Starting phenix.real_space_refine on Sun Jul 5 05:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.map" model { file = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jwy_22515/07_2026/7jwy_22515.cif" } resolution = 2.5 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= 0.000 sd= 0.001 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 111 5.16 5 C 16366 2.51 5 N 4200 2.21 5 O 5183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25860 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1057, 8262 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 51, 'TRANS': 1005} Chain breaks: 7 bond proxies already assigned to first conformer: 8442 Chain: "B" Number of atoms: 8293 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1061, 8288 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 52, 'TRANS': 1008} Chain breaks: 6 bond proxies already assigned to first conformer: 8471 Chain: "C" Number of atoms: 8285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 1060, 8280 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 7 bond proxies already assigned to first conformer: 8462 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 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 chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 10.06, per 1000 atoms: 0.39 Number of scatterers: 25860 At special positions: 0 Unit cell: (139.68, 130.077, 178.965, 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 111 16.00 O 5183 8.00 N 4200 7.00 C 16366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.07 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.06 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1074 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 2.0 seconds 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5968 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 24.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.159A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.547A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.553A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.661A pdb=" N LEU A 629 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.555A pdb=" N SER A 637 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.811A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.942A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.180A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.125A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.840A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.541A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.502A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.647A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.624A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.773A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.957A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.097A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.167A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.730A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.545A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.170A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.681A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.930A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.665A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.505A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.150A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.711A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.732A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.835A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.331A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.321A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.219A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.806A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.184A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.441A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.834A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.697A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.535A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.432A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.547A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.461A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.647A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.688A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.559A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.193A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.816A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.117A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.643A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.849A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.701A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.582A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.703A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.397A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.237A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 135 through 141 removed outlier: 7.380A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.294A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.134A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 539 removed outlier: 5.181A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.583A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.678A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.694A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.600A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 978 hydrogen bonds defined for protein. 2678 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: 6.41 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8120 1.34 - 1.48: 7503 1.48 - 1.62: 10549 1.62 - 1.76: 16 1.76 - 1.91: 119 Bond restraints: 26307 Sorted by residual: bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.350 0.171 3.30e-02 9.18e+02 2.70e+01 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.337 1.393 -0.057 1.11e-02 8.12e+03 2.60e+01 bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.648 0.160 3.30e-02 9.18e+02 2.34e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.49e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 26302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 35289 3.68 - 7.37: 462 7.37 - 11.05: 48 11.05 - 14.74: 3 14.74 - 18.42: 5 Bond angle restraints: 35807 Sorted by residual: angle pdb=" C ASP B 215 " pdb=" N LEU B 216 " pdb=" CA LEU B 216 " ideal model delta sigma weight residual 120.39 132.63 -12.24 1.39e+00 5.18e-01 7.75e+01 angle pdb=" CA CYS C 166 " pdb=" CB CYS C 166 " pdb=" SG CYS C 166 " ideal model delta sigma weight residual 114.40 132.82 -18.42 2.30e+00 1.89e-01 6.42e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 131.64 -17.24 2.30e+00 1.89e-01 5.62e+01 angle pdb=" C SER B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta sigma weight residual 121.54 135.28 -13.74 1.91e+00 2.74e-01 5.18e+01 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 130.43 -16.03 2.30e+00 1.89e-01 4.86e+01 ... (remaining 35802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 13727 17.57 - 35.14: 1194 35.14 - 52.70: 170 52.70 - 70.27: 49 70.27 - 87.84: 31 Dihedral angle restraints: 15171 sinusoidal: 5901 harmonic: 9270 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 23.36 69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.42 63.42 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 ... (remaining 15168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3090 0.077 - 0.153: 1029 0.153 - 0.230: 117 0.230 - 0.307: 13 0.307 - 0.384: 12 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C2 NAG A1311 " pdb=" C1 NAG A1311 " pdb=" C3 NAG A1311 " pdb=" N2 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 4258 not shown) Planarity restraints: 4601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.030 2.00e-02 2.50e+03 2.63e-02 1.72e+01 pdb=" CG TRP A 886 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.027 2.00e-02 2.50e+03 2.58e-02 1.66e+01 pdb=" CG TRP C 886 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 886 " 0.030 2.00e-02 2.50e+03 2.51e-02 1.58e+01 pdb=" CG TRP B 886 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 886 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 886 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 886 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 886 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 886 " 0.018 2.00e-02 2.50e+03 ... (remaining 4598 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4938 2.78 - 3.31: 20928 3.31 - 3.84: 41292 3.84 - 4.37: 48725 4.37 - 4.90: 84365 Nonbonded interactions: 200248 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" O LYS B 113 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU B1017 " pdb=" O HOH B1401 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 599 " pdb=" O PRO A 600 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR C 599 " pdb=" O PRO C 600 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OG SER C 297 " model vdw 2.284 3.040 ... (remaining 200243 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 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 954 or resid 956 through 1309)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1309)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 828 or resid 834 throu \ gh 954 or resid 956 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.620 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.011 0.171 26413 Z= 0.487 Angle : 1.249 18.456 36083 Z= 0.685 Chirality : 0.073 0.384 4261 Planarity : 0.008 0.072 4554 Dihedral : 13.918 87.839 9077 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.12), residues: 3135 helix: -1.38 (0.17), residues: 722 sheet: -0.50 (0.20), residues: 637 loop : -2.60 (0.11), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 328 TYR 0.023 0.004 TYR C 369 PHE 0.038 0.004 PHE B 238 TRP 0.065 0.006 TRP A 886 HIS 0.011 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.49 (26307) covalent geometry : angle 1.19910 / 0.67 (35807) SS BOND : bond 0.01279 / 0.84 ( 42) SS BOND : angle 3.81092 / 2.39 ( 84) hydrogen bonds : bond 0.21377 / 14.14 ( 959) hydrogen bonds : angle 7.33309 / 4.94 ( 2678) link_BETA1-4 : bond 0.01134 / 0.70 ( 17) link_BETA1-4 : angle 3.17314 / 1.94 ( 51) link_NAG-ASN : bond 0.00805 / 0.52 ( 47) link_NAG-ASN : angle 4.64447 / 2.91 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 ASP cc_start: 0.7181 (p0) cc_final: 0.6966 (p0) REVERT: B 985 ASP cc_start: 0.6743 (p0) cc_final: 0.6424 (p0) REVERT: C 904 TYR cc_start: 0.7328 (p90) cc_final: 0.6941 (p90) outliers start: 3 outliers final: 0 residues processed: 279 average time/residue: 0.6190 time to fit residues: 201.0204 Evaluate side-chains 204 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 211 ASN A 218 GLN A 370 ASN A 414 GLN A 501 ASN A 779 GLN A 901 GLN A1002 GLN A1113 GLN B 99 ASN B 519 HIS B 901 GLN B1113 GLN C 52 GLN C 81 ASN C 99 ASN C 121 ASN C 188 ASN C 218 GLN C 440 ASN C 501 ASN C 779 GLN C 901 GLN C1005 GLN C1113 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151608 restraints weight = 34879.905| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.21 r_work: 0.3152 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26413 Z= 0.156 Angle : 0.731 13.574 36083 Z= 0.380 Chirality : 0.048 0.222 4261 Planarity : 0.005 0.063 4554 Dihedral : 5.935 27.834 3410 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.04 % Allowed : 7.49 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3135 helix: 0.49 (0.20), residues: 723 sheet: 0.16 (0.20), residues: 652 loop : -2.13 (0.12), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 319 TYR 0.030 0.002 TYR C 904 PHE 0.030 0.002 PHE A 32 TRP 0.033 0.002 TRP B 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (26307) covalent geometry : angle 0.68356 / 0.37 (35807) SS BOND : bond 0.00538 / 0.35 ( 42) SS BOND : angle 2.50420 / 1.53 ( 84) hydrogen bonds : bond 0.07680 / 4.96 ( 959) hydrogen bonds : angle 5.80724 / 3.96 ( 2678) link_BETA1-4 : bond 0.00341 / 0.20 ( 17) link_BETA1-4 : angle 1.53034 / 0.93 ( 51) link_NAG-ASN : bond 0.00429 / 0.27 ( 47) link_NAG-ASN : angle 3.66700 / 2.37 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 613 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: A 614 ASP cc_start: 0.7706 (p0) cc_final: 0.7423 (p0) REVERT: A 921 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8094 (mppt) REVERT: B 453 TYR cc_start: 0.7937 (p90) cc_final: 0.7703 (p90) REVERT: B 776 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8497 (tmtm) REVERT: B 834 ILE cc_start: 0.1079 (OUTLIER) cc_final: 0.0823 (mm) REVERT: C 586 ASP cc_start: 0.6980 (m-30) cc_final: 0.6733 (m-30) REVERT: C 603 ASN cc_start: 0.8255 (m110) cc_final: 0.7445 (t0) REVERT: C 614 ASP cc_start: 0.7501 (p0) cc_final: 0.7221 (p0) REVERT: C 747 THR cc_start: 0.8590 (t) cc_final: 0.8390 (m) REVERT: C 904 TYR cc_start: 0.7798 (p90) cc_final: 0.7362 (p90) outliers start: 29 outliers final: 12 residues processed: 250 average time/residue: 0.5332 time to fit residues: 157.9998 Evaluate side-chains 222 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 204 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A1101 HIS A1135 ASN B 99 ASN C 99 ASN C 121 ASN C 218 GLN C 779 GLN C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152190 restraints weight = 32559.492| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.08 r_work: 0.3134 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (15 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 26413 Z= 0.210 Angle : 0.773 12.822 36083 Z= 0.403 Chirality : 0.051 0.233 4261 Planarity : 0.005 0.059 4554 Dihedral : 5.860 29.998 3410 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.73 % Allowed : 8.17 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3135 helix: 0.74 (0.20), residues: 721 sheet: 0.46 (0.20), residues: 666 loop : -1.99 (0.12), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.031 0.002 TYR C 904 PHE 0.029 0.002 PHE A 32 TRP 0.021 0.002 TRP C 886 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (26307) covalent geometry : angle 0.72996 / 0.39 (35807) SS BOND : bond 0.00592 / 0.37 ( 42) SS BOND : angle 3.02582 / 1.90 ( 84) hydrogen bonds : bond 0.08733 / 5.66 ( 959) hydrogen bonds : angle 5.69708 / 3.88 ( 2678) link_BETA1-4 : bond 0.00489 / 0.30 ( 17) link_BETA1-4 : angle 1.67137 / 1.00 ( 51) link_NAG-ASN : bond 0.00444 / 0.27 ( 47) link_NAG-ASN : angle 3.33090 / 2.15 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 TYR cc_start: 0.7838 (p90) cc_final: 0.7628 (p90) REVERT: A 564 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7260 (tp40) REVERT: A 613 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: A 614 ASP cc_start: 0.7917 (p0) cc_final: 0.7626 (p0) REVERT: A 776 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8728 (tmtm) REVERT: A 790 LYS cc_start: 0.8672 (tttm) cc_final: 0.8385 (ttmm) REVERT: A 979 ASP cc_start: 0.8195 (t0) cc_final: 0.7931 (t0) REVERT: A 1005 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8766 (mm-40) REVERT: B 453 TYR cc_start: 0.7870 (p90) cc_final: 0.7601 (p90) REVERT: B 776 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8714 (tmtm) REVERT: B 1017 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: C 239 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7343 (tm-30) REVERT: C 453 TYR cc_start: 0.7743 (p90) cc_final: 0.7509 (p90) REVERT: C 564 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.5745 (tm-30) REVERT: C 603 ASN cc_start: 0.8479 (m110) cc_final: 0.7531 (t0) REVERT: C 613 GLN cc_start: 0.8138 (mt0) cc_final: 0.7875 (mp10) REVERT: C 747 THR cc_start: 0.8727 (t) cc_final: 0.8527 (m) REVERT: C 904 TYR cc_start: 0.8088 (p90) cc_final: 0.7803 (p90) outliers start: 48 outliers final: 22 residues processed: 233 average time/residue: 0.5234 time to fit residues: 145.0900 Evaluate side-chains 222 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 168 optimal weight: 0.5980 chunk 167 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A1101 HIS B 99 ASN C 66 HIS C 99 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.203531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157352 restraints weight = 35633.128| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.20 r_work: 0.3223 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26413 Z= 0.122 Angle : 0.611 11.115 36083 Z= 0.319 Chirality : 0.045 0.222 4261 Planarity : 0.004 0.055 4554 Dihedral : 5.175 29.105 3410 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.04 % Allowed : 9.47 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3135 helix: 1.42 (0.21), residues: 722 sheet: 0.82 (0.19), residues: 693 loop : -1.79 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.029 0.001 TYR C 904 PHE 0.030 0.001 PHE A 32 TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26307) covalent geometry : angle 0.57700 / 0.31 (35807) SS BOND : bond 0.00450 / 0.29 ( 42) SS BOND : angle 2.22999 / 1.40 ( 84) hydrogen bonds : bond 0.06055 / 3.90 ( 959) hydrogen bonds : angle 5.22259 / 3.57 ( 2678) link_BETA1-4 : bond 0.00456 / 0.27 ( 17) link_BETA1-4 : angle 1.20573 / 0.75 ( 51) link_NAG-ASN : bond 0.00387 / 0.25 ( 47) link_NAG-ASN : angle 2.75616 / 1.77 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6751 (pttm) cc_final: 0.6494 (ptpt) REVERT: A 453 TYR cc_start: 0.8086 (p90) cc_final: 0.7870 (p90) REVERT: A 614 ASP cc_start: 0.7854 (p0) cc_final: 0.7588 (p0) REVERT: A 1092 GLU cc_start: 0.7637 (tp30) cc_final: 0.7323 (pp20) REVERT: B 453 TYR cc_start: 0.8108 (p90) cc_final: 0.7835 (p90) REVERT: B 603 ASN cc_start: 0.7873 (m110) cc_final: 0.7158 (t0) REVERT: B 776 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8304 (tmtm) REVERT: C 118 LEU cc_start: 0.8222 (tt) cc_final: 0.7909 (tm) REVERT: C 239 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: C 403 ARG cc_start: 0.6750 (ttp-170) cc_final: 0.6461 (mtp-110) REVERT: C 453 TYR cc_start: 0.7897 (p90) cc_final: 0.7664 (p90) REVERT: C 603 ASN cc_start: 0.8167 (m110) cc_final: 0.7358 (t0) outliers start: 29 outliers final: 11 residues processed: 260 average time/residue: 0.5125 time to fit residues: 159.3983 Evaluate side-chains 223 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 171 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 143 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A1101 HIS B 99 ASN C 99 ASN C 121 ASN C 779 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.200490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152589 restraints weight = 28225.017| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.96 r_work: 0.3173 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26413 Z= 0.172 Angle : 0.686 10.993 36083 Z= 0.358 Chirality : 0.049 0.227 4261 Planarity : 0.004 0.049 4554 Dihedral : 5.310 26.229 3410 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.80 % Allowed : 9.94 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3135 helix: 1.34 (0.20), residues: 725 sheet: 0.81 (0.20), residues: 659 loop : -1.73 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.024 0.002 TYR B 904 PHE 0.025 0.002 PHE A 32 TRP 0.019 0.002 TRP C 886 HIS 0.014 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (26307) covalent geometry : angle 0.65121 / 0.35 (35807) SS BOND : bond 0.00519 / 0.32 ( 42) SS BOND : angle 2.47935 / 1.53 ( 84) hydrogen bonds : bond 0.07782 / 5.04 ( 959) hydrogen bonds : angle 5.37400 / 3.67 ( 2678) link_BETA1-4 : bond 0.00412 / 0.26 ( 17) link_BETA1-4 : angle 1.41393 / 0.85 ( 51) link_NAG-ASN : bond 0.00404 / 0.25 ( 47) link_NAG-ASN : angle 2.89030 / 1.88 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6531 (pttm) cc_final: 0.6293 (ptpt) REVERT: A 453 TYR cc_start: 0.7828 (p90) cc_final: 0.7582 (p90) REVERT: A 614 ASP cc_start: 0.8010 (p0) cc_final: 0.7713 (p0) REVERT: A 776 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (tmtm) REVERT: A 850 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6460 (tp) REVERT: A 979 ASP cc_start: 0.8215 (t0) cc_final: 0.7906 (t0) REVERT: A 1005 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8737 (mm-40) REVERT: A 1092 GLU cc_start: 0.7889 (tp30) cc_final: 0.7184 (pp20) REVERT: B 453 TYR cc_start: 0.7894 (p90) cc_final: 0.7596 (p90) REVERT: B 564 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6581 (tp40) REVERT: B 776 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8581 (tmtm) REVERT: B 1017 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: C 239 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: C 271 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7072 (mt0) REVERT: C 453 TYR cc_start: 0.7714 (p90) cc_final: 0.7472 (p90) REVERT: C 564 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.5592 (tm-30) REVERT: C 603 ASN cc_start: 0.8399 (m110) cc_final: 0.7488 (t0) REVERT: C 613 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6124 (mp10) outliers start: 50 outliers final: 23 residues processed: 240 average time/residue: 0.5207 time to fit residues: 148.9986 Evaluate side-chains 239 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 108 optimal weight: 0.7980 chunk 236 optimal weight: 0.3980 chunk 306 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 208 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A1101 HIS B 99 ASN B1005 GLN C 99 ASN C 779 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.203026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157523 restraints weight = 41668.078| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.36 r_work: 0.3172 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26413 Z= 0.122 Angle : 0.598 10.529 36083 Z= 0.313 Chirality : 0.046 0.249 4261 Planarity : 0.004 0.049 4554 Dihedral : 4.950 24.759 3410 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.40 % Allowed : 10.26 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3135 helix: 1.67 (0.21), residues: 720 sheet: 0.94 (0.20), residues: 694 loop : -1.65 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.023 0.001 TYR B 904 PHE 0.027 0.001 PHE A 32 TRP 0.019 0.001 TRP C 886 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (26307) covalent geometry : angle 0.56754 / 0.31 (35807) SS BOND : bond 0.00527 / 0.36 ( 42) SS BOND : angle 2.06602 / 1.33 ( 84) hydrogen bonds : bond 0.06174 / 3.97 ( 959) hydrogen bonds : angle 5.11862 / 3.50 ( 2678) link_BETA1-4 : bond 0.00390 / 0.23 ( 17) link_BETA1-4 : angle 1.19991 / 0.74 ( 51) link_NAG-ASN : bond 0.00379 / 0.23 ( 47) link_NAG-ASN : angle 2.59777 / 1.69 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6598 (pttm) cc_final: 0.6383 (ptpt) REVERT: A 453 TYR cc_start: 0.7998 (p90) cc_final: 0.7727 (p90) REVERT: A 614 ASP cc_start: 0.7890 (p0) cc_final: 0.7600 (p0) REVERT: A 979 ASP cc_start: 0.7992 (t0) cc_final: 0.7684 (t0) REVERT: A 1092 GLU cc_start: 0.7791 (tp30) cc_final: 0.7263 (pp20) REVERT: B 453 TYR cc_start: 0.8083 (p90) cc_final: 0.7812 (p90) REVERT: B 529 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6685 (ptmm) REVERT: B 614 ASP cc_start: 0.7721 (p0) cc_final: 0.7316 (p0) REVERT: B 776 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8363 (tmtm) REVERT: C 118 LEU cc_start: 0.8169 (tt) cc_final: 0.7797 (tm) REVERT: C 239 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: C 271 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: C 453 TYR cc_start: 0.7837 (p90) cc_final: 0.7576 (p90) REVERT: C 564 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.5621 (tm-30) REVERT: C 586 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: C 603 ASN cc_start: 0.8235 (m110) cc_final: 0.7409 (t0) REVERT: C 933 LYS cc_start: 0.8634 (mttp) cc_final: 0.8135 (mmtm) outliers start: 39 outliers final: 18 residues processed: 242 average time/residue: 0.5683 time to fit residues: 163.1832 Evaluate side-chains 229 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 115 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 286 optimal weight: 0.3980 chunk 231 optimal weight: 7.9990 chunk 196 optimal weight: 0.5980 chunk 251 optimal weight: 30.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 ASN A1101 HIS B 99 ASN B1005 GLN C 30 ASN C 99 ASN C 779 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152447 restraints weight = 30786.144| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.03 r_work: 0.3158 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 26413 Z= 0.192 Angle : 0.704 10.387 36083 Z= 0.368 Chirality : 0.050 0.236 4261 Planarity : 0.005 0.050 4554 Dihedral : 5.261 26.096 3410 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.69 % Allowed : 10.55 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3135 helix: 1.32 (0.20), residues: 731 sheet: 0.90 (0.20), residues: 660 loop : -1.66 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.027 0.002 TYR B 904 PHE 0.023 0.002 PHE B 318 TRP 0.015 0.002 TRP C 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (26307) covalent geometry : angle 0.67057 / 0.36 (35807) SS BOND : bond 0.00558 / 0.36 ( 42) SS BOND : angle 2.53080 / 1.58 ( 84) hydrogen bonds : bond 0.08221 / 5.32 ( 959) hydrogen bonds : angle 5.37222 / 3.66 ( 2678) link_BETA1-4 : bond 0.00444 / 0.27 ( 17) link_BETA1-4 : angle 1.48272 / 0.89 ( 51) link_NAG-ASN : bond 0.00407 / 0.25 ( 47) link_NAG-ASN : angle 2.84953 / 1.87 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6534 (pttm) cc_final: 0.6279 (ptmt) REVERT: A 453 TYR cc_start: 0.7852 (p90) cc_final: 0.7559 (p90) REVERT: A 564 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7165 (tp40) REVERT: A 614 ASP cc_start: 0.8015 (p0) cc_final: 0.7708 (p0) REVERT: A 850 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6444 (tp) REVERT: A 979 ASP cc_start: 0.8180 (t0) cc_final: 0.7932 (t0) REVERT: A 1092 GLU cc_start: 0.7932 (tp30) cc_final: 0.7380 (pp20) REVERT: B 239 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 453 TYR cc_start: 0.7968 (p90) cc_final: 0.7633 (p90) REVERT: B 529 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6624 (ptmm) REVERT: B 614 ASP cc_start: 0.7890 (p0) cc_final: 0.7482 (p0) REVERT: B 776 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8617 (tmtm) REVERT: B 1017 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8061 (tp30) REVERT: C 239 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: C 271 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7065 (mt0) REVERT: C 417 LYS cc_start: 0.6316 (pmtt) cc_final: 0.6105 (ptpt) REVERT: C 453 TYR cc_start: 0.7769 (p90) cc_final: 0.7476 (p90) REVERT: C 564 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.5578 (tm-30) REVERT: C 586 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: C 603 ASN cc_start: 0.8423 (m110) cc_final: 0.7509 (t0) REVERT: C 613 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.6181 (mp10) outliers start: 47 outliers final: 26 residues processed: 241 average time/residue: 0.5413 time to fit residues: 155.9913 Evaluate side-chains 236 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 198 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 233 optimal weight: 0.0980 chunk 284 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 66 HIS C 99 ASN C 779 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151255 restraints weight = 30583.095| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.06 r_work: 0.3272 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 26413 Z= 0.128 Angle : 0.608 10.292 36083 Z= 0.318 Chirality : 0.046 0.231 4261 Planarity : 0.004 0.050 4554 Dihedral : 4.942 25.459 3410 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.44 % Allowed : 10.87 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3135 helix: 1.62 (0.20), residues: 731 sheet: 0.98 (0.20), residues: 693 loop : -1.57 (0.13), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.024 0.001 TYR B 904 PHE 0.026 0.001 PHE B 318 TRP 0.017 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (26307) covalent geometry : angle 0.57724 / 0.31 (35807) SS BOND : bond 0.00478 / 0.31 ( 42) SS BOND : angle 2.19461 / 1.36 ( 84) hydrogen bonds : bond 0.06445 / 4.15 ( 959) hydrogen bonds : angle 5.14535 / 3.52 ( 2678) link_BETA1-4 : bond 0.00392 / 0.23 ( 17) link_BETA1-4 : angle 1.23501 / 0.76 ( 51) link_NAG-ASN : bond 0.00374 / 0.23 ( 47) link_NAG-ASN : angle 2.58512 / 1.69 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6535 (pttm) cc_final: 0.6308 (ptmt) REVERT: A 453 TYR cc_start: 0.7817 (p90) cc_final: 0.7502 (p90) REVERT: A 614 ASP cc_start: 0.8013 (p0) cc_final: 0.7698 (p0) REVERT: A 979 ASP cc_start: 0.8104 (t0) cc_final: 0.7816 (t0) REVERT: A 1092 GLU cc_start: 0.7811 (tp30) cc_final: 0.7298 (pp20) REVERT: B 239 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 453 TYR cc_start: 0.7932 (p90) cc_final: 0.7655 (p90) REVERT: B 529 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6687 (ptmm) REVERT: B 564 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6462 (tp40) REVERT: B 614 ASP cc_start: 0.7826 (p0) cc_final: 0.7398 (p0) REVERT: B 776 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8464 (tmtm) REVERT: C 118 LEU cc_start: 0.8058 (tt) cc_final: 0.7664 (tm) REVERT: C 239 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: C 271 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: C 453 TYR cc_start: 0.7708 (p90) cc_final: 0.7461 (p90) REVERT: C 564 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.5463 (tm-30) REVERT: C 586 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: C 603 ASN cc_start: 0.8294 (m110) cc_final: 0.7410 (t0) outliers start: 40 outliers final: 21 residues processed: 230 average time/residue: 0.5524 time to fit residues: 151.0929 Evaluate side-chains 231 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 191 optimal weight: 2.9990 chunk 266 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 28 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 147 optimal weight: 0.0770 chunk 288 optimal weight: 0.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 66 HIS C 99 ASN C 779 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.207012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158850 restraints weight = 34498.559| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.06 r_work: 0.3332 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 26413 Z= 0.111 Angle : 0.563 9.883 36083 Z= 0.295 Chirality : 0.045 0.229 4261 Planarity : 0.004 0.050 4554 Dihedral : 4.651 24.614 3410 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.04 % Allowed : 11.38 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3135 helix: 1.84 (0.21), residues: 734 sheet: 1.07 (0.20), residues: 669 loop : -1.40 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.024 0.001 TYR B 904 PHE 0.027 0.001 PHE A 32 TRP 0.018 0.001 TRP C 886 HIS 0.009 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26307) covalent geometry : angle 0.53627 / 0.29 (35807) SS BOND : bond 0.00433 / 0.29 ( 42) SS BOND : angle 1.83385 / 1.15 ( 84) hydrogen bonds : bond 0.05423 / 3.49 ( 959) hydrogen bonds : angle 4.94402 / 3.39 ( 2678) link_BETA1-4 : bond 0.00406 / 0.23 ( 17) link_BETA1-4 : angle 1.12571 / 0.70 ( 51) link_NAG-ASN : bond 0.00366 / 0.23 ( 47) link_NAG-ASN : angle 2.39343 / 1.56 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6537 (pttm) cc_final: 0.6329 (ptmt) REVERT: A 614 ASP cc_start: 0.8092 (p0) cc_final: 0.7783 (p0) REVERT: A 979 ASP cc_start: 0.8118 (t0) cc_final: 0.7831 (t0) REVERT: A 1092 GLU cc_start: 0.7838 (tp30) cc_final: 0.7316 (pp20) REVERT: B 239 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7457 (tm-30) REVERT: B 335 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6984 (mt) REVERT: B 453 TYR cc_start: 0.7995 (p90) cc_final: 0.7750 (p90) REVERT: B 529 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6656 (ptmm) REVERT: B 564 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6490 (tp40) REVERT: B 614 ASP cc_start: 0.7852 (p0) cc_final: 0.7415 (p0) REVERT: B 776 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8434 (tmtm) REVERT: C 118 LEU cc_start: 0.8154 (tt) cc_final: 0.7801 (tm) REVERT: C 239 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: C 271 GLN cc_start: 0.7441 (mm-40) cc_final: 0.7236 (mp10) REVERT: C 453 TYR cc_start: 0.7774 (p90) cc_final: 0.7515 (p90) REVERT: C 564 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.5470 (tm-30) REVERT: C 586 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: C 603 ASN cc_start: 0.8265 (m110) cc_final: 0.7388 (t0) REVERT: C 868 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: C 933 LYS cc_start: 0.8651 (mttp) cc_final: 0.8161 (mmtm) outliers start: 29 outliers final: 14 residues processed: 237 average time/residue: 0.5648 time to fit residues: 159.5381 Evaluate side-chains 227 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B1005 GLN C 66 HIS C 99 ASN C 779 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.204787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161074 restraints weight = 47958.301| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.42 r_work: 0.3214 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 26413 Z= 0.134 Angle : 0.607 9.789 36083 Z= 0.318 Chirality : 0.046 0.238 4261 Planarity : 0.004 0.051 4554 Dihedral : 4.768 24.159 3410 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.08 % Allowed : 11.59 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3135 helix: 1.77 (0.20), residues: 740 sheet: 0.89 (0.20), residues: 683 loop : -1.38 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.025 0.001 TYR B 904 PHE 0.025 0.001 PHE B 318 TRP 0.016 0.002 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (26307) covalent geometry : angle 0.57890 / 0.31 (35807) SS BOND : bond 0.00447 / 0.29 ( 42) SS BOND : angle 2.12321 / 1.31 ( 84) hydrogen bonds : bond 0.06613 / 4.27 ( 959) hydrogen bonds : angle 5.04314 / 3.44 ( 2678) link_BETA1-4 : bond 0.00370 / 0.22 ( 17) link_BETA1-4 : angle 1.20876 / 0.73 ( 51) link_NAG-ASN : bond 0.00357 / 0.22 ( 47) link_NAG-ASN : angle 2.45210 / 1.61 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6270 Ramachandran restraints generated. 3135 Oldfield, 0 Emsley, 3135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6591 (pttm) cc_final: 0.6343 (ptmt) REVERT: A 614 ASP cc_start: 0.7999 (p0) cc_final: 0.7685 (p0) REVERT: A 979 ASP cc_start: 0.8022 (t0) cc_final: 0.7697 (t0) REVERT: A 1092 GLU cc_start: 0.7770 (tp30) cc_final: 0.7248 (pp20) REVERT: B 239 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 335 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7033 (mt) REVERT: B 453 TYR cc_start: 0.8110 (p90) cc_final: 0.7867 (p90) REVERT: B 564 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6518 (tp40) REVERT: B 614 ASP cc_start: 0.7790 (p0) cc_final: 0.7357 (p0) REVERT: B 776 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8449 (tmtm) REVERT: C 239 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: C 453 TYR cc_start: 0.7867 (p90) cc_final: 0.7583 (p90) REVERT: C 564 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.5504 (tm-30) REVERT: C 586 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: C 603 ASN cc_start: 0.8191 (m110) cc_final: 0.7408 (t0) REVERT: C 613 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.5981 (mp10) REVERT: C 933 LYS cc_start: 0.8622 (mttp) cc_final: 0.8158 (mmtm) outliers start: 30 outliers final: 18 residues processed: 233 average time/residue: 0.5487 time to fit residues: 151.5557 Evaluate side-chains 235 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 172 optimal weight: 0.4980 chunk 312 optimal weight: 1.9990 chunk 310 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 117 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 211 ASN A1101 HIS B 99 ASN B 121 ASN B 957 GLN B1005 GLN C 66 HIS C 99 ASN C 779 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.206511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.162002 restraints weight = 48168.777| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.45 r_work: 0.3264 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 26413 Z= 0.113 Angle : 0.568 9.722 36083 Z= 0.297 Chirality : 0.045 0.231 4261 Planarity : 0.004 0.051 4554 Dihedral : 4.603 23.733 3410 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.94 % Allowed : 11.74 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.15), residues: 3135 helix: 1.94 (0.20), residues: 734 sheet: 0.97 (0.20), residues: 649 loop : -1.31 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.026 0.001 TYR A 453 PHE 0.026 0.001 PHE A 32 TRP 0.017 0.001 TRP C 886 HIS 0.016 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (26307) covalent geometry : angle 0.54125 / 0.29 (35807) SS BOND : bond 0.00431 / 0.29 ( 42) SS BOND : angle 1.87592 / 1.17 ( 84) hydrogen bonds : bond 0.05698 / 3.66 ( 959) hydrogen bonds : angle 4.93298 / 3.38 ( 2678) link_BETA1-4 : bond 0.00406 / 0.24 ( 17) link_BETA1-4 : angle 1.12912 / 0.70 ( 51) link_NAG-ASN : bond 0.00362 / 0.22 ( 47) link_NAG-ASN : angle 2.34483 / 1.54 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11061.88 seconds wall clock time: 188 minutes 28.79 seconds (11308.79 seconds total)