Starting phenix.real_space_refine on Tue Aug 26 12:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xal_38201/08_2025/8xal_38201.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 178 5.16 5 C 23355 2.51 5 N 6071 2.21 5 O 7021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36625 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "B" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "C" Number of atoms: 8813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 8813 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 58, 'TRANS': 1070} Chain: "I" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "J" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "K" 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 10.12, per 1000 atoms: 0.28 Number of scatterers: 36625 At special positions: 0 Unit cell: (151.2, 165.24, 231.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 178 16.00 O 7021 8.00 N 6071 7.00 C 23355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS A 475 " - pdb=" SG CYS A 483 " distance=2.03 Simple disulfide: pdb=" SG CYS A 533 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS A 733 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A1027 " - pdb=" SG CYS A1038 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 533 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 666 " distance=2.03 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B1027 " - pdb=" SG CYS B1038 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 161 " distance=2.04 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 533 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.03 Simple disulfide: pdb=" SG CYS I 133 " - pdb=" SG CYS I 141 " distance=2.03 Simple disulfide: pdb=" SG CYS I 344 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 530 " - pdb=" SG CYS I 542 " distance=2.03 Simple disulfide: pdb=" SG CYS J 133 " - pdb=" SG CYS J 141 " distance=2.03 Simple disulfide: pdb=" SG CYS J 344 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 530 " - pdb=" SG CYS J 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1302 " - " ASN A 160 " " NAG A1303 " - " ASN A 277 " " NAG A1305 " - " ASN A 704 " " NAG A1306 " - " ASN A 712 " " NAG A1308 " - " ASN A1093 " " NAG A1309 " - " ASN A1129 " " NAG B1305 " - " ASN B 704 " " NAG B1306 " - " ASN B 712 " " NAG B1307 " - " ASN B1069 " " NAG B1308 " - " ASN B1093 " " NAG B1309 " - " ASN B1129 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 277 " " NAG C1303 " - " ASN C 704 " " NAG C1304 " - " ASN C 712 " " NAG C1306 " - " ASN C1093 " " NAG C1307 " - " ASN C1129 " " NAG I 903 " - " ASN I 322 " " NAG I 905 " - " ASN I 546 " " NAG K 1 " - " ASN I 90 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8580 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 54 sheets defined 34.6% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.565A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.975A pdb=" N TYR A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 741 through 751 removed outlier: 3.591A pdb=" N SER A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 777 Processing helix chain 'A' and resid 811 through 821 Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 861 through 879 Processing helix chain 'A' and resid 892 through 903 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.789A pdb=" N TYR A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 940 through 963 removed outlier: 3.645A pdb=" N LEU A 961 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'A' and resid 980 through 1027 removed outlier: 5.030A pdb=" N VAL A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 3.888A pdb=" N SER A1142 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.820A pdb=" N LYS B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 4.134A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.838A pdb=" N ASN B 383 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.131A pdb=" N SER B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 497 through 500 Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.644A pdb=" N VAL B 615 " --> pdb=" O CYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 737 Processing helix chain 'B' and resid 741 through 749 removed outlier: 3.685A pdb=" N SER B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 752 No H-bonds generated for 'chain 'B' and resid 750 through 752' Processing helix chain 'B' and resid 753 through 777 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 844 through 851 removed outlier: 3.798A pdb=" N LYS B 851 " --> pdb=" O ALA B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 879 Processing helix chain 'B' and resid 881 through 885 Processing helix chain 'B' and resid 892 through 903 Processing helix chain 'B' and resid 908 through 914 removed outlier: 3.655A pdb=" N TYR B 912 " --> pdb=" O GLN B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 940 through 962 Processing helix chain 'B' and resid 971 through 979 Processing helix chain 'B' and resid 980 through 1027 removed outlier: 4.208A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1140 removed outlier: 4.592A pdb=" N GLU B1139 " --> pdb=" O PRO B1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.526A pdb=" N TRP C 348 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.541A pdb=" N PHE C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 385 removed outlier: 3.755A pdb=" N LEU C 382 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN C 383 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 removed outlier: 4.052A pdb=" N SER C 403 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 406 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 417 Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.986A pdb=" N VAL C 615 " --> pdb=" O CYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 741 through 749 Processing helix chain 'C' and resid 753 through 778 Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 842 through 850 Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 903 Processing helix chain 'C' and resid 908 through 914 removed outlier: 3.629A pdb=" N TYR C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 Processing helix chain 'C' and resid 937 through 939 No H-bonds generated for 'chain 'C' and resid 937 through 939' Processing helix chain 'C' and resid 940 through 960 Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1027 Processing helix chain 'C' and resid 1122 through 1124 No H-bonds generated for 'chain 'C' and resid 1122 through 1124' Processing helix chain 'C' and resid 1135 through 1141 removed outlier: 4.412A pdb=" N GLU C1139 " --> pdb=" O PRO C1135 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 53 removed outlier: 3.719A pdb=" N HIS I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP I 38 " --> pdb=" O HIS I 34 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 80 removed outlier: 4.215A pdb=" N ASN I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET I 62 " --> pdb=" O ASN I 58 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN I 63 " --> pdb=" O VAL I 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN I 64 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 83 No H-bonds generated for 'chain 'I' and resid 81 through 83' Processing helix chain 'I' and resid 90 through 102 Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.640A pdb=" N SER I 106 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 129 Processing helix chain 'I' and resid 147 through 152 removed outlier: 3.812A pdb=" N GLU I 150 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 194 removed outlier: 3.885A pdb=" N LYS I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Proline residue: I 178 - end of helix Processing helix chain 'I' and resid 198 through 205 Processing helix chain 'I' and resid 220 through 232 removed outlier: 4.470A pdb=" N GLU I 224 " --> pdb=" O GLY I 220 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU I 231 " --> pdb=" O GLU I 227 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU I 232 " --> pdb=" O HIS I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 249 removed outlier: 4.221A pdb=" N MET I 249 " --> pdb=" O ARG I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 283 Processing helix chain 'I' and resid 293 through 300 Processing helix chain 'I' and resid 303 through 318 removed outlier: 3.700A pdb=" N PHE I 315 " --> pdb=" O ALA I 311 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL I 318 " --> pdb=" O PHE I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 331 Processing helix chain 'I' and resid 365 through 386 removed outlier: 3.977A pdb=" N HIS I 373 " --> pdb=" O PHE I 369 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS I 374 " --> pdb=" O LEU I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 412 removed outlier: 3.606A pdb=" N MET I 408 " --> pdb=" O VAL I 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA I 412 " --> pdb=" O MET I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 422 Processing helix chain 'I' and resid 434 through 445 removed outlier: 3.843A pdb=" N THR I 445 " --> pdb=" O LYS I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 465 removed outlier: 4.106A pdb=" N PHE I 452 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 485 removed outlier: 3.864A pdb=" N LYS I 476 " --> pdb=" O GLN I 472 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 502 Processing helix chain 'I' and resid 503 through 508 Processing helix chain 'I' and resid 512 through 532 removed outlier: 4.320A pdb=" N TYR I 516 " --> pdb=" O PHE I 512 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE I 523 " --> pdb=" O THR I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 542 removed outlier: 3.605A pdb=" N LYS I 541 " --> pdb=" O PRO I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 559 removed outlier: 3.545A pdb=" N GLY I 551 " --> pdb=" O SER I 547 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET I 557 " --> pdb=" O LYS I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 560 through 564 removed outlier: 4.247A pdb=" N GLU I 564 " --> pdb=" O GLY I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 565 through 572 Processing helix chain 'I' and resid 581 through 599 removed outlier: 3.599A pdb=" N LEU I 585 " --> pdb=" O VAL I 581 " (cutoff:3.500A) Proline residue: I 590 - end of helix removed outlier: 3.928A pdb=" N ASP I 597 " --> pdb=" O THR I 593 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN I 598 " --> pdb=" O TRP I 594 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 53 removed outlier: 3.565A pdb=" N SER J 47 " --> pdb=" O SER J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 79 removed outlier: 3.970A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN J 63 " --> pdb=" O VAL J 59 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY J 66 " --> pdb=" O MET J 62 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA J 71 " --> pdb=" O ASP J 67 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU J 73 " --> pdb=" O TRP J 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS J 74 " --> pdb=" O SER J 70 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN J 76 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 88 removed outlier: 3.747A pdb=" N GLU J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE J 88 " --> pdb=" O LEU J 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 84 through 88' Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'J' and resid 109 through 129 Processing helix chain 'J' and resid 148 through 153 removed outlier: 3.552A pdb=" N MET J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA J 153 " --> pdb=" O ASN J 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 148 through 153' Processing helix chain 'J' and resid 157 through 174 removed outlier: 3.930A pdb=" N TRP J 165 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 189 removed outlier: 3.728A pdb=" N GLU J 189 " --> pdb=" O VAL J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 194 removed outlier: 3.693A pdb=" N ASN J 194 " --> pdb=" O ALA J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 205 Processing helix chain 'J' and resid 218 through 226 removed outlier: 3.691A pdb=" N GLU J 224 " --> pdb=" O GLY J 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 251 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 263 through 268 removed outlier: 3.631A pdb=" N LEU J 266 " --> pdb=" O PRO J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 281 removed outlier: 3.874A pdb=" N SER J 280 " --> pdb=" O THR J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 300 Processing helix chain 'J' and resid 304 through 312 Processing helix chain 'J' and resid 365 through 386 removed outlier: 3.940A pdb=" N ALA J 384 " --> pdb=" O GLN J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 394 removed outlier: 4.290A pdb=" N ASN J 394 " --> pdb=" O PHE J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 397 through 404 removed outlier: 4.233A pdb=" N HIS J 401 " --> pdb=" O ASN J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 413 removed outlier: 3.654A pdb=" N SER J 409 " --> pdb=" O GLY J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 422 removed outlier: 3.747A pdb=" N ILE J 421 " --> pdb=" O HIS J 417 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY J 422 " --> pdb=" O LEU J 418 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 444 Processing helix chain 'J' and resid 445 through 447 No H-bonds generated for 'chain 'J' and resid 445 through 447' Processing helix chain 'J' and resid 448 through 464 removed outlier: 4.565A pdb=" N PHE J 452 " --> pdb=" O GLY J 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE J 464 " --> pdb=" O ARG J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 477 through 484 removed outlier: 4.403A pdb=" N LYS J 481 " --> pdb=" O TRP J 477 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG J 482 " --> pdb=" O TRP J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 507 removed outlier: 7.446A pdb=" N PHE J 504 " --> pdb=" O ALA J 501 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N HIS J 505 " --> pdb=" O SER J 502 " (cutoff:3.500A) Processing helix chain 'J' and resid 511 through 519 removed outlier: 4.254A pdb=" N ARG J 514 " --> pdb=" O SER J 511 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR J 517 " --> pdb=" O ARG J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 531 removed outlier: 3.552A pdb=" N GLN J 524 " --> pdb=" O LEU J 520 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN J 531 " --> pdb=" O GLU J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 553 Processing helix chain 'J' and resid 554 through 557 removed outlier: 3.706A pdb=" N MET J 557 " --> pdb=" O LEU J 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 554 through 557' Processing helix chain 'J' and resid 559 through 563 removed outlier: 3.704A pdb=" N LYS J 562 " --> pdb=" O ARG J 559 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER J 563 " --> pdb=" O LEU J 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 559 through 563' Processing helix chain 'J' and resid 565 through 570 removed outlier: 3.906A pdb=" N ALA J 569 " --> pdb=" O PRO J 565 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU J 570 " --> pdb=" O TRP J 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 565 through 570' Processing helix chain 'J' and resid 588 through 597 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 7.385A pdb=" N ASN A 58 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR A 264 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.694A pdb=" N GLY C 561 " --> pdb=" O ASP C 569 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASP C 569 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 7.794A pdb=" N THR A 269 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP A 285 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 271 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 283 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS A 273 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 80 removed outlier: 3.504A pdb=" N GLY A 102 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA A 238 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE A 96 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG A 97 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 121 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 165 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE A 123 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 163 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL A 125 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N CYS A 161 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 159 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 189 through 192 removed outlier: 6.203A pdb=" N SER A 200 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 311 removed outlier: 7.358A pdb=" N VAL A 590 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 323 removed outlier: 7.148A pdb=" N ILE A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.592A pdb=" N ASP A 393 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AB2, first strand: chain 'A' and resid 447 through 449 Processing sheet with id=AB3, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AB4, first strand: chain 'A' and resid 560 through 561 removed outlier: 7.658A pdb=" N PHE A 560 " --> pdb=" O PHE B 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 649 through 650 removed outlier: 5.944A pdb=" N GLU A 649 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR A 691 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 667 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 696 through 698 Processing sheet with id=AB7, first strand: chain 'A' and resid 706 through 717 removed outlier: 6.942A pdb=" N GLN A1066 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 713 " --> pdb=" O PRO A1064 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 715 " --> pdb=" O TYR A1062 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1062 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 717 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A1060 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1060 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 706 through 717 removed outlier: 6.942A pdb=" N GLN A1066 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 713 " --> pdb=" O PRO A1064 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 715 " --> pdb=" O TYR A1062 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A1062 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 717 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A1060 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A1101 " --> pdb=" O GLU A1106 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU A1106 " --> pdb=" O GLN A1101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 720 through 723 Processing sheet with id=AC1, first strand: chain 'A' and resid 729 through 731 Processing sheet with id=AC2, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.516A pdb=" N ILE A 783 " --> pdb=" O ASN C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1115 through 1117 Processing sheet with id=AC4, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AC5, first strand: chain 'B' and resid 45 through 52 Processing sheet with id=AC6, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.661A pdb=" N GLY B 256 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.574A pdb=" N GLY B 98 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA B 238 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 96 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.646A pdb=" N LEU B 136 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 220 through 224 removed outlier: 6.418A pdb=" N SER B 200 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 222 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 190 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 203 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 184 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG B 185 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B 89 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 88 " --> pdb=" O TYR B 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.009A pdb=" N VAL B 115 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 122 " --> pdb=" O VAL B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 306 through 314 removed outlier: 5.543A pdb=" N ILE B 307 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR B 594 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN B 309 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 592 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 320 through 323 Processing sheet with id=AD4, first strand: chain 'B' and resid 371 through 375 Processing sheet with id=AD5, first strand: chain 'B' and resid 389 through 398 Processing sheet with id=AD6, first strand: chain 'B' and resid 447 through 449 Processing sheet with id=AD7, first strand: chain 'B' and resid 648 through 650 removed outlier: 5.653A pdb=" N GLU B 649 " --> pdb=" O ALA B 689 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA B 667 " --> pdb=" O PRO B 660 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 706 through 717 removed outlier: 6.664A pdb=" N SER B 706 " --> pdb=" O THR B1071 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1071 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 708 " --> pdb=" O ASN B1069 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B1069 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1067 " --> pdb=" O PRO B 710 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 706 through 717 removed outlier: 6.664A pdb=" N SER B 706 " --> pdb=" O THR B1071 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1071 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 708 " --> pdb=" O ASN B1069 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN B1069 " --> pdb=" O ALA B 708 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B1067 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER B1050 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B1056 " --> pdb=" O PRO B1048 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU B1058 " --> pdb=" O SER B1046 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B1046 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B1060 " --> pdb=" O LEU B1044 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 729 through 731 Processing sheet with id=AE2, first strand: chain 'B' and resid 1115 through 1120 removed outlier: 4.418A pdb=" N ALA B1082 " --> pdb=" O SER B1118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1089 through 1092 Processing sheet with id=AE4, first strand: chain 'C' and resid 20 through 27 removed outlier: 3.704A pdb=" N TYR C 260 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 88 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER C 200 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 44 through 52 removed outlier: 4.038A pdb=" N ASP C 282 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AE7, first strand: chain 'C' and resid 79 through 80 removed outlier: 6.201A pdb=" N ALA C 238 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE C 96 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 97 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 163 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLU C 127 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 161 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN C 129 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ASN C 159 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 306 through 314 removed outlier: 5.413A pdb=" N ILE C 307 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR C 594 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN C 309 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 592 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY C 589 " --> pdb=" O GLN C 608 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 349 through 353 removed outlier: 5.627A pdb=" N ASN C 389 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU C 511 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 371 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 356 through 357 removed outlier: 6.979A pdb=" N CYS C 356 " --> pdb=" O CYS C 520 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AF3, first strand: chain 'C' and resid 649 through 651 removed outlier: 5.572A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 651 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 667 " --> pdb=" O PRO C 660 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 706 through 710 removed outlier: 3.678A pdb=" N ALA C1073 " --> pdb=" O PHE C1090 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C1090 " --> pdb=" O ALA C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 714 through 723 removed outlier: 3.620A pdb=" N MET C1045 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR C1062 " --> pdb=" O HIS C1043 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N HIS C1043 " --> pdb=" O TYR C1062 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 714 through 723 Processing sheet with id=AF7, first strand: chain 'C' and resid 729 through 731 Processing sheet with id=AF8, first strand: chain 'C' and resid 1115 through 1120 removed outlier: 4.367A pdb=" N ALA C1082 " --> pdb=" O SER C1118 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 347 through 349 1435 hydrogen bonds defined for protein. 3960 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: 8.00 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11773 1.35 - 1.47: 9408 1.47 - 1.59: 16106 1.59 - 1.71: 1 1.71 - 1.83: 250 Bond restraints: 37538 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB PRO C 204 " pdb=" CG PRO C 204 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.18e+01 bond pdb=" CG PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 1.503 1.406 0.097 3.40e-02 8.65e+02 8.06e+00 bond pdb=" N PRO C 204 " pdb=" CA PRO C 204 " ideal model delta sigma weight residual 1.479 1.431 0.048 1.71e-02 3.42e+03 7.86e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 ... (remaining 37533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 50911 3.63 - 7.27: 143 7.27 - 10.90: 20 10.90 - 14.54: 2 14.54 - 18.17: 2 Bond angle restraints: 51078 Sorted by residual: angle pdb=" CA PRO C 204 " pdb=" N PRO C 204 " pdb=" CD PRO C 204 " ideal model delta sigma weight residual 112.00 93.83 18.17 1.40e+00 5.10e-01 1.68e+02 angle pdb=" N ILE C 619 " pdb=" CA ILE C 619 " pdb=" C ILE C 619 " ideal model delta sigma weight residual 113.71 107.76 5.95 9.50e-01 1.11e+00 3.93e+01 angle pdb=" N PRO C 204 " pdb=" CD PRO C 204 " pdb=" CG PRO C 204 " ideal model delta sigma weight residual 103.20 93.88 9.32 1.50e+00 4.44e-01 3.86e+01 angle pdb=" CB MET I 360 " pdb=" CG MET I 360 " pdb=" SD MET I 360 " ideal model delta sigma weight residual 112.70 127.97 -15.27 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C ASN C 712 " pdb=" CA ASN C 712 " pdb=" CB ASN C 712 " ideal model delta sigma weight residual 109.89 118.36 -8.47 1.69e+00 3.50e-01 2.51e+01 ... (remaining 51073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 21215 25.60 - 51.19: 1286 51.19 - 76.79: 160 76.79 - 102.38: 74 102.38 - 127.98: 24 Dihedral angle restraints: 22759 sinusoidal: 9396 harmonic: 13363 Sorted by residual: dihedral pdb=" CB CYS I 530 " pdb=" SG CYS I 530 " pdb=" SG CYS I 542 " pdb=" CB CYS I 542 " ideal model delta sinusoidal sigma weight residual -86.00 -168.86 82.86 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS C 533 " pdb=" SG CYS C 533 " pdb=" SG CYS C 585 " pdb=" CB CYS C 585 " ideal model delta sinusoidal sigma weight residual 93.00 13.61 79.39 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS B 733 " pdb=" SG CYS B 733 " pdb=" SG CYS B 755 " pdb=" CB CYS B 755 " ideal model delta sinusoidal sigma weight residual -86.00 -141.88 55.88 1 1.00e+01 1.00e-02 4.22e+01 ... (remaining 22756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 5716 0.195 - 0.390: 6 0.390 - 0.585: 0 0.585 - 0.780: 0 0.780 - 0.976: 1 Chirality restraints: 5723 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 704 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 160 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.72e+00 ... (remaining 5720 not shown) Planarity restraints: 6602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 25 " 0.033 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR B 25 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR B 25 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TYR B 25 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 25 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 25 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR B 25 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 25 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 203 " -0.110 5.00e-02 4.00e+02 1.49e-01 3.57e+01 pdb=" N PRO C 204 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO C 204 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 204 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 704 " 0.055 2.00e-02 2.50e+03 5.05e-02 3.19e+01 pdb=" CG ASN B 704 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN B 704 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 704 " -0.056 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.055 2.00e-02 2.50e+03 ... (remaining 6599 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 728 2.66 - 3.22: 35523 3.22 - 3.78: 57032 3.78 - 4.34: 76590 4.34 - 4.90: 124180 Nonbonded interactions: 294053 Sorted by model distance: nonbonded pdb=" NE2 GLN I 81 " pdb=" N2 NAG I 902 " model vdw 2.104 2.560 nonbonded pdb=" O GLY B 491 " pdb=" OH TYR B 496 " model vdw 2.107 3.040 nonbonded pdb=" CD1 TYR B 25 " pdb=" O6 NAG B1301 " model vdw 2.126 2.672 nonbonded pdb=" OG1 THR B 22 " pdb=" O HIS B 63 " model vdw 2.145 3.040 nonbonded pdb=" O LEU J 444 " pdb=" OG1 THR J 449 " model vdw 2.179 3.040 ... (remaining 294048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1307) selection = (chain 'B' and resid 14 through 1307) selection = chain 'C' } ncs_group { reference = (chain 'I' and resid 19 through 614) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.340 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 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 : 0.003 0.172 37610 Z= 0.148 Angle : 0.647 20.588 51237 Z= 0.331 Chirality : 0.045 0.976 5723 Planarity : 0.004 0.149 6582 Dihedral : 17.096 127.977 14035 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 1.63 % Allowed : 18.45 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.13), residues: 4569 helix: 1.00 (0.15), residues: 1340 sheet: -0.33 (0.21), residues: 584 loop : -1.11 (0.12), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 341 TYR 0.099 0.001 TYR B 25 PHE 0.033 0.001 PHE B 270 TRP 0.029 0.001 TRP A 628 HIS 0.006 0.001 HIS I 401 Details of bonding type rmsd covalent geometry : bond 0.00314 (37538) covalent geometry : angle 0.62391 (51078) SS BOND : bond 0.00273 ( 48) SS BOND : angle 1.03855 ( 96) hydrogen bonds : bond 0.14080 ( 1408) hydrogen bonds : angle 6.58678 ( 3960) Misc. bond : bond 0.00566 ( 3) link_BETA1-4 : bond 0.00743 ( 1) link_BETA1-4 : angle 2.59119 ( 3) link_NAG-ASN : bond 0.00907 ( 20) link_NAG-ASN : angle 4.90998 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 110 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 897 MET cc_start: 0.7955 (tpt) cc_final: 0.7693 (mmm) REVERT: C 346 TYR cc_start: 0.8312 (p90) cc_final: 0.7995 (p90) REVERT: C 431 TRP cc_start: 0.6378 (p90) cc_final: 0.5900 (p90) REVERT: J 62 MET cc_start: 0.0500 (tpp) cc_final: -0.0892 (mmp) REVERT: J 383 MET cc_start: 0.2586 (mpt) cc_final: 0.2081 (mpt) outliers start: 65 outliers final: 58 residues processed: 173 average time/residue: 0.1714 time to fit residues: 51.9837 Evaluate side-chains 162 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 104 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 956 THR Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1025 SER Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1118 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 409 SER Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 141 CYS Chi-restraints excluded: chain J residue 293 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.2980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 50.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 539 ASN B 896 GLN B1006 GLN C 110 GLN C 183 ASN C 383 ASN C 432 ASN I 64 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.079176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.066960 restraints weight = 289540.231| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.82 r_work: 0.3715 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37610 Z= 0.126 Angle : 0.591 19.564 51237 Z= 0.293 Chirality : 0.044 0.449 5723 Planarity : 0.004 0.057 6582 Dihedral : 10.562 104.380 5708 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.47 % Favored : 94.51 % Rotamer: Outliers : 2.70 % Allowed : 16.75 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.13), residues: 4569 helix: 1.13 (0.15), residues: 1341 sheet: -0.41 (0.20), residues: 618 loop : -1.00 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 115 TYR 0.027 0.001 TYR B 25 PHE 0.035 0.001 PHE B 270 TRP 0.015 0.001 TRP A 628 HIS 0.005 0.001 HIS C 949 Details of bonding type rmsd covalent geometry : bond 0.00269 (37538) covalent geometry : angle 0.57191 (51078) SS BOND : bond 0.00278 ( 48) SS BOND : angle 1.15687 ( 96) hydrogen bonds : bond 0.04174 ( 1408) hydrogen bonds : angle 5.49067 ( 3960) Misc. bond : bond 0.00650 ( 3) link_BETA1-4 : bond 0.00549 ( 1) link_BETA1-4 : angle 2.70753 ( 3) link_NAG-ASN : bond 0.00844 ( 20) link_NAG-ASN : angle 4.11006 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 109 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7542 (ttp-110) REVERT: B 730 SER cc_start: 0.7264 (OUTLIER) cc_final: 0.5894 (t) REVERT: C 346 TYR cc_start: 0.9009 (p90) cc_final: 0.7979 (p90) REVERT: C 431 TRP cc_start: 0.6601 (p90) cc_final: 0.6340 (p90) REVERT: C 503 TYR cc_start: 0.7154 (m-80) cc_final: 0.6897 (m-80) REVERT: C 756 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6618 (m) REVERT: C 868 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7650 (m-10) REVERT: I 190 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8550 (tpp) REVERT: I 358 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8557 (tp) REVERT: I 360 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7400 (mmm) REVERT: I 455 MET cc_start: 0.7648 (pp-130) cc_final: 0.7445 (pp-130) REVERT: I 480 MET cc_start: 0.6363 (ttt) cc_final: 0.6082 (ttt) REVERT: I 609 ASP cc_start: 0.5994 (p0) cc_final: 0.5774 (p0) REVERT: J 62 MET cc_start: -0.0610 (tpp) cc_final: -0.1348 (mmp) REVERT: J 303 ASP cc_start: -0.1395 (OUTLIER) cc_final: -0.1947 (t0) outliers start: 108 outliers final: 50 residues processed: 206 average time/residue: 0.1976 time to fit residues: 71.8248 Evaluate side-chains 163 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 358 ILE Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 257 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 418 optimal weight: 40.0000 chunk 317 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 345 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 GLN A1137 GLN C 141 HIS C 183 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN I 42 GLN I 53 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 472 GLN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.078495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.065336 restraints weight = 306566.243| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.78 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 37610 Z= 0.214 Angle : 0.626 18.895 51237 Z= 0.314 Chirality : 0.045 0.468 5723 Planarity : 0.004 0.048 6582 Dihedral : 8.841 100.922 5669 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer: Outliers : 3.15 % Allowed : 16.62 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.13), residues: 4569 helix: 1.01 (0.14), residues: 1351 sheet: -0.64 (0.19), residues: 668 loop : -1.02 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 185 TYR 0.023 0.002 TYR B 25 PHE 0.031 0.002 PHE B 270 TRP 0.014 0.001 TRP I 163 HIS 0.005 0.001 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00462 (37538) covalent geometry : angle 0.60569 (51078) SS BOND : bond 0.00539 ( 48) SS BOND : angle 1.78793 ( 96) hydrogen bonds : bond 0.04515 ( 1408) hydrogen bonds : angle 5.55577 ( 3960) Misc. bond : bond 0.00533 ( 3) link_BETA1-4 : bond 0.00346 ( 1) link_BETA1-4 : angle 2.24343 ( 3) link_NAG-ASN : bond 0.00803 ( 20) link_NAG-ASN : angle 4.16191 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 108 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6546 (pp) REVERT: A 895 MET cc_start: 0.8305 (mmm) cc_final: 0.7758 (mtp) REVERT: B 730 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.5486 (t) REVERT: C 23 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: C 431 TRP cc_start: 0.6375 (p90) cc_final: 0.5946 (p90) REVERT: C 756 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7167 (m) REVERT: C 868 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: C 895 MET cc_start: 0.8277 (mmt) cc_final: 0.8029 (mmt) REVERT: I 190 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8200 (tpp) REVERT: I 445 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7580 (m) REVERT: I 609 ASP cc_start: 0.5974 (p0) cc_final: 0.5740 (p0) REVERT: J 62 MET cc_start: -0.1485 (tpp) cc_final: -0.1770 (mmp) REVERT: J 270 MET cc_start: 0.2957 (OUTLIER) cc_final: 0.1399 (tmm) REVERT: J 592 PHE cc_start: -0.5710 (OUTLIER) cc_final: -0.5932 (t80) outliers start: 126 outliers final: 82 residues processed: 221 average time/residue: 0.2151 time to fit residues: 81.7987 Evaluate side-chains 193 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 102 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 868 TYR Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 757 GLN Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 474 MET Chi-restraints excluded: chain J residue 592 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 157 optimal weight: 20.0000 chunk 282 optimal weight: 0.9990 chunk 198 optimal weight: 0.3980 chunk 372 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN B1006 GLN C 17 ASN C 120 ASN C 183 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 373 HIS ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 373 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.078157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.064984 restraints weight = 308858.569| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.69 r_work: 0.3630 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 37610 Z= 0.216 Angle : 0.621 18.304 51237 Z= 0.313 Chirality : 0.045 0.472 5723 Planarity : 0.004 0.049 6582 Dihedral : 8.090 97.363 5669 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.65 % Allowed : 17.05 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.12), residues: 4569 helix: 0.90 (0.14), residues: 1366 sheet: -0.75 (0.19), residues: 669 loop : -1.10 (0.13), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 900 TYR 0.020 0.002 TYR C1062 PHE 0.030 0.002 PHE J 525 TRP 0.016 0.001 TRP I 163 HIS 0.007 0.001 HIS J 373 Details of bonding type rmsd covalent geometry : bond 0.00464 (37538) covalent geometry : angle 0.60125 (51078) SS BOND : bond 0.00373 ( 48) SS BOND : angle 1.55936 ( 96) hydrogen bonds : bond 0.04407 ( 1408) hydrogen bonds : angle 5.53263 ( 3960) Misc. bond : bond 0.00553 ( 3) link_BETA1-4 : bond 0.00820 ( 1) link_BETA1-4 : angle 1.95082 ( 3) link_NAG-ASN : bond 0.00783 ( 20) link_NAG-ASN : angle 4.13343 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 105 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8611 (tp) REVERT: A 688 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6674 (pp) REVERT: B 23 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7755 (pp30) REVERT: B 274 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.2576 (m-80) REVERT: B 730 SER cc_start: 0.7315 (OUTLIER) cc_final: 0.5750 (t) REVERT: B 895 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7210 (mmm) REVERT: C 23 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7462 (pm20) REVERT: C 503 TYR cc_start: 0.7537 (m-80) cc_final: 0.7216 (m-80) REVERT: C 756 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6806 (m) REVERT: C 868 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: I 57 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: I 190 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8528 (tpp) REVERT: I 332 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: I 360 MET cc_start: 0.7713 (mmm) cc_final: 0.7304 (mmm) REVERT: I 480 MET cc_start: 0.6471 (ttt) cc_final: 0.6234 (ttt) REVERT: J 270 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.2446 (tmm) REVERT: J 360 MET cc_start: 0.3492 (ttt) cc_final: 0.3265 (tpp) REVERT: J 592 PHE cc_start: -0.6145 (OUTLIER) cc_final: -0.6380 (t80) outliers start: 146 outliers final: 95 residues processed: 235 average time/residue: 0.2029 time to fit residues: 83.3030 Evaluate side-chains 211 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 102 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 757 GLN Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 474 MET Chi-restraints excluded: chain J residue 592 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 392 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 406 optimal weight: 30.0000 chunk 311 optimal weight: 1.9990 chunk 118 optimal weight: 0.0970 chunk 385 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 187 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN C 183 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.078242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.066702 restraints weight = 279328.858| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.70 r_work: 0.3703 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37610 Z= 0.125 Angle : 0.576 18.039 51237 Z= 0.286 Chirality : 0.044 0.470 5723 Planarity : 0.004 0.057 6582 Dihedral : 7.549 96.199 5667 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.13), residues: 4569 helix: 1.13 (0.14), residues: 1357 sheet: -0.61 (0.20), residues: 652 loop : -1.07 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 185 TYR 0.016 0.001 TYR I 385 PHE 0.034 0.001 PHE C 754 TRP 0.016 0.001 TRP I 163 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00269 (37538) covalent geometry : angle 0.55670 (51078) SS BOND : bond 0.00302 ( 48) SS BOND : angle 1.37224 ( 96) hydrogen bonds : bond 0.03958 ( 1408) hydrogen bonds : angle 5.33780 ( 3960) Misc. bond : bond 0.00578 ( 3) link_BETA1-4 : bond 0.00542 ( 1) link_BETA1-4 : angle 2.33430 ( 3) link_NAG-ASN : bond 0.00760 ( 20) link_NAG-ASN : angle 3.97945 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 106 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 688 ILE cc_start: 0.7050 (OUTLIER) cc_final: 0.6759 (pp) REVERT: B 23 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: B 496 TYR cc_start: 0.1224 (OUTLIER) cc_final: 0.0037 (m-10) REVERT: B 730 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.6964 (p) REVERT: B 850 PHE cc_start: 0.7525 (m-80) cc_final: 0.7227 (m-10) REVERT: B 895 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.6821 (mmm) REVERT: C 23 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: C 503 TYR cc_start: 0.7388 (m-80) cc_final: 0.7140 (m-80) REVERT: C 756 THR cc_start: 0.6994 (OUTLIER) cc_final: 0.6699 (m) REVERT: C 868 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7676 (m-10) REVERT: C 895 MET cc_start: 0.8396 (mmt) cc_final: 0.8095 (mmt) REVERT: I 57 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: I 190 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8547 (tpp) REVERT: I 332 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7172 (tmm) REVERT: I 360 MET cc_start: 0.7738 (mmm) cc_final: 0.7383 (mmm) REVERT: J 270 MET cc_start: 0.3280 (OUTLIER) cc_final: 0.1871 (tmm) REVERT: J 303 ASP cc_start: -0.0806 (OUTLIER) cc_final: -0.1164 (t0) outliers start: 121 outliers final: 80 residues processed: 209 average time/residue: 0.1915 time to fit residues: 70.4154 Evaluate side-chains 197 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 103 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 431 TRP Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 757 GLN Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 474 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 394 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 64 optimal weight: 0.0070 chunk 400 optimal weight: 50.0000 chunk 328 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 424 optimal weight: 50.0000 chunk 79 optimal weight: 0.4980 overall best weight: 1.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN C 183 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.078223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.066073 restraints weight = 293715.438| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.69 r_work: 0.3688 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37610 Z= 0.141 Angle : 0.567 17.576 51237 Z= 0.283 Chirality : 0.044 0.476 5723 Planarity : 0.004 0.051 6582 Dihedral : 7.113 94.924 5660 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.20 % Allowed : 17.30 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4569 helix: 1.13 (0.14), residues: 1360 sheet: -0.60 (0.19), residues: 675 loop : -1.06 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.017 0.001 TYR C1062 PHE 0.029 0.001 PHE B 270 TRP 0.017 0.001 TRP I 163 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00304 (37538) covalent geometry : angle 0.54973 (51078) SS BOND : bond 0.00300 ( 48) SS BOND : angle 1.14092 ( 96) hydrogen bonds : bond 0.03957 ( 1408) hydrogen bonds : angle 5.29272 ( 3960) Misc. bond : bond 0.00572 ( 3) link_BETA1-4 : bond 0.00634 ( 1) link_BETA1-4 : angle 2.21977 ( 3) link_NAG-ASN : bond 0.00798 ( 20) link_NAG-ASN : angle 3.91173 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 106 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 254 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8242 (p) REVERT: A 688 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6638 (pp) REVERT: B 23 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7810 (pp30) REVERT: B 496 TYR cc_start: 0.1128 (OUTLIER) cc_final: 0.0051 (m-10) REVERT: B 730 SER cc_start: 0.7217 (OUTLIER) cc_final: 0.5768 (t) REVERT: B 850 PHE cc_start: 0.7488 (m-80) cc_final: 0.7187 (m-10) REVERT: B 895 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.6813 (mmm) REVERT: C 23 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: C 503 TYR cc_start: 0.7474 (m-80) cc_final: 0.7216 (m-80) REVERT: C 756 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6781 (m) REVERT: C 868 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: I 57 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: I 190 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8546 (tpp) REVERT: I 332 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7036 (tmm) REVERT: I 360 MET cc_start: 0.7686 (mmm) cc_final: 0.7339 (mmm) REVERT: J 270 MET cc_start: 0.3315 (OUTLIER) cc_final: 0.1944 (tmm) REVERT: J 303 ASP cc_start: -0.0851 (OUTLIER) cc_final: -0.1206 (t0) REVERT: J 592 PHE cc_start: -0.6018 (OUTLIER) cc_final: -0.6227 (t80) outliers start: 128 outliers final: 95 residues processed: 217 average time/residue: 0.2082 time to fit residues: 79.4308 Evaluate side-chains 216 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 105 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 35 TYR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 387 PHE Chi-restraints excluded: chain C residue 431 TRP Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 757 GLN Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 332 MET Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 447 VAL Chi-restraints excluded: chain J residue 474 MET Chi-restraints excluded: chain J residue 592 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 117 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 396 optimal weight: 30.0000 chunk 229 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 438 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN B 896 GLN B1120 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1043 HIS ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.077268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.063489 restraints weight = 316033.623| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.40 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.127 37610 Z= 0.552 Angle : 0.921 16.443 51237 Z= 0.481 Chirality : 0.056 0.519 5723 Planarity : 0.006 0.066 6582 Dihedral : 8.394 94.007 5658 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.53 % Allowed : 17.55 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.12), residues: 4569 helix: -0.10 (0.13), residues: 1389 sheet: -1.20 (0.19), residues: 648 loop : -1.54 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 900 TYR 0.037 0.004 TYR B 260 PHE 0.036 0.003 PHE C 170 TRP 0.053 0.002 TRP I 478 HIS 0.009 0.002 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.01193 (37538) covalent geometry : angle 0.90384 (51078) SS BOND : bond 0.00742 ( 48) SS BOND : angle 1.96093 ( 96) hydrogen bonds : bond 0.06298 ( 1408) hydrogen bonds : angle 6.43523 ( 3960) Misc. bond : bond 0.00456 ( 3) link_BETA1-4 : bond 0.00127 ( 1) link_BETA1-4 : angle 1.68307 ( 3) link_NAG-ASN : bond 0.00902 ( 20) link_NAG-ASN : angle 4.77974 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 107 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 254 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8489 (p) REVERT: A 688 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6397 (pp) REVERT: A 895 MET cc_start: 0.8309 (mmm) cc_final: 0.7905 (mtp) REVERT: B 148 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.3798 (pmm) REVERT: B 274 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.2528 (m-80) REVERT: B 282 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5572 (m-30) REVERT: B 496 TYR cc_start: 0.1006 (OUTLIER) cc_final: -0.0077 (m-10) REVERT: B 730 SER cc_start: 0.5951 (OUTLIER) cc_final: 0.4605 (t) REVERT: C 23 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: C 503 TYR cc_start: 0.7715 (m-80) cc_final: 0.7432 (m-80) REVERT: C 550 SER cc_start: 0.4969 (OUTLIER) cc_final: 0.4735 (p) REVERT: C 868 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: C 895 MET cc_start: 0.8338 (mmt) cc_final: 0.8077 (mmp) REVERT: I 57 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7747 (pp20) REVERT: I 190 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8521 (tpp) REVERT: I 360 MET cc_start: 0.7678 (mmm) cc_final: 0.7449 (mmm) REVERT: I 478 TRP cc_start: 0.7555 (m100) cc_final: 0.7313 (m100) REVERT: J 159 ASN cc_start: 0.3771 (m-40) cc_final: 0.3498 (t0) outliers start: 141 outliers final: 94 residues processed: 230 average time/residue: 0.2098 time to fit residues: 84.9580 Evaluate side-chains 207 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 100 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 542 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 608 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 347 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 265 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 356 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 196 optimal weight: 0.0270 chunk 407 optimal weight: 0.0470 chunk 452 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 331 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 GLN B 94 ASN B 896 GLN C 120 ASN C 141 HIS C 183 ASN I 42 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.077512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.063459 restraints weight = 314334.136| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.87 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37610 Z= 0.137 Angle : 0.618 16.988 51237 Z= 0.310 Chirality : 0.045 0.468 5723 Planarity : 0.004 0.063 6582 Dihedral : 7.117 93.295 5654 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 18.27 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.12), residues: 4569 helix: 0.70 (0.14), residues: 1374 sheet: -1.06 (0.19), residues: 646 loop : -1.27 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 314 TYR 0.018 0.001 TYR I 385 PHE 0.055 0.001 PHE C 366 TRP 0.019 0.001 TRP I 163 HIS 0.014 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00292 (37538) covalent geometry : angle 0.59910 (51078) SS BOND : bond 0.00529 ( 48) SS BOND : angle 1.61662 ( 96) hydrogen bonds : bond 0.04279 ( 1408) hydrogen bonds : angle 5.60317 ( 3960) Misc. bond : bond 0.00577 ( 3) link_BETA1-4 : bond 0.00733 ( 1) link_BETA1-4 : angle 1.95897 ( 3) link_NAG-ASN : bond 0.00710 ( 20) link_NAG-ASN : angle 4.03730 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 105 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 274 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.2492 (m-80) REVERT: B 496 TYR cc_start: 0.1328 (OUTLIER) cc_final: 0.0182 (m-10) REVERT: B 850 PHE cc_start: 0.7198 (m-80) cc_final: 0.6140 (m-80) REVERT: B 895 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7115 (mmm) REVERT: C 23 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: C 503 TYR cc_start: 0.7547 (m-80) cc_final: 0.7232 (m-80) REVERT: C 756 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6695 (m) REVERT: C 868 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7465 (m-10) REVERT: C 895 MET cc_start: 0.8263 (mmt) cc_final: 0.7934 (mmt) REVERT: I 57 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: I 123 MET cc_start: 0.7136 (mmt) cc_final: 0.6932 (mmm) REVERT: I 190 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8411 (tpp) REVERT: I 323 MET cc_start: 0.5727 (mmm) cc_final: 0.5134 (mmm) REVERT: J 159 ASN cc_start: 0.4160 (m-40) cc_final: 0.3799 (t0) REVERT: J 303 ASP cc_start: -0.1026 (OUTLIER) cc_final: -0.1306 (t0) REVERT: J 474 MET cc_start: 0.8349 (tpp) cc_final: 0.7761 (tmm) outliers start: 100 outliers final: 74 residues processed: 192 average time/residue: 0.1971 time to fit residues: 66.0694 Evaluate side-chains 187 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 103 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 274 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 757 GLN Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 160 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 393 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN C 183 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.077230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.063593 restraints weight = 314315.487| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.68 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37610 Z= 0.178 Angle : 0.611 16.458 51237 Z= 0.307 Chirality : 0.045 0.476 5723 Planarity : 0.004 0.060 6582 Dihedral : 6.742 92.828 5652 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.50 % Allowed : 18.60 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.12), residues: 4569 helix: 0.80 (0.14), residues: 1380 sheet: -1.03 (0.19), residues: 648 loop : -1.25 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.019 0.001 TYR C1062 PHE 0.057 0.001 PHE C 366 TRP 0.058 0.001 TRP I 478 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00385 (37538) covalent geometry : angle 0.59316 (51078) SS BOND : bond 0.00333 ( 48) SS BOND : angle 1.49952 ( 96) hydrogen bonds : bond 0.04306 ( 1408) hydrogen bonds : angle 5.55327 ( 3960) Misc. bond : bond 0.00571 ( 3) link_BETA1-4 : bond 0.00499 ( 1) link_BETA1-4 : angle 1.91869 ( 3) link_NAG-ASN : bond 0.00707 ( 20) link_NAG-ASN : angle 3.91274 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 102 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8298 (p) REVERT: A 688 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6499 (pp) REVERT: B 496 TYR cc_start: 0.0805 (OUTLIER) cc_final: -0.0105 (m-10) REVERT: B 850 PHE cc_start: 0.7353 (m-80) cc_final: 0.6207 (m-80) REVERT: B 895 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.6889 (mmm) REVERT: C 23 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: C 503 TYR cc_start: 0.7699 (m-80) cc_final: 0.7387 (m-80) REVERT: C 756 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.7189 (m) REVERT: C 868 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7435 (m-10) REVERT: C 895 MET cc_start: 0.8130 (mmt) cc_final: 0.7794 (mmt) REVERT: I 57 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: I 123 MET cc_start: 0.7200 (mmt) cc_final: 0.6919 (mmm) REVERT: I 190 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8379 (tpp) REVERT: I 323 MET cc_start: 0.6401 (mmm) cc_final: 0.5814 (mmm) REVERT: J 159 ASN cc_start: 0.3906 (m-40) cc_final: 0.3546 (t0) REVERT: J 270 MET cc_start: 0.3291 (OUTLIER) cc_final: 0.1631 (mmp) REVERT: J 303 ASP cc_start: -0.0914 (OUTLIER) cc_final: -0.1178 (t0) REVERT: J 474 MET cc_start: 0.8301 (tpp) cc_final: 0.7848 (tmm) outliers start: 100 outliers final: 78 residues processed: 189 average time/residue: 0.1952 time to fit residues: 65.2497 Evaluate side-chains 189 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 100 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 270 MET Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 301 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 77 optimal weight: 0.0870 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 896 GLN C 944 GLN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.077253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.064056 restraints weight = 315338.532| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 5.08 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37610 Z= 0.133 Angle : 0.598 16.894 51237 Z= 0.296 Chirality : 0.044 0.468 5723 Planarity : 0.004 0.062 6582 Dihedral : 6.471 91.983 5652 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.30 % Allowed : 18.80 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.12), residues: 4569 helix: 0.93 (0.14), residues: 1378 sheet: -0.89 (0.19), residues: 637 loop : -1.19 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 185 TYR 0.016 0.001 TYR C1062 PHE 0.055 0.001 PHE C 366 TRP 0.025 0.001 TRP I 163 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00287 (37538) covalent geometry : angle 0.58098 (51078) SS BOND : bond 0.00281 ( 48) SS BOND : angle 1.46095 ( 96) hydrogen bonds : bond 0.04007 ( 1408) hydrogen bonds : angle 5.40802 ( 3960) Misc. bond : bond 0.00582 ( 3) link_BETA1-4 : bond 0.00570 ( 1) link_BETA1-4 : angle 2.06285 ( 3) link_NAG-ASN : bond 0.00731 ( 20) link_NAG-ASN : angle 3.81063 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9138 Ramachandran restraints generated. 4569 Oldfield, 0 Emsley, 4569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 102 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8193 (p) REVERT: A 688 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6530 (pp) REVERT: B 496 TYR cc_start: 0.0792 (OUTLIER) cc_final: -0.0078 (m-10) REVERT: B 850 PHE cc_start: 0.7234 (m-80) cc_final: 0.6137 (m-80) REVERT: B 895 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.6771 (mmm) REVERT: C 23 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: C 756 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7102 (m) REVERT: C 868 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: C 895 MET cc_start: 0.8155 (mmt) cc_final: 0.7833 (mmt) REVERT: I 57 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: I 123 MET cc_start: 0.7105 (mmt) cc_final: 0.6851 (mmm) REVERT: I 190 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: I 323 MET cc_start: 0.6430 (mmm) cc_final: 0.5831 (mmm) REVERT: I 589 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: J 159 ASN cc_start: 0.4036 (m-40) cc_final: 0.3654 (t0) REVERT: J 270 MET cc_start: 0.3268 (ptp) cc_final: 0.1653 (mmp) REVERT: J 303 ASP cc_start: -0.0890 (OUTLIER) cc_final: -0.1179 (t0) REVERT: J 383 MET cc_start: 0.2523 (mpp) cc_final: 0.2249 (mpp) REVERT: J 474 MET cc_start: 0.8257 (tpp) cc_final: 0.7808 (tmm) outliers start: 92 outliers final: 76 residues processed: 184 average time/residue: 0.2133 time to fit residues: 68.9170 Evaluate side-chains 187 residues out of total 3995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 100 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 835 CYS Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 868 TYR Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 539 ASN Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 757 GLN Chi-restraints excluded: chain B residue 851 LYS Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 895 MET Chi-restraints excluded: chain B residue 962 SER Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 1009 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 585 CYS Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 646 ILE Chi-restraints excluded: chain C residue 682 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 726 MET Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 864 MET Chi-restraints excluded: chain C residue 865 ILE Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1095 THR Chi-restraints excluded: chain C residue 1131 THR Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 223 ILE Chi-restraints excluded: chain I residue 241 HIS Chi-restraints excluded: chain I residue 271 TRP Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 MET Chi-restraints excluded: chain I residue 401 HIS Chi-restraints excluded: chain I residue 445 THR Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 534 LYS Chi-restraints excluded: chain I residue 542 CYS Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 584 LEU Chi-restraints excluded: chain I residue 589 GLU Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 293 VAL Chi-restraints excluded: chain J residue 303 ASP Chi-restraints excluded: chain J residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 255 optimal weight: 0.0980 chunk 194 optimal weight: 0.0040 chunk 394 optimal weight: 0.0870 chunk 337 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 445 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 427 optimal weight: 8.9990 chunk 238 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 GLN B 445 ASN B 896 GLN B1006 GLN C 183 ASN ** I 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 472 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.077918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.064178 restraints weight = 313141.097| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 5.08 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 37610 Z= 0.105 Angle : 0.562 15.645 51237 Z= 0.278 Chirality : 0.044 0.455 5723 Planarity : 0.004 0.064 6582 Dihedral : 5.993 90.437 5652 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.93 % Allowed : 19.07 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.13), residues: 4569 helix: 1.17 (0.14), residues: 1367 sheet: -0.59 (0.20), residues: 637 loop : -1.08 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 73 TYR 0.019 0.001 TYR B1062 PHE 0.052 0.001 PHE C 366 TRP 0.081 0.001 TRP I 478 HIS 0.006 0.001 HIS J 241 Details of bonding type rmsd covalent geometry : bond 0.00225 (37538) covalent geometry : angle 0.54699 (51078) SS BOND : bond 0.00225 ( 48) SS BOND : angle 1.28576 ( 96) hydrogen bonds : bond 0.03575 ( 1408) hydrogen bonds : angle 5.10050 ( 3960) Misc. bond : bond 0.00594 ( 3) link_BETA1-4 : bond 0.00562 ( 1) link_BETA1-4 : angle 2.40648 ( 3) link_NAG-ASN : bond 0.00735 ( 20) link_NAG-ASN : angle 3.52479 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10239.43 seconds wall clock time: 176 minutes 8.05 seconds (10568.05 seconds total)