.37 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: 3.42 Conformation dependent library (CDL) restraints added in 1.9 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: 1.39 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: 9.96 Time building geometry restraints manager: 4.57 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: 20861 17.93 - 35.86: 1795 35.86 - 53.78: 234 53.78 - 71.71: 60 71.71 - 89.64: 63 Dihedral angle restraints: 23013 sinusoidal: 9126 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 23010 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: 0.12 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: 13.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 48.960 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 14.024 89.639 13923 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/Z covalent geometry : bond 0.00359 / 0.17 (39552) covalent geometry : angle 0.54381 / 0.28 (53769) SS BOND : bond 0.00196 / 0.13 ( 48) SS BOND : angle 1.13701 / 0.68 ( 96) hydrogen bonds : bond 0.20444 / 13.72 ( 1653) hydrogen bonds : angle 7.07214 / 4.95 ( 4689) metal coordination : bond 0.00126 / 0.08 ( 6) link_BETA1-4 : bond 0.00369 / 0.16 ( 3) link_BETA1-4 : angle 2.11911 / 1.37 ( 9) link_NAG-ASN : bond 0.00775 / 0.48 ( 51) link_NAG-ASN : angle 4.54557 / 2.85 ( 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 : 1.568 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: 0.2339 time to fit residues: 89.3558 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 : 1.202 ------------------------------------------------------------------------------- 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... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 370 ASN A 422 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** D 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.116035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067693 restraints weight = 161703.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065748 restraints weight = 108548.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066142 restraints weight = 89457.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066108 restraints weight = 68776.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066377 restraints weight = 65423.317| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 39660 Z= 0.282 Angle : 0.711 15.739 54027 Z= 0.352 Chirality : 0.045 0.350 6081 Planarity : 0.004 0.040 6876 Dihedral : 4.449 27.334 5097 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.48 % Allowed : 6.87 % Favored : 92.65 % 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: -0.23 (0.12), residues: 4686 helix: 1.77 (0.12), residues: 1662 sheet: -0.68 (0.19), residues: 729 loop : -1.47 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.030 0.001 TYR C1067 PHE 0.023 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/Z covalent geometry : bond 0.00642 / 0.28 (39552) covalent geometry : angle 0.67145 / 0.34 (53769) SS BOND : bond 0.00451 / 0.36 ( 48) SS BOND : angle 1.32899 / 0.80 ( 96) hydrogen bonds : bond 0.05465 / 3.63 ( 1653) hydrogen bonds : angle 5.79841 / 4.07 ( 4689) metal coordination : bond 0.00436 / 0.24 ( 6) link_BETA1-4 : bond 0.00529 / 0.21 ( 3) link_BETA1-4 : angle 1.89883 / 1.23 ( 9) link_NAG-ASN : bond 0.00600 / 0.36 ( 51) link_NAG-ASN : angle 4.31345 / 2.73 ( 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 179 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.417 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: A 135 PHE cc_start: 0.8683 (m-80) cc_final: 0.8473 (m-80) REVERT: D 516 TYR cc_start: 0.8118 (t80) cc_final: 0.7014 (m-80) REVERT: E 332 MET cc_start: 0.5469 (ppp) cc_final: 0.5115 (ppp) REVERT: E 360 MET cc_start: 0.8913 (mtp) cc_final: 0.8322 (tpp) REVERT: E 366 MET cc_start: 0.8225 (tpp) cc_final: 0.7458 (mmm) REVERT: F 249 MET cc_start: 0.5858 (mtt) cc_final: 0.5100 (mmt) REVERT: F 270 MET cc_start: 0.7830 (ttp) cc_final: 0.7420 (ptm) REVERT: F 332 MET cc_start: 0.6676 (ppp) cc_final: 0.6363 (ppp) REVERT: F 471 ASP cc_start: 0.9556 (t0) cc_final: 0.9292 (p0) REVERT: F 474 MET cc_start: 0.7425 (mmp) cc_final: 0.7018 (mmm) REVERT: F 516 TYR cc_start: 0.8151 (t80) cc_final: 0.7050 (m-80) REVERT: B 175 PHE cc_start: 0.8458 (m-80) cc_final: 0.8072 (m-80) REVERT: B 740 MET cc_start: 0.9025 (tpt) cc_final: 0.8537 (tpp) REVERT: C 175 PHE cc_start: 0.8496 (m-80) cc_final: 0.8118 (m-80) REVERT: C 902 MET cc_start: 0.9219 (tpt) cc_final: 0.8945 (tpt) outliers start: 20 outliers final: 15 residues processed: 167 average time/residue: 0.2386 time to fit residues: 66.0830 Evaluate side-chains 157 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 463 optimal weight: 0.6980 chunk 236 optimal weight: 30.0000 chunk 389 optimal weight: 0.9980 chunk 360 optimal weight: 0.5980 chunk 457 optimal weight: 0.5980 chunk 443 optimal weight: 0.0050 chunk 80 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN D 472 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 ** 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 = 0.4209 r_free = 0.4209 target = 0.117822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070806 restraints weight = 161953.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.069505 restraints weight = 103923.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.069684 restraints weight = 86609.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069810 restraints weight = 78057.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070078 restraints weight = 65279.889| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39660 Z= 0.114 Angle : 0.592 13.688 54027 Z= 0.289 Chirality : 0.043 0.357 6081 Planarity : 0.004 0.045 6876 Dihedral : 4.173 21.334 5097 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 8.83 % Favored : 90.50 % 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: 0.12 (0.12), residues: 4686 helix: 2.01 (0.13), residues: 1653 sheet: -0.36 (0.19), residues: 747 loop : -1.27 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.014 0.001 TYR C1067 PHE 0.016 0.001 PHE E 315 TRP 0.016 0.001 TRP E 271 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (39552) covalent geometry : angle 0.55366 / 0.28 (53769) SS BOND : bond 0.00231 / 0.17 ( 48) SS BOND : angle 1.67166 / 1.12 ( 96) hydrogen bonds : bond 0.04400 / 2.92 ( 1653) hydrogen bonds : angle 5.26126 / 3.69 ( 4689) metal coordination : bond 0.00601 / 0.33 ( 6) link_BETA1-4 : bond 0.00839 / 0.39 ( 3) link_BETA1-4 : angle 1.85437 / 1.20 ( 9) link_NAG-ASN : bond 0.00570 / 0.33 ( 51) link_NAG-ASN : angle 3.77595 / 2.42 ( 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 181 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.536 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: D 249 MET cc_start: 0.5534 (mtt) cc_final: 0.5017 (mmm) REVERT: D 270 MET cc_start: 0.8192 (ptm) cc_final: 0.7175 (pmm) REVERT: D 462 MET cc_start: 0.5924 (ptt) cc_final: 0.5170 (mmt) REVERT: D 516 TYR cc_start: 0.7996 (t80) cc_final: 0.7040 (m-80) REVERT: D 557 MET cc_start: 0.8931 (ppp) cc_final: 0.8693 (ppp) REVERT: D 558 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9029 (mt) REVERT: E 270 MET cc_start: 0.6795 (ptm) cc_final: 0.5430 (pmm) REVERT: E 332 MET cc_start: 0.4959 (ppp) cc_final: 0.4008 (ppp) REVERT: E 366 MET cc_start: 0.7942 (tpp) cc_final: 0.7285 (mmm) REVERT: E 480 MET cc_start: 0.6012 (ptt) cc_final: 0.5555 (ptt) REVERT: F 249 MET cc_start: 0.5858 (mtt) cc_final: 0.5104 (mmm) REVERT: F 270 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7063 (pmm) REVERT: F 332 MET cc_start: 0.6125 (ppp) cc_final: 0.5741 (ppp) REVERT: F 366 MET cc_start: 0.6477 (tpp) cc_final: 0.5848 (mmm) REVERT: F 471 ASP cc_start: 0.9477 (t0) cc_final: 0.9207 (p0) REVERT: F 557 MET cc_start: 0.8773 (ppp) cc_final: 0.8370 (ppp) REVERT: F 558 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9020 (mt) REVERT: B 740 MET cc_start: 0.8913 (tpt) cc_final: 0.8410 (tpp) REVERT: C 175 PHE cc_start: 0.8305 (m-80) cc_final: 0.8087 (m-80) outliers start: 28 outliers final: 14 residues processed: 169 average time/residue: 0.2198 time to fit residues: 63.7486 Evaluate side-chains 164 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 297 MET Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 579 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 91 LEU Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 518 LEU 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: 0.6980 chunk 36 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 457 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 371 optimal weight: 4.9990 chunk 120 optimal weight: 30.0000 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.116117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067567 restraints weight = 161716.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066745 restraints weight = 100544.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067393 restraints weight = 79352.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067134 restraints weight = 66381.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.067398 restraints weight = 63529.087| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 39660 Z= 0.217 Angle : 0.630 10.895 54027 Z= 0.310 Chirality : 0.043 0.356 6081 Planarity : 0.004 0.042 6876 Dihedral : 4.278 24.101 5097 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.77 % Allowed : 10.91 % Favored : 88.32 % 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: -0.09 (0.12), residues: 4686 helix: 1.73 (0.13), residues: 1680 sheet: -0.43 (0.18), residues: 729 loop : -1.35 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 214 TYR 0.023 0.001 TYR C1067 PHE 0.016 0.001 PHE B 43 TRP 0.013 0.001 TRP E 271 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (39552) covalent geometry : angle 0.59990 / 0.30 (53769) SS BOND : bond 0.00276 / 0.19 ( 48) SS BOND : angle 1.55119 / 0.98 ( 96) hydrogen bonds : bond 0.04561 / 3.04 ( 1653) hydrogen bonds : angle 5.32649 / 3.73 ( 4689) metal coordination : bond 0.00199 / 0.11 ( 6) link_BETA1-4 : bond 0.00402 / 0.19 ( 3) link_BETA1-4 : angle 1.67162 / 1.08 ( 9) link_NAG-ASN : bond 0.00477 / 0.27 ( 51) link_NAG-ASN : angle 3.45664 / 2.29 ( 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 178 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.409 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: D 249 MET cc_start: 0.5686 (mtt) cc_final: 0.4735 (mmm) REVERT: D 270 MET cc_start: 0.8020 (ptm) cc_final: 0.7075 (pmm) REVERT: D 366 MET cc_start: 0.7011 (tpp) cc_final: 0.6735 (tpp) REVERT: D 408 MET cc_start: 0.7452 (ptp) cc_final: 0.7009 (ptt) REVERT: D 462 MET cc_start: 0.6194 (ptt) cc_final: 0.5471 (mmt) REVERT: D 474 MET cc_start: 0.8176 (mmp) cc_final: 0.7603 (mmm) REVERT: D 516 TYR cc_start: 0.7916 (t80) cc_final: 0.7120 (m-80) REVERT: E 270 MET cc_start: 0.6942 (ptm) cc_final: 0.5581 (pmm) REVERT: E 366 MET cc_start: 0.7892 (tpp) cc_final: 0.7331 (mmm) REVERT: E 480 MET cc_start: 0.5289 (ptt) cc_final: 0.4660 (ptt) REVERT: E 516 TYR cc_start: 0.6525 (t80) cc_final: 0.5790 (m-80) REVERT: E 557 MET cc_start: 0.8807 (ppp) cc_final: 0.8494 (ppp) REVERT: E 558 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9019 (mt) REVERT: F 249 MET cc_start: 0.5695 (mtt) cc_final: 0.5034 (mmm) REVERT: F 270 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6940 (pmm) REVERT: F 376 MET cc_start: 0.8831 (ptp) cc_final: 0.8485 (ptp) REVERT: F 408 MET cc_start: 0.7343 (ptp) cc_final: 0.6850 (ptt) REVERT: F 455 MET cc_start: 0.7232 (ppp) cc_final: 0.6793 (ppp) REVERT: F 462 MET cc_start: 0.6260 (ptt) cc_final: 0.5601 (mmt) REVERT: F 474 MET cc_start: 0.8146 (mmp) cc_final: 0.6955 (mmm) REVERT: F 480 MET cc_start: 0.6619 (ptt) cc_final: 0.5451 (ptt) REVERT: F 516 TYR cc_start: 0.8017 (t80) cc_final: 0.7199 (m-80) REVERT: B 427 ASP cc_start: 0.9168 (m-30) cc_final: 0.8891 (m-30) REVERT: B 434 ILE cc_start: 0.9204 (mm) cc_final: 0.8590 (tp) REVERT: B 740 MET cc_start: 0.8942 (tpt) cc_final: 0.8518 (tpp) outliers start: 32 outliers final: 19 residues processed: 166 average time/residue: 0.2148 time to fit residues: 61.9045 Evaluate side-chains 159 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 781 VAL Chi-restraints excluded: chain A residue 1104 VAL 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 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 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 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 112 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 470 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 396 optimal weight: 0.8980 chunk 309 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4288 r_free = 0.4288 target = 0.119378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.075381 restraints weight = 163149.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073709 restraints weight = 97900.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073954 restraints weight = 82810.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.073880 restraints weight = 78792.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074090 restraints weight = 67396.906| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39660 Z= 0.126 Angle : 0.564 10.112 54027 Z= 0.277 Chirality : 0.042 0.355 6081 Planarity : 0.003 0.055 6876 Dihedral : 4.131 22.075 5097 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.93 % Allowed : 11.73 % Favored : 87.34 % 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: 0.13 (0.12), residues: 4686 helix: 1.94 (0.13), residues: 1677 sheet: -0.24 (0.19), residues: 729 loop : -1.27 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 983 TYR 0.016 0.001 TYR C1067 PHE 0.015 0.001 PHE C 135 TRP 0.012 0.001 TRP E 271 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (39552) covalent geometry : angle 0.53694 / 0.27 (53769) SS BOND : bond 0.00179 / 0.12 ( 48) SS BOND : angle 1.15210 / 0.72 ( 96) hydrogen bonds : bond 0.04026 / 2.68 ( 1653) hydrogen bonds : angle 5.09851 / 3.57 ( 4689) metal coordination : bond 0.00050 / 0.02 ( 6) link_BETA1-4 : bond 0.00586 / 0.26 ( 3) link_BETA1-4 : angle 1.81708 / 1.18 ( 9) link_NAG-ASN : bond 0.00474 / 0.26 ( 51) link_NAG-ASN : angle 3.18099 / 2.11 ( 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 187 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.397 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: 0.9243 (mm) cc_final: 0.8644 (tp) REVERT: D 249 MET cc_start: 0.6355 (mtt) cc_final: 0.5700 (mmm) REVERT: D 270 MET cc_start: 0.7902 (ptm) cc_final: 0.7106 (pmm) REVERT: D 408 MET cc_start: 0.7616 (ptp) cc_final: 0.7146 (ptt) REVERT: D 462 MET cc_start: 0.6139 (ptt) cc_final: 0.5548 (mmt) REVERT: D 516 TYR cc_start: 0.8196 (t80) cc_final: 0.7397 (m-80) REVERT: D 557 MET cc_start: 0.8863 (ppp) cc_final: 0.8604 (ppp) REVERT: D 558 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9192 (mt) REVERT: E 270 MET cc_start: 0.6959 (ptm) cc_final: 0.5592 (pmm) REVERT: E 332 MET cc_start: 0.5774 (ppp) cc_final: 0.4910 (ppp) REVERT: E 366 MET cc_start: 0.8206 (tpp) cc_final: 0.7459 (mmm) REVERT: E 480 MET cc_start: 0.5439 (ptt) cc_final: 0.4946 (ptt) REVERT: E 516 TYR cc_start: 0.6833 (t80) cc_final: 0.6235 (m-80) REVERT: E 557 MET cc_start: 0.8883 (ppp) cc_final: 0.8645 (ppp) REVERT: E 558 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9206 (mt) REVERT: F 249 MET cc_start: 0.6142 (mtt) cc_final: 0.5424 (mmm) REVERT: F 332 MET cc_start: 0.6410 (ppp) cc_final: 0.6072 (ppp) REVERT: F 376 MET cc_start: 0.8850 (ptp) cc_final: 0.8611 (ptp) REVERT: F 408 MET cc_start: 0.7385 (ptp) cc_final: 0.7088 (ptt) REVERT: F 462 MET cc_start: 0.6377 (ptt) cc_final: 0.5786 (mmt) REVERT: F 474 MET cc_start: 0.8283 (mmp) cc_final: 0.7583 (mmm) REVERT: F 480 MET cc_start: 0.6681 (ptt) cc_final: 0.5619 (ptt) REVERT: F 516 TYR cc_start: 0.8232 (t80) cc_final: 0.7478 (m-80) REVERT: F 558 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9179 (mt) REVERT: B 427 ASP cc_start: 0.9392 (m-30) cc_final: 0.9177 (m-30) REVERT: B 434 ILE cc_start: 0.9245 (mm) cc_final: 0.8637 (tp) REVERT: B 740 MET cc_start: 0.9012 (tpt) cc_final: 0.8536 (tpp) REVERT: C 105 ILE cc_start: 0.9380 (tp) cc_final: 0.9102 (mm) outliers start: 39 outliers final: 21 residues processed: 175 average time/residue: 0.2163 time to fit residues: 66.7454 Evaluate side-chains 169 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 294 ASP 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 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 B residue 118 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 294 ASP 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 1104 VAL 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: 0.9980 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 353 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 433 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN F 599 ASN B 188 ASN C 188 ASN ** C 544 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 = 0.4198 r_free = 0.4198 target = 0.117217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071814 restraints weight = 162078.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.069823 restraints weight = 115311.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069740 restraints weight = 105380.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069715 restraints weight = 95531.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069910 restraints weight = 84337.433| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39660 Z= 0.123 Angle : 0.557 11.427 54027 Z= 0.273 Chirality : 0.042 0.351 6081 Planarity : 0.003 0.054 6876 Dihedral : 4.052 21.581 5097 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.27 % Allowed : 12.20 % Favored : 86.53 % 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: 0.21 (0.12), residues: 4686 helix: 1.99 (0.13), residues: 1692 sheet: -0.22 (0.18), residues: 735 loop : -1.22 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.015 0.001 TYR C1067 PHE 0.014 0.001 PHE B 135 TRP 0.019 0.001 TRP F 271 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (39552) covalent geometry : angle 0.53118 / 0.27 (53769) SS BOND : bond 0.00171 / 0.11 ( 48) SS BOND : angle 1.09271 / 0.67 ( 96) hydrogen bonds : bond 0.03842 / 2.57 ( 1653) hydrogen bonds : angle 5.02324 / 3.51 ( 4689) metal coordination : bond 0.00087 / 0.04 ( 6) link_BETA1-4 : bond 0.00493 / 0.22 ( 3) link_BETA1-4 : angle 1.81498 / 1.18 ( 9) link_NAG-ASN : bond 0.00457 / 0.25 ( 51) link_NAG-ASN : angle 3.04516 / 2.03 ( 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 201 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.441 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: 0.9249 (mm) cc_final: 0.8683 (tp) REVERT: D 249 MET cc_start: 0.6397 (mtt) cc_final: 0.5800 (mmm) REVERT: D 270 MET cc_start: 0.8000 (ptm) cc_final: 0.7065 (pmm) REVERT: D 332 MET cc_start: 0.6309 (ppp) cc_final: 0.5785 (ppp) REVERT: D 366 MET cc_start: 0.7284 (tpp) cc_final: 0.7062 (tpp) REVERT: D 408 MET cc_start: 0.7772 (ptp) cc_final: 0.7561 (ptt) REVERT: D 462 MET cc_start: 0.6182 (ptt) cc_final: 0.5551 (mmt) REVERT: D 474 MET cc_start: 0.8081 (mmp) cc_final: 0.7323 (mmm) REVERT: D 557 MET cc_start: 0.8904 (ppp) cc_final: 0.8704 (ppp) REVERT: D 558 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9120 (mt) REVERT: E 82 MET cc_start: 0.9457 (ptp) cc_final: 0.9069 (ppp) REVERT: E 152 MET cc_start: 0.1674 (OUTLIER) cc_final: 0.1045 (tmm) REVERT: E 270 MET cc_start: 0.6907 (ptm) cc_final: 0.5983 (ptm) REVERT: E 332 MET cc_start: 0.5591 (ppp) cc_final: 0.4664 (ppp) REVERT: E 366 MET cc_start: 0.8141 (tpp) cc_final: 0.7481 (mmm) REVERT: E 480 MET cc_start: 0.5390 (ptt) cc_final: 0.4883 (ptt) REVERT: E 558 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9090 (mt) REVERT: F 249 MET cc_start: 0.6154 (mtt) cc_final: 0.5360 (mmm) REVERT: F 270 MET cc_start: 0.7843 (pmm) cc_final: 0.7537 (pmm) REVERT: F 332 MET cc_start: 0.6351 (ppp) cc_final: 0.5912 (ppp) REVERT: F 376 MET cc_start: 0.8843 (ptp) cc_final: 0.8550 (ptp) REVERT: F 408 MET cc_start: 0.7425 (ptp) cc_final: 0.7067 (ptt) REVERT: F 455 MET cc_start: 0.7178 (ppp) cc_final: 0.6775 (ppp) REVERT: F 462 MET cc_start: 0.6501 (ptt) cc_final: 0.6082 (mmt) REVERT: F 474 MET cc_start: 0.8353 (mmp) cc_final: 0.8133 (mmt) REVERT: F 558 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9124 (mt) REVERT: B 105 ILE cc_start: 0.9395 (tp) cc_final: 0.9173 (mm) REVERT: B 427 ASP cc_start: 0.9330 (m-30) cc_final: 0.9115 (m-30) REVERT: B 434 ILE cc_start: 0.9268 (mm) cc_final: 0.8668 (tp) REVERT: B 740 MET cc_start: 0.8898 (tpt) cc_final: 0.8464 (tpp) REVERT: C 105 ILE cc_start: 0.9357 (tp) cc_final: 0.9087 (mm) REVERT: C 434 ILE cc_start: 0.9236 (mm) cc_final: 0.8686 (tp) outliers start: 53 outliers final: 35 residues processed: 191 average time/residue: 0.2108 time to fit residues: 70.8160 Evaluate side-chains 186 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 660 TYR 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 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 228 HIS Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 365 THR 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 753 LEU 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 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 1104 VAL 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: 0.8980 chunk 39 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 chunk 386 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 173 optimal weight: 20.0000 chunk 402 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.116136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070893 restraints weight = 161885.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068177 restraints weight = 106530.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068714 restraints weight = 114516.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068504 restraints weight = 101953.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068691 restraints weight = 92574.984| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 39660 Z= 0.184 Angle : 0.598 10.781 54027 Z= 0.294 Chirality : 0.043 0.351 6081 Planarity : 0.004 0.052 6876 Dihedral : 4.158 23.019 5097 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.41 % Allowed : 13.02 % Favored : 85.57 % 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: 0.09 (0.12), residues: 4686 helix: 1.86 (0.13), residues: 1695 sheet: -0.28 (0.18), residues: 729 loop : -1.28 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE B 43 TRP 0.012 0.001 TRP F 271 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (39552) covalent geometry : angle 0.57346 / 0.29 (53769) SS BOND : bond 0.00238 / 0.16 ( 48) SS BOND : angle 1.25104 / 0.76 ( 96) hydrogen bonds : bond 0.04113 / 2.75 ( 1653) hydrogen bonds : angle 5.11741 / 3.58 ( 4689) metal coordination : bond 0.00058 / 0.02 ( 6) link_BETA1-4 : bond 0.00325 / 0.14 ( 3) link_BETA1-4 : angle 1.75986 / 1.14 ( 9) link_NAG-ASN : bond 0.00434 / 0.24 ( 51) link_NAG-ASN : angle 3.07401 / 2.05 ( 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 210 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 1.331 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: 0.9231 (tp) cc_final: 0.8978 (mm) REVERT: A 398 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.6539 (m-30) REVERT: A 434 ILE cc_start: 0.9225 (mm) cc_final: 0.8684 (tp) REVERT: A 725 GLU cc_start: 0.8521 (tt0) cc_final: 0.7800 (pt0) REVERT: A 754 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9382 (mm) REVERT: D 249 MET cc_start: 0.6284 (mtt) cc_final: 0.5691 (mmm) REVERT: D 270 MET cc_start: 0.7993 (ptm) cc_final: 0.7055 (pmm) REVERT: D 332 MET cc_start: 0.5378 (ppp) cc_final: 0.4777 (ppp) REVERT: D 408 MET cc_start: 0.7849 (ptp) cc_final: 0.6338 (ppp) REVERT: D 462 MET cc_start: 0.6357 (ptt) cc_final: 0.5616 (mmt) REVERT: D 474 MET cc_start: 0.8120 (mmp) cc_final: 0.7312 (mmm) REVERT: D 516 TYR cc_start: 0.8156 (t80) cc_final: 0.7189 (m-10) REVERT: D 558 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9040 (mt) REVERT: E 82 MET cc_start: 0.9458 (ptp) cc_final: 0.9069 (ppp) REVERT: E 152 MET cc_start: 0.2001 (OUTLIER) cc_final: 0.1419 (tmm) REVERT: E 270 MET cc_start: 0.7067 (ptm) cc_final: 0.6009 (ptm) REVERT: E 332 MET cc_start: 0.5232 (ppp) cc_final: 0.4288 (ppp) REVERT: E 366 MET cc_start: 0.8122 (tpp) cc_final: 0.7464 (mmm) REVERT: E 480 MET cc_start: 0.5540 (ptt) cc_final: 0.5094 (ptt) REVERT: E 557 MET cc_start: 0.8798 (ppp) cc_final: 0.8480 (ppp) REVERT: E 558 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9041 (mt) REVERT: F 249 MET cc_start: 0.6077 (mtt) cc_final: 0.5040 (mmm) REVERT: F 270 MET cc_start: 0.7875 (pmm) cc_final: 0.7589 (pmm) REVERT: F 332 MET cc_start: 0.6090 (ppp) cc_final: 0.5867 (ppp) REVERT: F 376 MET cc_start: 0.8733 (ptp) cc_final: 0.8455 (ptp) REVERT: F 408 MET cc_start: 0.7390 (ptp) cc_final: 0.7173 (ptt) REVERT: F 462 MET cc_start: 0.6579 (ptt) cc_final: 0.6058 (mmt) REVERT: F 474 MET cc_start: 0.8347 (mmp) cc_final: 0.8101 (mmt) REVERT: F 480 MET cc_start: 0.6120 (ptt) cc_final: 0.4898 (ptt) REVERT: F 557 MET cc_start: 0.8569 (ppp) cc_final: 0.8197 (ppp) REVERT: F 558 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9033 (mt) REVERT: B 105 ILE cc_start: 0.9365 (tp) cc_final: 0.9129 (mm) REVERT: B 294 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: B 427 ASP cc_start: 0.9243 (m-30) cc_final: 0.8997 (m-30) REVERT: B 434 ILE cc_start: 0.9254 (mm) cc_final: 0.8652 (tp) REVERT: B 740 MET cc_start: 0.8852 (tpt) cc_final: 0.8466 (tpp) REVERT: C 398 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: C 434 ILE cc_start: 0.9267 (mm) cc_final: 0.8709 (tp) REVERT: C 740 MET cc_start: 0.8789 (tpt) cc_final: 0.8565 (tpt) outliers start: 59 outliers final: 40 residues processed: 200 average time/residue: 0.2067 time to fit residues: 72.3771 Evaluate side-chains 193 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 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 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 1104 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 423 LEU 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 358 ILE Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 558 LEU 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 478 THR Chi-restraints excluded: chain B residue 518 LEU 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 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 573 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 177 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 448 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN E 472 GLN B 360 ASN C 360 ASN ** C 544 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 = 0.4171 r_free = 0.4171 target = 0.115600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072819 restraints weight = 162563.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067656 restraints weight = 108180.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068034 restraints weight = 97588.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068245 restraints weight = 86920.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.068273 restraints weight = 78183.376| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2431 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= 0.220 Angle : 0.627 13.188 54027 Z= 0.309 Chirality : 0.043 0.357 6081 Planarity : 0.004 0.052 6876 Dihedral : 4.267 24.344 5097 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.46 % Allowed : 13.38 % 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: -0.03 (0.12), residues: 4686 helix: 1.75 (0.13), residues: 1695 sheet: -0.41 (0.18), residues: 729 loop : -1.30 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.024 0.001 TYR C1067 PHE 0.015 0.001 PHE B 43 TRP 0.011 0.001 TRP F 271 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (39552) covalent geometry : angle 0.60330 / 0.30 (53769) SS BOND : bond 0.00259 / 0.17 ( 48) SS BOND : angle 1.31044 / 0.80 ( 96) hydrogen bonds : bond 0.04266 / 2.85 ( 1653) hydrogen bonds : angle 5.23065 / 3.65 ( 4689) metal coordination : bond 0.00057 / 0.02 ( 6) link_BETA1-4 : bond 0.00362 / 0.16 ( 3) link_BETA1-4 : angle 1.75826 / 1.14 ( 9) link_NAG-ASN : bond 0.00442 / 0.23 ( 51) link_NAG-ASN : angle 3.12115 / 2.08 ( 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 202 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 141 time to evaluate : 1.572 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 105 ILE cc_start: 0.9263 (tp) cc_final: 0.9005 (mm) REVERT: A 294 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: A 398 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: A 434 ILE cc_start: 0.9278 (mm) cc_final: 0.8711 (tp) REVERT: A 725 GLU cc_start: 0.8188 (tt0) cc_final: 0.7509 (pt0) REVERT: D 249 MET cc_start: 0.6280 (mtt) cc_final: 0.5878 (mmt) REVERT: D 270 MET cc_start: 0.7954 (ptm) cc_final: 0.7033 (pmm) REVERT: D 332 MET cc_start: 0.5549 (ppp) cc_final: 0.5001 (ppp) REVERT: D 408 MET cc_start: 0.7860 (ptp) cc_final: 0.7342 (ptm) REVERT: D 462 MET cc_start: 0.6452 (ptt) cc_final: 0.5859 (mmt) REVERT: D 474 MET cc_start: 0.8116 (mmp) cc_final: 0.7444 (mmm) REVERT: D 480 MET cc_start: 0.5612 (ptt) cc_final: 0.4643 (ptt) REVERT: D 516 TYR cc_start: 0.8212 (t80) cc_final: 0.7249 (m-10) REVERT: D 557 MET cc_start: 0.8751 (ppp) cc_final: 0.8395 (ppp) REVERT: D 558 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9104 (mt) REVERT: E 82 MET cc_start: 0.9468 (ptp) cc_final: 0.9106 (ppp) REVERT: E 152 MET cc_start: 0.1981 (OUTLIER) cc_final: 0.1459 (tmm) REVERT: E 270 MET cc_start: 0.7170 (ptm) cc_final: 0.6149 (ptm) REVERT: E 332 MET cc_start: 0.5291 (ppp) cc_final: 0.4291 (ppp) REVERT: E 366 MET cc_start: 0.8194 (tpp) cc_final: 0.7524 (mmm) REVERT: E 408 MET cc_start: 0.8791 (pmm) cc_final: 0.8226 (pmm) REVERT: E 557 MET cc_start: 0.8836 (ppp) cc_final: 0.8576 (ppp) REVERT: E 558 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9090 (mt) REVERT: F 249 MET cc_start: 0.6124 (mtt) cc_final: 0.5124 (mmm) REVERT: F 270 MET cc_start: 0.7811 (pmm) cc_final: 0.7349 (pmm) REVERT: F 332 MET cc_start: 0.6286 (ppp) cc_final: 0.6003 (ppp) REVERT: F 462 MET cc_start: 0.6687 (ptt) cc_final: 0.6075 (mmt) REVERT: F 474 MET cc_start: 0.8288 (mmp) cc_final: 0.7997 (mmt) REVERT: F 480 MET cc_start: 0.6161 (ptt) cc_final: 0.4937 (ptt) REVERT: F 558 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9098 (mt) REVERT: B 105 ILE cc_start: 0.9362 (tp) cc_final: 0.9101 (mm) REVERT: B 294 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: B 398 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: B 434 ILE cc_start: 0.9265 (mm) cc_final: 0.8651 (tp) REVERT: B 740 MET cc_start: 0.8943 (tpt) cc_final: 0.8551 (tpp) REVERT: C 398 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7278 (m-30) REVERT: C 434 ILE cc_start: 0.9288 (mm) cc_final: 0.8763 (tp) REVERT: C 740 MET cc_start: 0.8939 (tpt) cc_final: 0.8685 (tpt) outliers start: 61 outliers final: 39 residues processed: 190 average time/residue: 0.2153 time to fit residues: 71.8681 Evaluate side-chains 183 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 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 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 358 ILE 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 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 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 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 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 660 TYR 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 1050 MET 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: 5.9990 chunk 210 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 429 optimal weight: 2.9990 chunk 407 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 297 optimal weight: 0.8980 chunk 433 optimal weight: 0.5980 chunk 387 optimal weight: 0.4980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.116276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.071403 restraints weight = 161232.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068912 restraints weight = 106274.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069047 restraints weight = 104931.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069453 restraints weight = 84081.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069508 restraints weight = 78464.799| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39660 Z= 0.156 Angle : 0.588 11.291 54027 Z= 0.288 Chirality : 0.043 0.359 6081 Planarity : 0.003 0.051 6876 Dihedral : 4.184 22.697 5097 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.51 % Allowed : 13.50 % Favored : 85.00 % 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: 1.86 (0.13), residues: 1695 sheet: -0.34 (0.18), residues: 735 loop : -1.22 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 983 TYR 0.020 0.001 TYR C1067 PHE 0.041 0.001 PHE E 315 TRP 0.010 0.001 TRP E 271 HIS 0.010 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (39552) covalent geometry : angle 0.56410 / 0.28 (53769) SS BOND : bond 0.00200 / 0.13 ( 48) SS BOND : angle 1.17248 / 0.72 ( 96) hydrogen bonds : bond 0.03971 / 2.65 ( 1653) hydrogen bonds : angle 5.11908 / 3.57 ( 4689) metal coordination : bond 0.00123 / 0.09 ( 6) link_BETA1-4 : bond 0.00536 / 0.22 ( 3) link_BETA1-4 : angle 1.81821 / 1.18 ( 9) link_NAG-ASN : bond 0.00412 / 0.22 ( 51) link_NAG-ASN : angle 3.03912 / 2.03 ( 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 201 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 138 time to evaluate : 1.518 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 105 ILE cc_start: 0.9218 (tp) cc_final: 0.8969 (mm) REVERT: A 398 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: A 434 ILE cc_start: 0.9259 (mm) cc_final: 0.8696 (tp) REVERT: A 725 GLU cc_start: 0.8534 (tt0) cc_final: 0.7833 (pt0) REVERT: A 754 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9384 (mm) REVERT: D 249 MET cc_start: 0.6471 (mtt) cc_final: 0.5889 (mmt) REVERT: D 270 MET cc_start: 0.7873 (ptm) cc_final: 0.6927 (pmm) REVERT: D 332 MET cc_start: 0.5362 (ppp) cc_final: 0.4772 (ppp) REVERT: D 366 MET cc_start: 0.7329 (tpp) cc_final: 0.6977 (tpp) REVERT: D 408 MET cc_start: 0.7823 (ptp) cc_final: 0.6438 (ppp) REVERT: D 462 MET cc_start: 0.6430 (ptt) cc_final: 0.5853 (mmt) REVERT: D 474 MET cc_start: 0.8102 (mmp) cc_final: 0.7420 (mmm) REVERT: D 480 MET cc_start: 0.5553 (ptt) cc_final: 0.4596 (ptt) REVERT: D 516 TYR cc_start: 0.8255 (t80) cc_final: 0.7343 (m-10) REVERT: D 557 MET cc_start: 0.8785 (ppp) cc_final: 0.8494 (ppp) REVERT: E 82 MET cc_start: 0.9476 (ptp) cc_final: 0.9134 (ppp) REVERT: E 152 MET cc_start: 0.2083 (OUTLIER) cc_final: 0.1615 (tmm) REVERT: E 190 MET cc_start: 0.9353 (ppp) cc_final: 0.9112 (pmm) REVERT: E 270 MET cc_start: 0.7157 (ptm) cc_final: 0.6165 (ptm) REVERT: E 332 MET cc_start: 0.5261 (ppp) cc_final: 0.4211 (ppp) REVERT: E 366 MET cc_start: 0.8209 (tpp) cc_final: 0.7499 (mmm) REVERT: E 408 MET cc_start: 0.8727 (pmm) cc_final: 0.8224 (pmm) REVERT: E 455 MET cc_start: 0.5858 (ppp) cc_final: 0.5581 (ppp) REVERT: E 462 MET cc_start: 0.5284 (ptt) cc_final: 0.4699 (mmt) REVERT: E 557 MET cc_start: 0.8893 (ppp) cc_final: 0.8602 (ppp) REVERT: E 558 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9113 (mt) REVERT: F 249 MET cc_start: 0.6152 (mtt) cc_final: 0.5157 (mmm) REVERT: F 270 MET cc_start: 0.7727 (pmm) cc_final: 0.7378 (pmm) REVERT: F 332 MET cc_start: 0.6138 (ppp) cc_final: 0.5838 (ppp) REVERT: F 462 MET cc_start: 0.6679 (ptt) cc_final: 0.6071 (mmt) REVERT: F 474 MET cc_start: 0.8268 (mmp) cc_final: 0.7909 (mmt) REVERT: F 480 MET cc_start: 0.6097 (ptt) cc_final: 0.4870 (ptt) REVERT: F 557 MET cc_start: 0.8580 (ppp) cc_final: 0.8152 (ppp) REVERT: F 558 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9116 (mt) REVERT: B 105 ILE cc_start: 0.9376 (tp) cc_final: 0.9149 (mm) REVERT: B 294 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: B 398 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: B 434 ILE cc_start: 0.9259 (mm) cc_final: 0.8656 (tp) REVERT: B 740 MET cc_start: 0.8827 (tpt) cc_final: 0.8450 (tpp) REVERT: C 398 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: C 434 ILE cc_start: 0.9273 (mm) cc_final: 0.8732 (tp) REVERT: C 513 LEU cc_start: 0.9763 (mt) cc_final: 0.9521 (pt) REVERT: C 740 MET cc_start: 0.8824 (tpt) cc_final: 0.8610 (tpt) outliers start: 63 outliers final: 43 residues processed: 192 average time/residue: 0.2073 time to fit residues: 70.5689 Evaluate side-chains 189 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 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 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 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 152 MET 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 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 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 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 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 573 THR Chi-restraints excluded: chain C residue 660 TYR 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: 6.9990 chunk 88 optimal weight: 1.9990 chunk 321 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 356 optimal weight: 0.6980 chunk 451 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 277 optimal weight: 1.9990 chunk 122 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.117049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072519 restraints weight = 160880.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069738 restraints weight = 106123.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069997 restraints weight = 110677.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.069931 restraints weight = 96182.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070291 restraints weight = 81105.474| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39660 Z= 0.113 Angle : 0.571 12.018 54027 Z= 0.279 Chirality : 0.043 0.351 6081 Planarity : 0.003 0.053 6876 Dihedral : 4.039 21.404 5097 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 13.76 % Favored : 85.07 % 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: 0.26 (0.13), residues: 4686 helix: 1.97 (0.13), residues: 1695 sheet: -0.16 (0.19), residues: 735 loop : -1.16 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 559 TYR 0.025 0.001 TYR D 385 PHE 0.025 0.001 PHE E 452 TRP 0.011 0.001 TRP E 271 HIS 0.006 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (39552) covalent geometry : angle 0.54891 / 0.27 (53769) SS BOND : bond 0.00169 / 0.11 ( 48) SS BOND : angle 1.06446 / 0.65 ( 96) hydrogen bonds : bond 0.03662 / 2.45 ( 1653) hydrogen bonds : angle 4.99162 / 3.48 ( 4689) metal coordination : bond 0.00161 / 0.07 ( 6) link_BETA1-4 : bond 0.00468 / 0.20 ( 3) link_BETA1-4 : angle 1.83505 / 1.20 ( 9) link_NAG-ASN : bond 0.00437 / 0.23 ( 51) link_NAG-ASN : angle 2.91284 / 1.93 ( 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 192 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9292 (mm) cc_final: 0.8814 (tp) REVERT: A 513 LEU cc_start: 0.9731 (mt) cc_final: 0.9463 (pt) REVERT: A 725 GLU cc_start: 0.8495 (tt0) cc_final: 0.8000 (pt0) REVERT: A 754 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9380 (mm) REVERT: D 249 MET cc_start: 0.6521 (mtt) cc_final: 0.5919 (mmt) REVERT: D 332 MET cc_start: 0.5534 (ppp) cc_final: 0.4900 (ppp) REVERT: D 366 MET cc_start: 0.7294 (tpp) cc_final: 0.6926 (tpp) REVERT: D 408 MET cc_start: 0.7682 (ptp) cc_final: 0.6451 (ppp) REVERT: D 462 MET cc_start: 0.6403 (ptt) cc_final: 0.5857 (mmt) REVERT: D 474 MET cc_start: 0.8029 (mmp) cc_final: 0.7350 (mmm) REVERT: D 480 MET cc_start: 0.5460 (ptt) cc_final: 0.4770 (ptt) REVERT: D 516 TYR cc_start: 0.8267 (t80) cc_final: 0.7395 (m-80) REVERT: D 557 MET cc_start: 0.8733 (ppp) cc_final: 0.8507 (ppp) REVERT: E 82 MET cc_start: 0.9499 (ptp) cc_final: 0.9174 (ppp) REVERT: E 152 MET cc_start: 0.1664 (OUTLIER) cc_final: 0.1296 (tmm) REVERT: E 270 MET cc_start: 0.7178 (ptm) cc_final: 0.6209 (ptm) REVERT: E 332 MET cc_start: 0.5452 (ppp) cc_final: 0.4508 (ppp) REVERT: E 366 MET cc_start: 0.8208 (tpp) cc_final: 0.7497 (mmm) REVERT: E 408 MET cc_start: 0.8792 (pmm) cc_final: 0.8314 (pmm) REVERT: E 462 MET cc_start: 0.5144 (ptt) cc_final: 0.4584 (mmt) REVERT: E 557 MET cc_start: 0.8927 (ppp) cc_final: 0.8650 (ppp) REVERT: E 558 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9124 (mt) REVERT: F 249 MET cc_start: 0.6149 (mtt) cc_final: 0.5119 (mmm) REVERT: F 270 MET cc_start: 0.7628 (pmm) cc_final: 0.7258 (pmm) REVERT: F 332 MET cc_start: 0.6234 (ppp) cc_final: 0.5922 (ppp) REVERT: F 462 MET cc_start: 0.6559 (ptt) cc_final: 0.6091 (mmt) REVERT: F 474 MET cc_start: 0.8241 (mmp) cc_final: 0.7894 (mmt) REVERT: F 480 MET cc_start: 0.6075 (ptt) cc_final: 0.4850 (ptt) REVERT: F 557 MET cc_start: 0.8629 (ppp) cc_final: 0.8226 (ppp) REVERT: F 558 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9129 (mt) REVERT: B 105 ILE cc_start: 0.9365 (tp) cc_final: 0.9111 (mm) REVERT: B 294 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: B 434 ILE cc_start: 0.9302 (mm) cc_final: 0.8733 (tp) REVERT: B 513 LEU cc_start: 0.9769 (mt) cc_final: 0.9540 (pt) REVERT: B 740 MET cc_start: 0.8954 (tpt) cc_final: 0.8556 (tpp) REVERT: C 398 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7088 (m-30) REVERT: C 434 ILE cc_start: 0.9246 (mm) cc_final: 0.8702 (tp) REVERT: C 513 LEU cc_start: 0.9768 (mt) cc_final: 0.9526 (pt) REVERT: C 740 MET cc_start: 0.8920 (tpt) cc_final: 0.8671 (tpt) outliers start: 49 outliers final: 39 residues processed: 185 average time/residue: 0.2181 time to fit residues: 71.7418 Evaluate side-chains 180 residues out of total 4179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 267 VAL 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 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 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 152 MET 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 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR 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 267 VAL 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 660 TYR 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 60 optimal weight: 0.6980 chunk 239 optimal weight: 30.0000 chunk 454 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 chunk 374 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 458 optimal weight: 0.8980 chunk 310 optimal weight: 6.9990 chunk 470 optimal weight: 0.3980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.117270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073607 restraints weight = 161672.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069946 restraints weight = 107214.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070261 restraints weight = 104327.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070647 restraints weight = 78518.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070736 restraints weight = 73777.423| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39660 Z= 0.109 Angle : 0.564 10.869 54027 Z= 0.276 Chirality : 0.043 0.347 6081 Planarity : 0.003 0.054 6876 Dihedral : 3.978 20.955 5097 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.17 % Allowed : 13.97 % Favored : 84.85 % 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: 0.33 (0.13), residues: 4686 helix: 2.04 (0.13), residues: 1680 sheet: -0.10 (0.19), residues: 735 loop : -1.11 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.013 0.001 TYR C1067 PHE 0.027 0.001 PHE E 315 TRP 0.016 0.001 TRP A 104 HIS 0.007 0.001 HIS F 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (39552) covalent geometry : angle 0.54269 / 0.27 (53769) SS BOND : bond 0.00178 / 0.11 ( 48) SS BOND : angle 1.04767 / 0.64 ( 96) hydrogen bonds : bond 0.03548 / 2.36 ( 1653) hydrogen bonds : angle 4.96143 / 3.47 ( 4689) metal coordination : bond 0.00027 / 0.01 ( 6) link_BETA1-4 : bond 0.00496 / 0.22 ( 3) link_BETA1-4 : angle 1.83459 / 1.19 ( 9) link_NAG-ASN : bond 0.00441 / 0.23 ( 51) link_NAG-ASN : angle 2.84372 / 1.89 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7191.02 seconds wall clock time: 124 minutes 58.77 seconds (7498.77 seconds total)