Starting phenix.real_space_refine on Fri Feb 23 13:19:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_14236.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_14236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_14236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_14236.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1a_14236/02_2024/7r1a_14236.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38616 Number of models: 1 Model: "" Number of chains: 15 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: "E" 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: "F" 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: "B" 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: "C" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 20.10, per 1000 atoms: 0.52 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 E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 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 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 15.77 Conformation dependent library (CDL) restraints added in 6.8 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: 4.99 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: 18.93 Time building geometry restraints manager: 16.76 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: 100.26 - 107.00: 1222 107.00 - 113.75: 21914 113.75 - 120.50: 14877 120.50 - 127.25: 15307 127.25 - 134.00: 449 Bond angle restraints: 53769 Sorted by residual: angle pdb=" N GLY E 147 " pdb=" CA GLY E 147 " pdb=" C GLY E 147 " ideal model delta sigma weight residual 112.79 106.22 6.57 1.20e+00 6.94e-01 3.00e+01 angle pdb=" N GLY F 147 " pdb=" CA GLY F 147 " pdb=" C GLY F 147 " ideal model delta sigma weight residual 112.79 106.24 6.55 1.20e+00 6.94e-01 2.98e+01 angle pdb=" N GLY D 147 " pdb=" CA GLY D 147 " pdb=" C GLY D 147 " ideal model delta sigma weight residual 112.79 106.25 6.54 1.20e+00 6.94e-01 2.97e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 112.83 118.22 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 112.83 118.20 -5.37 1.22e+00 6.72e-01 1.93e+01 ... (remaining 53764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21851 17.93 - 35.86: 1855 35.86 - 53.78: 300 53.78 - 71.71: 78 71.71 - 89.64: 63 Dihedral angle restraints: 24147 sinusoidal: 10260 harmonic: 13887 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.93 -85.07 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.93 -85.07 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.94 -85.06 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 24144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5570 0.081 - 0.162: 490 0.162 - 0.244: 15 0.244 - 0.325: 0 0.325 - 0.406: 6 Chirality restraints: 6081 Sorted by residual: chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 6078 not shown) Planarity restraints: 6927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU D 35 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU D 35 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA D 36 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 35 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU F 35 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU F 35 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA F 36 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 35 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLU E 35 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU E 35 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 36 " 0.019 2.00e-02 2.50e+03 ... (remaining 6924 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 827 2.69 - 3.24: 38200 3.24 - 3.79: 58886 3.79 - 4.35: 75318 4.35 - 4.90: 126531 Nonbonded interactions: 299762 Sorted by model distance: nonbonded pdb=" OD1 ASN E 103 " pdb=" OG SER E 106 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASN F 103 " pdb=" OG SER F 106 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASN D 103 " pdb=" OG SER D 106 " model vdw 2.135 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.167 2.440 ... (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 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: 22.450 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: 0.050 Extract box with map and model: 28.880 Check model and map are aligned: 0.610 Set scattering table: 0.340 Process input model: 111.740 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39552 Z= 0.232 Angle : 0.544 7.712 53769 Z= 0.276 Chirality : 0.044 0.406 6081 Planarity : 0.004 0.045 6876 Dihedral : 14.136 89.639 15057 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP F 459 HIS 0.008 0.001 HIS F 378 PHE 0.014 0.001 PHE A 43 TYR 0.015 0.001 TYR B1067 ARG 0.003 0.000 ARG D 177 *********************** 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 fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8891 (m-80) cc_final: 0.8660 (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: 0.8402 (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: 0.9213 (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: 0.5214 time to fit residues: 197.0191 Evaluate side-chains 159 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 240 optimal weight: 0.0020 chunk 190 optimal weight: 4.9990 chunk 369 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 274 optimal weight: 0.4980 chunk 427 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 370 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN D 472 GLN E 98 GLN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** 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 925 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39552 Z= 0.180 Angle : 0.557 10.282 53769 Z= 0.284 Chirality : 0.043 0.365 6081 Planarity : 0.004 0.045 6876 Dihedral : 6.971 58.508 6231 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.31 % Allowed : 6.44 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4686 helix: 2.06 (0.13), residues: 1662 sheet: -0.24 (0.19), residues: 738 loop : -1.41 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 271 HIS 0.007 0.001 HIS E 378 PHE 0.022 0.001 PHE C 135 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG B 346 *********************** 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 189 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 4.782 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: A 135 PHE cc_start: 0.8687 (m-80) cc_final: 0.8458 (m-80) REVERT: A 774 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8323 (mm-40) REVERT: D 383 MET cc_start: 0.9720 (ptp) cc_final: 0.9369 (ppp) REVERT: D 516 TYR cc_start: 0.8026 (t80) cc_final: 0.6941 (m-80) REVERT: E 152 MET cc_start: 0.1927 (ptt) cc_final: 0.1282 (ppp) REVERT: E 270 MET cc_start: 0.7369 (ttm) cc_final: 0.6861 (ptt) REVERT: E 332 MET cc_start: 0.5247 (ppp) cc_final: 0.4900 (ppp) REVERT: E 366 MET cc_start: 0.8012 (tpp) cc_final: 0.7381 (mmm) REVERT: E 516 TYR cc_start: 0.6405 (t80) cc_final: 0.5365 (m-80) REVERT: F 249 MET cc_start: 0.5533 (mtt) cc_final: 0.4859 (mmm) REVERT: F 270 MET cc_start: 0.7770 (ttp) cc_final: 0.7517 (ptm) REVERT: F 332 MET cc_start: 0.6291 (ppp) cc_final: 0.5988 (ppp) REVERT: F 383 MET cc_start: 0.9716 (ptp) cc_final: 0.9471 (ppp) REVERT: F 474 MET cc_start: 0.7670 (mmp) cc_final: 0.6711 (mmm) REVERT: F 516 TYR cc_start: 0.8048 (t80) cc_final: 0.6973 (m-80) REVERT: B 740 MET cc_start: 0.8981 (tpt) cc_final: 0.8763 (tpt) REVERT: C 175 PHE cc_start: 0.8449 (m-80) cc_final: 0.8224 (m-80) outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.5224 time to fit residues: 157.6502 Evaluate side-chains 162 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 355 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 428 optimal weight: 2.9990 chunk 462 optimal weight: 0.5980 chunk 381 optimal weight: 5.9990 chunk 424 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 343 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 472 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39552 Z= 0.215 Angle : 0.547 11.546 53769 Z= 0.276 Chirality : 0.042 0.359 6081 Planarity : 0.004 0.043 6876 Dihedral : 6.574 53.834 6231 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.62 % Allowed : 8.83 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 4686 helix: 2.08 (0.13), residues: 1653 sheet: -0.34 (0.19), residues: 735 loop : -1.33 (0.13), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 271 HIS 0.008 0.001 HIS D 378 PHE 0.014 0.001 PHE E 315 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 *********************** 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 175 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 4.988 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: A 135 PHE cc_start: 0.8677 (m-80) cc_final: 0.8467 (m-80) REVERT: D 249 MET cc_start: 0.5592 (mtt) cc_final: 0.5110 (mmm) REVERT: D 270 MET cc_start: 0.7889 (ptm) cc_final: 0.7126 (pmm) REVERT: D 366 MET cc_start: 0.7366 (tpp) cc_final: 0.7125 (tpp) REVERT: D 383 MET cc_start: 0.9739 (ptp) cc_final: 0.9499 (ppp) REVERT: D 455 MET cc_start: 0.6654 (ppp) cc_final: 0.6381 (ppp) REVERT: D 462 MET cc_start: 0.6005 (ptt) cc_final: 0.5222 (mmt) REVERT: D 516 TYR cc_start: 0.8033 (t80) cc_final: 0.7087 (m-80) REVERT: D 558 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9038 (mt) REVERT: E 152 MET cc_start: 0.2084 (ptt) cc_final: 0.1545 (tmm) REVERT: E 270 MET cc_start: 0.7445 (ttm) cc_final: 0.6974 (ptm) REVERT: E 332 MET cc_start: 0.5027 (ppp) cc_final: 0.4157 (ppp) REVERT: E 366 MET cc_start: 0.7956 (tpp) cc_final: 0.7282 (mmm) REVERT: E 480 MET cc_start: 0.6032 (ptt) cc_final: 0.5634 (ptt) REVERT: E 557 MET cc_start: 0.8929 (ppp) cc_final: 0.8646 (ppp) REVERT: E 558 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9119 (mt) REVERT: F 249 MET cc_start: 0.5722 (mtt) cc_final: 0.4980 (mmm) REVERT: F 270 MET cc_start: 0.7385 (ttp) cc_final: 0.7029 (ptm) REVERT: F 332 MET cc_start: 0.6152 (ppp) cc_final: 0.5762 (ppp) REVERT: F 383 MET cc_start: 0.9735 (ptp) cc_final: 0.9523 (ppp) REVERT: F 557 MET cc_start: 0.8821 (ppp) cc_final: 0.8579 (ppp) REVERT: F 558 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9027 (mt) REVERT: B 427 ASP cc_start: 0.9296 (m-30) cc_final: 0.9061 (m-30) REVERT: B 740 MET cc_start: 0.8973 (tpt) cc_final: 0.8757 (tpt) REVERT: C 175 PHE cc_start: 0.8506 (m-80) cc_final: 0.8273 (m-80) outliers start: 26 outliers final: 14 residues processed: 163 average time/residue: 0.5080 time to fit residues: 140.4677 Evaluate side-chains 157 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 558 LEU 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 E residue 579 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 316 SER 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 423 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 287 optimal weight: 8.9990 chunk 430 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 407 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 39552 Z= 0.317 Angle : 0.595 12.326 53769 Z= 0.298 Chirality : 0.043 0.364 6081 Planarity : 0.004 0.039 6876 Dihedral : 6.379 53.764 6231 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.93 % Allowed : 10.77 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4686 helix: 1.87 (0.13), residues: 1671 sheet: -0.48 (0.18), residues: 747 loop : -1.32 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 271 HIS 0.006 0.001 HIS F 378 PHE 0.015 0.001 PHE B 43 TYR 0.024 0.001 TYR C1067 ARG 0.011 0.000 ARG B1107 *********************** 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 184 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 4.722 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: A 135 PHE cc_start: 0.8682 (m-80) cc_final: 0.8479 (m-80) REVERT: A 398 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: A 725 GLU cc_start: 0.8239 (tt0) cc_final: 0.7852 (tt0) REVERT: D 249 MET cc_start: 0.5938 (mtt) cc_final: 0.5246 (mmm) REVERT: D 270 MET cc_start: 0.7854 (ptm) cc_final: 0.7226 (pmm) REVERT: D 332 MET cc_start: 0.6204 (ppp) cc_final: 0.5806 (ppp) REVERT: D 383 MET cc_start: 0.9737 (ptp) cc_final: 0.9528 (ppp) REVERT: D 462 MET cc_start: 0.6186 (ptt) cc_final: 0.5405 (mmt) REVERT: D 474 MET cc_start: 0.8088 (mmp) cc_final: 0.7440 (mmm) REVERT: D 516 TYR cc_start: 0.8124 (t80) cc_final: 0.7314 (m-80) REVERT: D 558 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9082 (mt) REVERT: E 152 MET cc_start: 0.2213 (ptt) cc_final: 0.1208 (tmm) REVERT: E 249 MET cc_start: 0.4776 (mtt) cc_final: 0.3974 (mmm) REVERT: E 270 MET cc_start: 0.7552 (ttm) cc_final: 0.6710 (ptm) REVERT: E 366 MET cc_start: 0.7980 (tpp) cc_final: 0.7331 (mmm) REVERT: E 516 TYR cc_start: 0.6741 (t80) cc_final: 0.6045 (m-80) REVERT: E 558 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9157 (mt) REVERT: F 249 MET cc_start: 0.5847 (mtt) cc_final: 0.5169 (mmm) REVERT: F 332 MET cc_start: 0.6300 (ppp) cc_final: 0.6075 (ppp) REVERT: F 455 MET cc_start: 0.7206 (ppp) cc_final: 0.6403 (ppp) REVERT: F 462 MET cc_start: 0.5954 (ptt) cc_final: 0.5315 (mmt) REVERT: F 474 MET cc_start: 0.8170 (mmp) cc_final: 0.7541 (mmm) REVERT: F 516 TYR cc_start: 0.8163 (t80) cc_final: 0.7348 (m-80) REVERT: F 558 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9001 (mt) REVERT: B 740 MET cc_start: 0.8981 (tpt) cc_final: 0.8548 (tpp) REVERT: C 175 PHE cc_start: 0.8590 (m-80) cc_final: 0.8352 (m-80) outliers start: 39 outliers final: 20 residues processed: 169 average time/residue: 0.4807 time to fit residues: 139.6755 Evaluate side-chains 164 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 4.435 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 558 LEU 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 316 SER Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 909 ILE 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 379 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 388 optimal weight: 0.7980 chunk 314 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 408 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 39552 Z= 0.438 Angle : 0.676 13.307 53769 Z= 0.339 Chirality : 0.044 0.386 6081 Planarity : 0.004 0.045 6876 Dihedral : 6.412 54.100 6231 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.53 % Allowed : 12.54 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4686 helix: 1.58 (0.13), residues: 1680 sheet: -0.74 (0.18), residues: 744 loop : -1.41 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 271 HIS 0.010 0.001 HIS F 378 PHE 0.017 0.002 PHE B 43 TYR 0.029 0.001 TYR B1067 ARG 0.005 0.000 ARG A 983 *********************** 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 207 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 143 time to evaluate : 4.507 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 398 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: A 434 ILE cc_start: 0.9238 (mm) cc_final: 0.8587 (tp) REVERT: A 725 GLU cc_start: 0.8251 (tt0) cc_final: 0.7882 (tt0) REVERT: A 754 LEU cc_start: 0.9654 (OUTLIER) cc_final: 0.9434 (mm) REVERT: D 190 MET cc_start: 0.9314 (ppp) cc_final: 0.8695 (tpp) REVERT: D 249 MET cc_start: 0.6142 (mtt) cc_final: 0.5577 (mmm) REVERT: D 332 MET cc_start: 0.6300 (ppp) cc_final: 0.5816 (ppp) REVERT: D 383 MET cc_start: 0.9756 (ptp) cc_final: 0.9546 (ppp) REVERT: D 408 MET cc_start: 0.7876 (ptp) cc_final: 0.7355 (ptt) REVERT: D 462 MET cc_start: 0.6511 (ptt) cc_final: 0.5870 (mmt) REVERT: D 474 MET cc_start: 0.8077 (mmp) cc_final: 0.7374 (mmm) REVERT: D 480 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.4660 (ptt) REVERT: E 82 MET cc_start: 0.9479 (ptp) cc_final: 0.9200 (mpp) REVERT: E 152 MET cc_start: 0.2286 (ptt) cc_final: 0.1558 (tmm) REVERT: E 249 MET cc_start: 0.4948 (mtt) cc_final: 0.4147 (mmm) REVERT: E 270 MET cc_start: 0.7826 (ttm) cc_final: 0.7301 (ptm) REVERT: E 332 MET cc_start: 0.5700 (ppp) cc_final: 0.4745 (ppp) REVERT: E 366 MET cc_start: 0.8181 (tpp) cc_final: 0.7468 (mmm) REVERT: E 557 MET cc_start: 0.9016 (ppp) cc_final: 0.8727 (ppp) REVERT: E 558 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9209 (mt) REVERT: F 190 MET cc_start: 0.9297 (ppp) cc_final: 0.8594 (tpp) REVERT: F 249 MET cc_start: 0.5955 (mtt) cc_final: 0.5231 (mmm) REVERT: F 270 MET cc_start: 0.7886 (pmm) cc_final: 0.7653 (pmm) REVERT: F 332 MET cc_start: 0.6725 (ppp) cc_final: 0.6410 (ppp) REVERT: F 408 MET cc_start: 0.7577 (ptp) cc_final: 0.7085 (ptt) REVERT: F 462 MET cc_start: 0.6130 (ptt) cc_final: 0.5298 (mmt) REVERT: F 516 TYR cc_start: 0.8307 (t80) cc_final: 0.7555 (m-80) REVERT: F 557 MET cc_start: 0.8905 (ppp) cc_final: 0.8668 (ppp) REVERT: F 558 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9091 (mt) REVERT: B 398 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: B 427 ASP cc_start: 0.9361 (m-30) cc_final: 0.9110 (m-30) REVERT: B 434 ILE cc_start: 0.9278 (mm) cc_final: 0.8673 (tp) REVERT: B 740 MET cc_start: 0.8952 (tpt) cc_final: 0.8587 (tpp) REVERT: C 175 PHE cc_start: 0.8686 (m-80) cc_final: 0.8303 (m-80) REVERT: C 398 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7079 (m-30) REVERT: C 754 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9398 (mm) outliers start: 64 outliers final: 43 residues processed: 189 average time/residue: 0.4814 time to fit residues: 157.5500 Evaluate side-chains 184 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 133 time to evaluate : 4.941 ------------------------------------------------------------------------------- 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 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 909 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 480 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 62 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 471 ASP 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 377 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1116 THR 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 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 20.0000 chunk 409 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 112 optimal weight: 40.0000 chunk 455 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 239 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.164 39552 Z= 0.754 Angle : 0.886 14.502 53769 Z= 0.448 Chirality : 0.050 0.443 6081 Planarity : 0.005 0.062 6876 Dihedral : 6.920 55.436 6231 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.75 % Allowed : 14.19 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4686 helix: 0.96 (0.12), residues: 1689 sheet: -1.13 (0.18), residues: 753 loop : -1.69 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 886 HIS 0.008 0.002 HIS A1064 PHE 0.026 0.003 PHE B1042 TYR 0.039 0.002 TYR C1067 ARG 0.007 0.001 ARG B1107 *********************** 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 251 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 136 time to evaluate : 4.789 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 398 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: A 434 ILE cc_start: 0.9292 (mm) cc_final: 0.8651 (tp) REVERT: A 725 GLU cc_start: 0.8302 (tt0) cc_final: 0.7933 (tt0) REVERT: D 249 MET cc_start: 0.6302 (mtt) cc_final: 0.5832 (mmt) REVERT: D 270 MET cc_start: 0.7890 (ptm) cc_final: 0.7457 (pmm) REVERT: D 332 MET cc_start: 0.6358 (ppp) cc_final: 0.5797 (ppp) REVERT: D 408 MET cc_start: 0.7808 (ptp) cc_final: 0.7202 (ptt) REVERT: D 474 MET cc_start: 0.7922 (mmp) cc_final: 0.7270 (mmm) REVERT: D 480 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.4755 (ptt) REVERT: D 558 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9196 (mt) REVERT: E 249 MET cc_start: 0.5255 (mtt) cc_final: 0.4431 (mmm) REVERT: E 270 MET cc_start: 0.8001 (ttm) cc_final: 0.7765 (ptm) REVERT: E 332 MET cc_start: 0.6053 (ppp) cc_final: 0.5007 (ppp) REVERT: E 366 MET cc_start: 0.8308 (tpp) cc_final: 0.7787 (mmm) REVERT: E 557 MET cc_start: 0.9148 (ppp) cc_final: 0.8943 (ppp) REVERT: E 558 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9234 (mt) REVERT: F 249 MET cc_start: 0.6204 (mtt) cc_final: 0.5416 (mmm) REVERT: F 270 MET cc_start: 0.8031 (pmm) cc_final: 0.7609 (pmm) REVERT: F 332 MET cc_start: 0.6961 (ppp) cc_final: 0.6548 (ppp) REVERT: F 408 MET cc_start: 0.7570 (ptp) cc_final: 0.7085 (ptt) REVERT: F 462 MET cc_start: 0.6746 (ptt) cc_final: 0.5898 (mmt) REVERT: F 558 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9146 (mt) REVERT: B 398 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.6634 (m-30) REVERT: B 434 ILE cc_start: 0.9275 (mm) cc_final: 0.8661 (tp) REVERT: B 725 GLU cc_start: 0.8199 (tt0) cc_final: 0.7850 (tt0) REVERT: B 740 MET cc_start: 0.8944 (tpt) cc_final: 0.8676 (tpp) REVERT: B 1107 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7619 (ttm-80) REVERT: C 398 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: C 434 ILE cc_start: 0.9297 (mm) cc_final: 0.8738 (tp) outliers start: 115 outliers final: 75 residues processed: 232 average time/residue: 0.4638 time to fit residues: 188.2369 Evaluate side-chains 214 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 131 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE 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 294 ASP Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 558 LEU 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 62 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1008 VAL 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 B residue 1116 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 101 ILE 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 549 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 597 VAL 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 874 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 259 optimal weight: 20.0000 chunk 332 optimal weight: 0.8980 chunk 257 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 453 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 chunk 276 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 39552 Z= 0.309 Angle : 0.630 12.689 53769 Z= 0.312 Chirality : 0.044 0.437 6081 Planarity : 0.004 0.041 6876 Dihedral : 6.433 54.591 6231 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.96 % Allowed : 15.70 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 4686 helix: 1.39 (0.13), residues: 1698 sheet: -0.84 (0.18), residues: 732 loop : -1.48 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 459 HIS 0.006 0.001 HIS D 374 PHE 0.014 0.001 PHE B 43 TYR 0.023 0.001 TYR B1067 ARG 0.011 0.000 ARG A1107 *********************** 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 224 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 142 time to evaluate : 4.410 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 294 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: A 398 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: A 434 ILE cc_start: 0.9234 (mm) cc_final: 0.8621 (tp) REVERT: A 725 GLU cc_start: 0.8220 (tt0) cc_final: 0.7860 (tt0) REVERT: A 754 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9419 (mm) REVERT: D 249 MET cc_start: 0.6222 (mtt) cc_final: 0.5763 (mmt) REVERT: D 332 MET cc_start: 0.6308 (ppp) cc_final: 0.5276 (ppp) REVERT: D 366 MET cc_start: 0.7567 (tpp) cc_final: 0.7359 (tpp) REVERT: D 408 MET cc_start: 0.7923 (ptp) cc_final: 0.7520 (ptt) REVERT: D 462 MET cc_start: 0.6640 (ptt) cc_final: 0.5810 (mmt) REVERT: D 474 MET cc_start: 0.7956 (mmp) cc_final: 0.7259 (mmm) REVERT: D 557 MET cc_start: 0.8878 (ppp) cc_final: 0.8628 (ppp) REVERT: D 558 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9171 (mt) REVERT: E 249 MET cc_start: 0.5284 (mtt) cc_final: 0.4481 (mmm) REVERT: E 332 MET cc_start: 0.5988 (ppp) cc_final: 0.4910 (ppp) REVERT: E 366 MET cc_start: 0.8363 (tpp) cc_final: 0.7543 (mmm) REVERT: E 462 MET cc_start: 0.5429 (ptt) cc_final: 0.4642 (mmt) REVERT: E 557 MET cc_start: 0.9147 (ppp) cc_final: 0.8943 (ppp) REVERT: E 558 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9212 (mt) REVERT: F 249 MET cc_start: 0.6194 (mtt) cc_final: 0.5437 (mmm) REVERT: F 270 MET cc_start: 0.7931 (pmm) cc_final: 0.7353 (pmm) REVERT: F 332 MET cc_start: 0.6910 (ppp) cc_final: 0.6436 (ppp) REVERT: F 408 MET cc_start: 0.7599 (ptp) cc_final: 0.7297 (ptt) REVERT: F 455 MET cc_start: 0.7610 (ppp) cc_final: 0.7145 (ppp) REVERT: F 462 MET cc_start: 0.6659 (ptt) cc_final: 0.5835 (mmt) REVERT: F 558 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9142 (mt) REVERT: F 572 ASN cc_start: 0.8226 (m-40) cc_final: 0.8017 (m-40) REVERT: B 105 ILE cc_start: 0.9317 (tp) cc_final: 0.9068 (mm) REVERT: B 398 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: B 434 ILE cc_start: 0.9242 (mm) cc_final: 0.8652 (tp) REVERT: B 740 MET cc_start: 0.8903 (tpt) cc_final: 0.8617 (tpp) REVERT: C 398 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: C 434 ILE cc_start: 0.9293 (mm) cc_final: 0.8748 (tp) outliers start: 82 outliers final: 51 residues processed: 211 average time/residue: 0.4497 time to fit residues: 165.5505 Evaluate side-chains 194 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 135 time to evaluate : 4.429 ------------------------------------------------------------------------------- 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 316 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 579 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 471 ASP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 597 VAL 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 805 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 288 optimal weight: 0.5980 chunk 309 optimal weight: 0.7980 chunk 224 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 356 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39552 Z= 0.166 Angle : 0.562 11.043 53769 Z= 0.279 Chirality : 0.043 0.408 6081 Planarity : 0.003 0.040 6876 Dihedral : 6.010 56.594 6231 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.70 % Allowed : 16.01 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 4686 helix: 1.79 (0.13), residues: 1695 sheet: -0.59 (0.18), residues: 729 loop : -1.31 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP E 271 HIS 0.005 0.001 HIS E 378 PHE 0.016 0.001 PHE B 135 TYR 0.014 0.001 TYR B1067 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 144 time to evaluate : 4.802 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 90 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8841 (m) REVERT: A 398 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.6544 (m-30) REVERT: A 434 ILE cc_start: 0.9209 (mm) cc_final: 0.8642 (tp) REVERT: A 513 LEU cc_start: 0.9742 (mt) cc_final: 0.9411 (pt) REVERT: D 190 MET cc_start: 0.9390 (ppp) cc_final: 0.8510 (tpp) REVERT: D 249 MET cc_start: 0.6372 (mtt) cc_final: 0.5801 (mmm) REVERT: D 270 MET cc_start: 0.7674 (ptm) cc_final: 0.7157 (ppp) REVERT: D 332 MET cc_start: 0.6291 (ppp) cc_final: 0.5161 (ppp) REVERT: D 366 MET cc_start: 0.7425 (tpp) cc_final: 0.7169 (tpp) REVERT: D 408 MET cc_start: 0.7900 (ptp) cc_final: 0.7679 (ptt) REVERT: D 455 MET cc_start: 0.7254 (ppp) cc_final: 0.6185 (ppp) REVERT: D 462 MET cc_start: 0.6744 (ptt) cc_final: 0.5564 (mmt) REVERT: D 474 MET cc_start: 0.8081 (mmp) cc_final: 0.7472 (mmm) REVERT: D 480 MET cc_start: 0.6026 (ptt) cc_final: 0.4981 (ppp) REVERT: D 516 TYR cc_start: 0.8328 (t80) cc_final: 0.7437 (m-10) REVERT: D 557 MET cc_start: 0.8858 (ppp) cc_final: 0.8585 (ppp) REVERT: D 558 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9139 (mt) REVERT: E 82 MET cc_start: 0.9546 (ptp) cc_final: 0.9205 (ppp) REVERT: E 249 MET cc_start: 0.5287 (mtt) cc_final: 0.4579 (mmt) REVERT: E 270 MET cc_start: 0.6488 (ptm) cc_final: 0.5672 (ptp) REVERT: E 332 MET cc_start: 0.5797 (ppp) cc_final: 0.4709 (ppp) REVERT: E 366 MET cc_start: 0.8256 (tpp) cc_final: 0.7575 (mmm) REVERT: E 462 MET cc_start: 0.5547 (ptt) cc_final: 0.4830 (mmt) REVERT: E 557 MET cc_start: 0.9090 (ppp) cc_final: 0.8870 (ppp) REVERT: E 558 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9230 (mt) REVERT: F 190 MET cc_start: 0.9329 (ppp) cc_final: 0.8346 (tpp) REVERT: F 249 MET cc_start: 0.6125 (mtt) cc_final: 0.5402 (mmm) REVERT: F 366 MET cc_start: 0.6893 (tpp) cc_final: 0.6575 (mmm) REVERT: F 408 MET cc_start: 0.7538 (ptp) cc_final: 0.7319 (ptt) REVERT: F 455 MET cc_start: 0.7477 (ppp) cc_final: 0.6983 (ppp) REVERT: F 462 MET cc_start: 0.6509 (ptt) cc_final: 0.5695 (mmt) REVERT: F 558 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9132 (mt) REVERT: B 90 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8713 (m) REVERT: B 105 ILE cc_start: 0.9274 (tp) cc_final: 0.9007 (mm) REVERT: B 434 ILE cc_start: 0.9242 (mm) cc_final: 0.8631 (tp) REVERT: B 740 MET cc_start: 0.8880 (tpt) cc_final: 0.8530 (tpp) REVERT: B 1107 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7050 (mmt90) REVERT: C 398 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: C 434 ILE cc_start: 0.9263 (mm) cc_final: 0.8720 (tp) REVERT: C 513 LEU cc_start: 0.9760 (mt) cc_final: 0.9509 (pt) outliers start: 71 outliers final: 42 residues processed: 202 average time/residue: 0.4827 time to fit residues: 168.6660 Evaluate side-chains 193 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 CYS 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 1071 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 579 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 471 ASP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1008 VAL 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 205 SER Chi-restraints excluded: chain C residue 284 THR 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 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 30.0000 chunk 434 optimal weight: 1.9990 chunk 396 optimal weight: 0.9980 chunk 423 optimal weight: 0.5980 chunk 254 optimal weight: 7.9990 chunk 184 optimal weight: 30.0000 chunk 332 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 chunk 421 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39552 Z= 0.211 Angle : 0.571 10.625 53769 Z= 0.283 Chirality : 0.043 0.387 6081 Planarity : 0.003 0.038 6876 Dihedral : 5.903 56.152 6231 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.46 % Allowed : 16.15 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4686 helix: 1.81 (0.13), residues: 1698 sheet: -0.52 (0.18), residues: 729 loop : -1.29 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 271 HIS 0.005 0.001 HIS D 374 PHE 0.014 0.001 PHE B 43 TYR 0.018 0.001 TYR B 904 ARG 0.008 0.000 ARG A1107 *********************** 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 205 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 144 time to evaluate : 4.531 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: A 90 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 434 ILE cc_start: 0.9250 (mm) cc_final: 0.8725 (tp) REVERT: A 513 LEU cc_start: 0.9733 (mt) cc_final: 0.9443 (pt) REVERT: D 249 MET cc_start: 0.6476 (mtt) cc_final: 0.6007 (mmt) REVERT: D 270 MET cc_start: 0.7564 (ptm) cc_final: 0.7237 (pmm) REVERT: D 332 MET cc_start: 0.6198 (ppp) cc_final: 0.5031 (ppp) REVERT: D 366 MET cc_start: 0.7414 (tpp) cc_final: 0.7165 (tpp) REVERT: D 408 MET cc_start: 0.7982 (ptp) cc_final: 0.6494 (ppp) REVERT: D 455 MET cc_start: 0.7307 (ppp) cc_final: 0.6297 (ppp) REVERT: D 462 MET cc_start: 0.6767 (ptt) cc_final: 0.5573 (mmt) REVERT: D 480 MET cc_start: 0.6453 (ptt) cc_final: 0.5599 (ppp) REVERT: D 516 TYR cc_start: 0.8336 (t80) cc_final: 0.7466 (m-80) REVERT: D 557 MET cc_start: 0.8870 (ppp) cc_final: 0.8578 (ppp) REVERT: D 558 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9100 (mt) REVERT: E 82 MET cc_start: 0.9553 (ptp) cc_final: 0.9216 (ppp) REVERT: E 152 MET cc_start: 0.1165 (ppp) cc_final: 0.0789 (tmm) REVERT: E 249 MET cc_start: 0.5373 (mtt) cc_final: 0.4700 (mmt) REVERT: E 270 MET cc_start: 0.6284 (ptm) cc_final: 0.5959 (ptm) REVERT: E 366 MET cc_start: 0.8283 (tpp) cc_final: 0.7562 (mmm) REVERT: E 408 MET cc_start: 0.8805 (pmm) cc_final: 0.8179 (pmm) REVERT: E 462 MET cc_start: 0.5682 (ptt) cc_final: 0.4967 (mmt) REVERT: E 474 MET cc_start: 0.8236 (tpp) cc_final: 0.7928 (tpp) REVERT: E 557 MET cc_start: 0.9095 (ppp) cc_final: 0.8895 (ppp) REVERT: E 558 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9233 (mt) REVERT: F 190 MET cc_start: 0.9337 (ppp) cc_final: 0.8378 (tpp) REVERT: F 249 MET cc_start: 0.6193 (mtt) cc_final: 0.5460 (mmm) REVERT: F 366 MET cc_start: 0.6873 (tpp) cc_final: 0.6567 (mmm) REVERT: F 455 MET cc_start: 0.7490 (ppp) cc_final: 0.7078 (ppp) REVERT: F 462 MET cc_start: 0.6517 (ptt) cc_final: 0.5690 (mmt) REVERT: F 474 MET cc_start: 0.8461 (mmt) cc_final: 0.8076 (mmm) REVERT: F 558 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9145 (mt) REVERT: B 90 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8695 (m) REVERT: B 105 ILE cc_start: 0.9283 (tp) cc_final: 0.9018 (mm) REVERT: B 434 ILE cc_start: 0.9241 (mm) cc_final: 0.8629 (tp) REVERT: B 740 MET cc_start: 0.8898 (tpt) cc_final: 0.8539 (tpp) REVERT: C 398 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: C 434 ILE cc_start: 0.9266 (mm) cc_final: 0.8726 (tp) REVERT: C 513 LEU cc_start: 0.9758 (mt) cc_final: 0.9516 (pt) REVERT: C 740 MET cc_start: 0.8891 (tpt) cc_final: 0.8555 (tpt) outliers start: 61 outliers final: 44 residues processed: 193 average time/residue: 0.4617 time to fit residues: 155.5840 Evaluate side-chains 191 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 579 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 471 ASP Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 0.5980 chunk 447 optimal weight: 0.5980 chunk 273 optimal weight: 6.9990 chunk 212 optimal weight: 0.0870 chunk 310 optimal weight: 20.0000 chunk 469 optimal weight: 0.7980 chunk 431 optimal weight: 0.6980 chunk 373 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 288 optimal weight: 0.3980 chunk 229 optimal weight: 20.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39552 Z= 0.149 Angle : 0.552 10.651 53769 Z= 0.274 Chirality : 0.043 0.379 6081 Planarity : 0.003 0.039 6876 Dihedral : 5.713 57.367 6231 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.22 % Allowed : 16.46 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4686 helix: 1.96 (0.13), residues: 1692 sheet: -0.41 (0.18), residues: 738 loop : -1.22 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 271 HIS 0.009 0.001 HIS F 378 PHE 0.012 0.001 PHE C 43 TYR 0.012 0.001 TYR C1067 ARG 0.007 0.000 ARG B1107 ********************** 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 197 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 4.618 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: 0.9265 (mm) cc_final: 0.8758 (tp) REVERT: A 513 LEU cc_start: 0.9731 (mt) cc_final: 0.9438 (pt) REVERT: A 740 MET cc_start: 0.8849 (tpt) cc_final: 0.8532 (tpt) REVERT: D 123 MET cc_start: 0.1158 (ppp) cc_final: 0.0816 (ppp) REVERT: D 249 MET cc_start: 0.6522 (mtt) cc_final: 0.5953 (mmm) REVERT: D 332 MET cc_start: 0.6245 (ppp) cc_final: 0.5052 (ppp) REVERT: D 366 MET cc_start: 0.7353 (tpp) cc_final: 0.7098 (tpp) REVERT: D 408 MET cc_start: 0.7911 (ptp) cc_final: 0.6427 (ppp) REVERT: D 455 MET cc_start: 0.7294 (ppp) cc_final: 0.6043 (ppp) REVERT: D 462 MET cc_start: 0.6767 (ptt) cc_final: 0.5585 (mmt) REVERT: D 474 MET cc_start: 0.7787 (mmp) cc_final: 0.7542 (mmp) REVERT: D 480 MET cc_start: 0.6467 (ptt) cc_final: 0.5649 (ppp) REVERT: D 512 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: D 516 TYR cc_start: 0.8354 (t80) cc_final: 0.7521 (m-80) REVERT: D 557 MET cc_start: 0.8839 (ppp) cc_final: 0.8532 (ppp) REVERT: D 558 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9092 (mt) REVERT: E 82 MET cc_start: 0.9545 (ptp) cc_final: 0.9197 (ppp) REVERT: E 152 MET cc_start: 0.1310 (ppp) cc_final: 0.0896 (tmm) REVERT: E 249 MET cc_start: 0.5353 (mtt) cc_final: 0.4698 (mmt) REVERT: E 270 MET cc_start: 0.6172 (ptm) cc_final: 0.5747 (ptm) REVERT: E 360 MET cc_start: 0.7960 (mmt) cc_final: 0.7595 (mmp) REVERT: E 366 MET cc_start: 0.8308 (tpp) cc_final: 0.7654 (mmm) REVERT: E 408 MET cc_start: 0.8801 (pmm) cc_final: 0.8300 (pmm) REVERT: E 462 MET cc_start: 0.5674 (ptt) cc_final: 0.5001 (mmt) REVERT: E 474 MET cc_start: 0.8036 (tpp) cc_final: 0.7798 (tpp) REVERT: E 558 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9224 (mt) REVERT: F 190 MET cc_start: 0.9332 (ppp) cc_final: 0.8368 (tpp) REVERT: F 249 MET cc_start: 0.6223 (mtt) cc_final: 0.5490 (mmm) REVERT: F 366 MET cc_start: 0.6802 (tpp) cc_final: 0.6494 (mmm) REVERT: F 455 MET cc_start: 0.7481 (ppp) cc_final: 0.7073 (ppp) REVERT: F 462 MET cc_start: 0.6573 (ptt) cc_final: 0.5743 (mmt) REVERT: F 474 MET cc_start: 0.8516 (mmt) cc_final: 0.8136 (mmm) REVERT: F 512 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: F 557 MET cc_start: 0.8620 (ppp) cc_final: 0.8206 (ppp) REVERT: F 558 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9132 (mt) REVERT: B 90 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 105 ILE cc_start: 0.9279 (tp) cc_final: 0.9045 (mm) REVERT: B 434 ILE cc_start: 0.9268 (mm) cc_final: 0.8668 (tp) REVERT: B 740 MET cc_start: 0.8912 (tpt) cc_final: 0.8554 (tpp) REVERT: C 398 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.6551 (m-30) REVERT: C 434 ILE cc_start: 0.9247 (mm) cc_final: 0.8747 (tp) REVERT: C 513 LEU cc_start: 0.9770 (mt) cc_final: 0.9504 (pt) REVERT: C 740 MET cc_start: 0.8873 (tpt) cc_final: 0.8547 (tpt) outliers start: 51 outliers final: 40 residues processed: 188 average time/residue: 0.4579 time to fit residues: 149.9276 Evaluate side-chains 187 residues out of total 4179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 579 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 512 PHE Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 579 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 284 THR 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 573 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 1107 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 344 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 384 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.116485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072541 restraints weight = 162726.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069332 restraints weight = 105592.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069796 restraints weight = 106791.339| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39552 Z= 0.197 Angle : 0.566 12.276 53769 Z= 0.281 Chirality : 0.043 0.362 6081 Planarity : 0.003 0.037 6876 Dihedral : 5.665 56.386 6231 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.29 % Allowed : 16.44 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.13), residues: 4686 helix: 1.95 (0.13), residues: 1689 sheet: -0.35 (0.18), residues: 732 loop : -1.26 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 271 HIS 0.006 0.001 HIS F 374 PHE 0.014 0.001 PHE C 43 TYR 0.015 0.001 TYR B 904 ARG 0.008 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6155.26 seconds wall clock time: 115 minutes 58.70 seconds (6958.70 seconds total)