Starting phenix.real_space_refine on Sat Aug 8 04:46:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xur_38681/08_2026/8xur_38681.map" } resolution = 3.85 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= 0.057 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 115 5.16 5 C 16442 2.51 5 N 4198 2.21 5 O 5037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25792 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" 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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 183 Unusual residues: {'IDU': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 5.29, per 1000 atoms: 0.21 Number of scatterers: 25792 At special positions: 0 Unit cell: (147.66, 136.96, 189.39, 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 115 16.00 O 5037 8.00 N 4198 7.00 C 16442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 122 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG A1311 " - " ASN A 282 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG B1311 " - " ASN B 354 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 343 " " NAG C1312 " - " ASN C 354 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C1098 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 729.0 milliseconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 52 sheets defined 25.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.900A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.791A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.969A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.858A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.704A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.789A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.582A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.997A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.855A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.992A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.549A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.876A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.598A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.829A pdb=" N VAL B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.362A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.623A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.661A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.051A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.757A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.890A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.649A pdb=" N VAL C 407 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 627 removed outlier: 3.586A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 840 through 844 removed outlier: 4.408A pdb=" N ILE C 844 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.581A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.436A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.743A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.503A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 9.725A pdb=" N ASN A 61 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A 268 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR A 63 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR A 266 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 65 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 264 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.601A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.621A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.385A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.990A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.296A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.932A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.915A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.629A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.812A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.844A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.207A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.198A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.586A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.577A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.998A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.914A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.568A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 120 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.311A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.541A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.837A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.918A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.950A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.965A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.590A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.549A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 5.601A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.377A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD9, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.527A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE3, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.657A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.039A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.506A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.543A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.105A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.542A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.638A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.608A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.335A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.813A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1094 through 1097 878 hydrogen bonds defined for protein. 2412 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: 6.27 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4621 1.33 - 1.45: 7162 1.45 - 1.57: 14467 1.57 - 1.70: 1 1.70 - 1.82: 141 Bond restraints: 26392 Sorted by residual: bond pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.13e+01 bond pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.84e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.80e+01 bond pdb=" CA ALA C 344 " pdb=" CB ALA C 344 " ideal model delta sigma weight residual 1.542 1.509 0.033 8.90e-03 1.26e+04 1.41e+01 bond pdb=" N VAL B 126 " pdb=" CA VAL B 126 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 ... (remaining 26387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 34169 2.09 - 4.18: 1518 4.18 - 6.27: 192 6.27 - 8.35: 37 8.35 - 10.44: 5 Bond angle restraints: 35921 Sorted by residual: angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" C ASN A 282 " ideal model delta sigma weight residual 111.02 103.17 7.85 1.22e+00 6.72e-01 4.14e+01 angle pdb=" O LYS A 557 " pdb=" C LYS A 557 " pdb=" N LYS A 558 " ideal model delta sigma weight residual 122.68 115.72 6.96 1.18e+00 7.18e-01 3.48e+01 angle pdb=" C CYS C 590 " pdb=" CA CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sigma weight residual 116.54 110.12 6.42 1.15e+00 7.56e-01 3.12e+01 angle pdb=" C LYS A 557 " pdb=" N LYS A 558 " pdb=" CA LYS A 558 " ideal model delta sigma weight residual 123.13 112.69 10.44 1.89e+00 2.80e-01 3.05e+01 angle pdb=" N CYS A 136 " pdb=" CA CYS A 136 " pdb=" C CYS A 136 " ideal model delta sigma weight residual 114.56 107.69 6.87 1.27e+00 6.20e-01 2.93e+01 ... (remaining 35916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 14701 23.09 - 46.18: 1411 46.18 - 69.27: 179 69.27 - 92.35: 113 92.35 - 115.44: 101 Dihedral angle restraints: 16505 sinusoidal: 7229 harmonic: 9276 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.81 83.19 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 26.05 66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual 93.00 33.06 59.94 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 16502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 4179 0.181 - 0.361: 52 0.361 - 0.542: 0 0.542 - 0.722: 2 0.722 - 0.903: 4 Chirality restraints: 4237 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-02 2.50e+03 1.23e+03 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 ... (remaining 4234 not shown) Planarity restraints: 4607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.274 2.00e-02 2.50e+03 2.29e-01 6.56e+02 pdb=" C7 NAG C1306 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.383 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.220 2.00e-02 2.50e+03 1.90e-01 4.53e+02 pdb=" C7 NAG B1303 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.320 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.209 2.00e-02 2.50e+03 1.74e-01 3.79e+02 pdb=" C7 NAG A1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.149 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " -0.014 2.00e-02 2.50e+03 ... (remaining 4604 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 439 2.63 - 3.20: 24011 3.20 - 3.77: 40380 3.77 - 4.33: 54058 4.33 - 4.90: 87188 Nonbonded interactions: 206076 Sorted by model distance: nonbonded pdb=" OD1 ASN B 532 " pdb=" N LEU B 533 " model vdw 2.064 3.120 nonbonded pdb=" NE2 GLN C 173 " pdb=" O PRO C 174 " model vdw 2.138 3.120 nonbonded pdb=" OD1 ASP B 40 " pdb=" N LYS B 41 " model vdw 2.157 3.120 nonbonded pdb=" O PHE C1075 " pdb=" OG1 THR C1076 " model vdw 2.171 3.040 nonbonded pdb=" O PHE B1075 " pdb=" OG1 THR B1076 " model vdw 2.174 3.040 ... (remaining 206071 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' selection = chain 'B' selection = (chain 'C' and resid 23 through 1311) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.960 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 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 : 0.006 0.059 26493 Z= 0.377 Angle : 0.978 17.595 36185 Z= 0.561 Chirality : 0.066 0.903 4237 Planarity : 0.012 0.369 4559 Dihedral : 20.665 115.442 10430 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.76 % Favored : 91.67 % Rotamer: Outliers : 1.69 % Allowed : 25.91 % Favored : 72.40 % 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: -1.86 (0.14), residues: 3159 helix: 0.83 (0.20), residues: 694 sheet: -1.06 (0.21), residues: 562 loop : -2.21 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1107 TYR 0.023 0.001 TYR A 365 PHE 0.035 0.001 PHE B 168 TRP 0.050 0.002 TRP B 633 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.38 (26392) covalent geometry : angle 0.92899 / 0.55 (35921) SS BOND : bond 0.00587 / 0.27 ( 39) SS BOND : angle 1.91010 / 1.39 ( 78) hydrogen bonds : bond 0.20526 / 13.25 ( 874) hydrogen bonds : angle 8.40534 / 5.72 ( 2412) link_BETA1-4 : bond 0.00491 / 0.32 ( 14) link_BETA1-4 : angle 2.73143 / 1.60 ( 42) link_NAG-ASN : bond 0.00811 / 0.55 ( 48) link_NAG-ASN : angle 4.57164 / 3.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 653 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9425 (tp) cc_final: 0.9203 (tt) REVERT: A 159 VAL cc_start: 0.7050 (OUTLIER) cc_final: 0.6749 (m) REVERT: A 173 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7152 (tt0) REVERT: A 353 TRP cc_start: 0.5114 (OUTLIER) cc_final: 0.3966 (p-90) REVERT: A 464 PHE cc_start: 0.6020 (p90) cc_final: 0.5521 (p90) REVERT: A 465 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.4722 (mm-30) REVERT: A 598 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7350 (mm) REVERT: A 624 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7470 (tt) REVERT: A 690 GLN cc_start: 0.4988 (mm110) cc_final: 0.4553 (mm110) REVERT: A 759 PHE cc_start: 0.7455 (t80) cc_final: 0.6482 (t80) REVERT: A 773 GLU cc_start: 0.7861 (tt0) cc_final: 0.7536 (tt0) REVERT: A 950 ASP cc_start: 0.7830 (t0) cc_final: 0.6722 (t0) REVERT: A 1143 LEU cc_start: 0.7035 (mt) cc_final: 0.6797 (pp) REVERT: B 170 TYR cc_start: 0.6643 (t80) cc_final: 0.6169 (t80) REVERT: B 303 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7832 (pp) REVERT: B 385 THR cc_start: 0.8988 (m) cc_final: 0.8720 (p) REVERT: B 421 TYR cc_start: 0.6307 (m-80) cc_final: 0.6102 (m-10) REVERT: B 493 GLN cc_start: 0.3813 (tm-30) cc_final: 0.3486 (mm-40) REVERT: B 547 THR cc_start: 0.5825 (OUTLIER) cc_final: 0.5237 (t) REVERT: B 1050 MET cc_start: 0.6347 (mtm) cc_final: 0.5856 (mtm) REVERT: C 177 MET cc_start: 0.0798 (mmp) cc_final: 0.0025 (mtm) REVERT: C 342 PHE cc_start: 0.5803 (m-80) cc_final: 0.5602 (m-80) REVERT: C 515 PHE cc_start: 0.8198 (m-80) cc_final: 0.7794 (m-80) REVERT: C 582 LEU cc_start: 0.8490 (mt) cc_final: 0.7720 (tp) REVERT: C 759 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6409 (t80) REVERT: C 777 ASN cc_start: 0.8637 (m-40) cc_final: 0.8174 (m110) REVERT: C 977 LEU cc_start: 0.8285 (mm) cc_final: 0.7945 (mm) outliers start: 47 outliers final: 13 residues processed: 694 average time/residue: 0.1496 time to fit residues: 167.7694 Evaluate side-chains 360 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 339 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 759 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 556 ASN A 628 GLN A 777 ASN A1108 ASN B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN B 957 GLN B1002 GLN B1005 GLN B1125 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 314 GLN C 321 GLN C 360 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.093958 restraints weight = 102766.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.096439 restraints weight = 56665.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.098059 restraints weight = 37122.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.099081 restraints weight = 27621.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.099800 restraints weight = 22754.754| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26493 Z= 0.183 Angle : 0.896 17.228 36185 Z= 0.422 Chirality : 0.054 0.646 4237 Planarity : 0.006 0.069 4559 Dihedral : 13.237 112.438 4750 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.44 % Favored : 92.47 % Rotamer: Outliers : 5.91 % Allowed : 25.51 % Favored : 68.58 % 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: -1.84 (0.14), residues: 3159 helix: 0.81 (0.20), residues: 706 sheet: -1.09 (0.20), residues: 621 loop : -2.20 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 328 TYR 0.024 0.002 TYR C 917 PHE 0.049 0.002 PHE C 133 TRP 0.021 0.002 TRP B 452 HIS 0.011 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (26392) covalent geometry : angle 0.81327 / 0.40 (35921) SS BOND : bond 0.00341 / 0.19 ( 39) SS BOND : angle 1.93613 / 1.26 ( 78) hydrogen bonds : bond 0.05162 / 3.34 ( 874) hydrogen bonds : angle 6.37558 / 4.38 ( 2412) link_BETA1-4 : bond 0.00451 / 0.24 ( 14) link_BETA1-4 : angle 3.81240 / 2.39 ( 42) link_NAG-ASN : bond 0.00773 / 0.52 ( 48) link_NAG-ASN : angle 5.51113 / 3.40 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 359 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9445 (tp) cc_final: 0.9202 (tt) REVERT: A 159 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6818 (m) REVERT: A 173 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7138 (tt0) REVERT: A 369 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 421 TYR cc_start: 0.7043 (m-10) cc_final: 0.6375 (m-10) REVERT: A 463 PRO cc_start: 0.6088 (Cg_exo) cc_final: 0.5788 (Cg_endo) REVERT: A 464 PHE cc_start: 0.5978 (p90) cc_final: 0.5401 (p90) REVERT: A 465 GLU cc_start: 0.5514 (OUTLIER) cc_final: 0.5195 (mm-30) REVERT: A 534 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7015 (m) REVERT: A 759 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7307 (t80) REVERT: A 773 GLU cc_start: 0.8476 (tt0) cc_final: 0.8260 (tt0) REVERT: A 954 HIS cc_start: 0.8395 (m-70) cc_final: 0.7999 (m-70) REVERT: A 1005 GLN cc_start: 0.9044 (mm110) cc_final: 0.8638 (mm-40) REVERT: A 1143 LEU cc_start: 0.6832 (mt) cc_final: 0.6500 (pp) REVERT: B 84 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5866 (mp) REVERT: B 170 TYR cc_start: 0.6842 (t80) cc_final: 0.6237 (t80) REVERT: B 200 TYR cc_start: 0.5243 (OUTLIER) cc_final: 0.4096 (t80) REVERT: B 374 PHE cc_start: 0.3319 (OUTLIER) cc_final: 0.3080 (m-80) REVERT: B 421 TYR cc_start: 0.6504 (m-80) cc_final: 0.6233 (m-10) REVERT: B 570 VAL cc_start: 0.8277 (m) cc_final: 0.7836 (p) REVERT: B 651 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6790 (mm) REVERT: B 819 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 856 ASN cc_start: 0.8526 (m110) cc_final: 0.7976 (p0) REVERT: B 902 MET cc_start: 0.8275 (tpt) cc_final: 0.7711 (tpt) REVERT: B 909 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6665 (tp) REVERT: B 1002 GLN cc_start: 0.8973 (tt0) cc_final: 0.8747 (tm-30) REVERT: B 1050 MET cc_start: 0.6703 (mtm) cc_final: 0.6435 (mtm) REVERT: C 50 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 54 LEU cc_start: 0.8836 (mm) cc_final: 0.8615 (mt) REVERT: C 177 MET cc_start: 0.0539 (mmp) cc_final: -0.0085 (mtm) REVERT: C 239 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6800 (mm110) REVERT: C 342 PHE cc_start: 0.6058 (m-80) cc_final: 0.5714 (m-80) REVERT: C 387 LEU cc_start: 0.9332 (mt) cc_final: 0.9123 (mt) REVERT: C 515 PHE cc_start: 0.8607 (m-80) cc_final: 0.8099 (m-80) REVERT: C 559 PHE cc_start: 0.1917 (OUTLIER) cc_final: 0.1358 (m-80) REVERT: C 565 PHE cc_start: 0.7703 (m-10) cc_final: 0.7249 (m-80) REVERT: C 571 ASP cc_start: 0.6335 (t0) cc_final: 0.6061 (t0) REVERT: C 582 LEU cc_start: 0.8573 (mt) cc_final: 0.7786 (tp) REVERT: C 697 MET cc_start: 0.8009 (mpp) cc_final: 0.7298 (mpp) REVERT: C 759 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7205 (t80) REVERT: C 776 LYS cc_start: 0.9011 (tppt) cc_final: 0.8779 (tppt) REVERT: C 977 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8108 (mm) REVERT: C 1019 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8572 (tpp80) REVERT: C 1037 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7324 (p) outliers start: 164 outliers final: 58 residues processed: 482 average time/residue: 0.1295 time to fit residues: 103.6726 Evaluate side-chains 354 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 279 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1061 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 314 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 218 GLN A 370 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 GLN A 901 GLN A 926 GLN A1036 GLN B 218 GLN B 360 ASN B 487 ASN B 493 GLN B 505 HIS B 506 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1125 ASN C 99 ASN C 173 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 628 GLN C1036 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072994 restraints weight = 102040.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075053 restraints weight = 57767.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076434 restraints weight = 39497.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.077348 restraints weight = 30430.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.077957 restraints weight = 25515.739| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 26493 Z= 0.325 Angle : 1.023 16.762 36185 Z= 0.509 Chirality : 0.058 0.669 4237 Planarity : 0.007 0.100 4559 Dihedral : 9.559 117.541 4734 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.31 % Favored : 90.60 % Rotamer: Outliers : 7.50 % Allowed : 25.01 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.14), residues: 3159 helix: 0.40 (0.19), residues: 690 sheet: -1.40 (0.21), residues: 582 loop : -2.35 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 355 TYR 0.030 0.003 TYR B 279 PHE 0.053 0.003 PHE A 338 TRP 0.026 0.003 TRP A 353 HIS 0.016 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.32 (26392) covalent geometry : angle 0.95651 / 0.49 (35921) SS BOND : bond 0.00681 / 0.39 ( 39) SS BOND : angle 2.33575 / 1.50 ( 78) hydrogen bonds : bond 0.06722 / 4.41 ( 874) hydrogen bonds : angle 6.41878 / 4.37 ( 2412) link_BETA1-4 : bond 0.01030 / 0.68 ( 14) link_BETA1-4 : angle 3.27939 / 2.13 ( 42) link_NAG-ASN : bond 0.01082 / 0.73 ( 48) link_NAG-ASN : angle 5.34795 / 3.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 279 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8644 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 341 VAL cc_start: 0.9443 (t) cc_final: 0.9223 (p) REVERT: A 369 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8053 (t80) REVERT: A 402 ILE cc_start: 0.7384 (tp) cc_final: 0.6933 (tp) REVERT: A 464 PHE cc_start: 0.5850 (p90) cc_final: 0.5579 (p90) REVERT: A 571 ASP cc_start: 0.8749 (t0) cc_final: 0.8291 (t0) REVERT: A 759 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7960 (t80) REVERT: A 786 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8193 (ptpp) REVERT: A 904 TYR cc_start: 0.7079 (m-10) cc_final: 0.6232 (m-80) REVERT: A 950 ASP cc_start: 0.8630 (t0) cc_final: 0.8412 (t0) REVERT: A 981 LEU cc_start: 0.8998 (tp) cc_final: 0.8579 (pp) REVERT: A 1005 GLN cc_start: 0.8920 (mm110) cc_final: 0.8563 (mm-40) REVERT: B 170 TYR cc_start: 0.7427 (t80) cc_final: 0.6988 (t80) REVERT: B 200 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.3972 (t80) REVERT: B 425 LEU cc_start: 0.6440 (mt) cc_final: 0.5742 (mp) REVERT: B 495 TYR cc_start: -0.1485 (OUTLIER) cc_final: -0.1808 (m-80) REVERT: B 643 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: B 774 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8234 (mm-40) REVERT: B 856 ASN cc_start: 0.8509 (m110) cc_final: 0.8172 (p0) REVERT: B 939 PHE cc_start: 0.8528 (t80) cc_final: 0.8314 (t80) REVERT: C 177 MET cc_start: 0.0972 (mmp) cc_final: 0.0077 (mtm) REVERT: C 342 PHE cc_start: 0.6523 (m-80) cc_final: 0.5424 (m-80) REVERT: C 387 LEU cc_start: 0.9432 (mt) cc_final: 0.9152 (mt) REVERT: C 515 PHE cc_start: 0.8729 (m-80) cc_final: 0.8201 (m-80) REVERT: C 559 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4316 (m-80) REVERT: C 571 ASP cc_start: 0.7236 (t0) cc_final: 0.6911 (t0) REVERT: C 582 LEU cc_start: 0.8589 (mt) cc_final: 0.7632 (tp) REVERT: C 759 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8157 (t80) REVERT: C 969 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8792 (mtpp) REVERT: C 977 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 996 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9399 (mp) REVERT: C 1019 ARG cc_start: 0.8989 (tpp80) cc_final: 0.8611 (tpp80) REVERT: C 1029 MET cc_start: 0.9101 (tpp) cc_final: 0.8893 (tpp) outliers start: 208 outliers final: 99 residues processed: 458 average time/residue: 0.1308 time to fit residues: 100.1208 Evaluate side-chains 323 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 213 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 439 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 206 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 307 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1011 GLN A1036 GLN B 26 GLN B 487 ASN B 540 ASN B 563 GLN B 564 GLN B 580 GLN B 777 ASN B 784 GLN B1125 ASN C 239 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.096238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072723 restraints weight = 101816.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074828 restraints weight = 57035.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076235 restraints weight = 38821.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.077162 restraints weight = 29856.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.077770 restraints weight = 25049.953| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26493 Z= 0.160 Angle : 0.819 16.249 36185 Z= 0.392 Chirality : 0.052 0.617 4237 Planarity : 0.005 0.066 4559 Dihedral : 8.500 107.785 4727 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.40 % Rotamer: Outliers : 5.37 % Allowed : 26.56 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.14), residues: 3159 helix: 0.87 (0.20), residues: 698 sheet: -1.19 (0.20), residues: 621 loop : -2.21 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.023 0.002 TYR A 655 PHE 0.037 0.002 PHE A 338 TRP 0.023 0.002 TRP B 452 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (26392) covalent geometry : angle 0.74609 / 0.37 (35921) SS BOND : bond 0.00518 / 0.31 ( 39) SS BOND : angle 2.23319 / 1.64 ( 78) hydrogen bonds : bond 0.05223 / 3.43 ( 874) hydrogen bonds : angle 5.81250 / 3.97 ( 2412) link_BETA1-4 : bond 0.00281 / 0.18 ( 14) link_BETA1-4 : angle 2.89994 / 1.81 ( 42) link_NAG-ASN : bond 0.00793 / 0.53 ( 48) link_NAG-ASN : angle 4.94795 / 3.10 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 255 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9514 (tp) cc_final: 0.9199 (tt) REVERT: A 133 PHE cc_start: 0.7421 (t80) cc_final: 0.6500 (t80) REVERT: A 314 GLN cc_start: 0.8601 (tt0) cc_final: 0.8077 (tm-30) REVERT: A 369 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8065 (t80) REVERT: A 402 ILE cc_start: 0.6716 (tp) cc_final: 0.6133 (tp) REVERT: A 453 TYR cc_start: 0.7919 (p90) cc_final: 0.7257 (p90) REVERT: A 464 PHE cc_start: 0.5751 (p90) cc_final: 0.5545 (p90) REVERT: A 495 TYR cc_start: 0.5364 (OUTLIER) cc_final: 0.4717 (t80) REVERT: A 571 ASP cc_start: 0.8724 (t0) cc_final: 0.8305 (t0) REVERT: A 643 PHE cc_start: 0.7304 (t80) cc_final: 0.6980 (t80) REVERT: A 759 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 786 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8343 (ptpp) REVERT: A 950 ASP cc_start: 0.8656 (t0) cc_final: 0.8429 (t0) REVERT: A 1005 GLN cc_start: 0.9006 (mm110) cc_final: 0.8699 (mm-40) REVERT: B 95 THR cc_start: 0.6239 (OUTLIER) cc_final: 0.6027 (m) REVERT: B 104 TRP cc_start: 0.5615 (m-90) cc_final: 0.5288 (m-90) REVERT: B 170 TYR cc_start: 0.7256 (t80) cc_final: 0.6805 (t80) REVERT: B 200 TYR cc_start: 0.5237 (OUTLIER) cc_final: 0.4587 (t80) REVERT: B 214 ARG cc_start: 0.7445 (mtt180) cc_final: 0.6550 (mmt180) REVERT: B 360 ASN cc_start: 0.9008 (m-40) cc_final: 0.8628 (p0) REVERT: B 456 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4960 (m-80) REVERT: B 909 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7844 (tp) REVERT: B 939 PHE cc_start: 0.8512 (t80) cc_final: 0.8266 (t80) REVERT: B 1041 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7631 (t0) REVERT: C 104 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8018 (m100) REVERT: C 177 MET cc_start: 0.0976 (mmp) cc_final: 0.0212 (mtt) REVERT: C 387 LEU cc_start: 0.9429 (mt) cc_final: 0.9142 (mt) REVERT: C 515 PHE cc_start: 0.8703 (m-80) cc_final: 0.8192 (m-80) REVERT: C 559 PHE cc_start: 0.5825 (OUTLIER) cc_final: 0.4650 (m-80) REVERT: C 571 ASP cc_start: 0.7157 (t0) cc_final: 0.6837 (t0) REVERT: C 582 LEU cc_start: 0.8539 (mt) cc_final: 0.7595 (tp) REVERT: C 712 ILE cc_start: 0.6213 (OUTLIER) cc_final: 0.5790 (pt) REVERT: C 759 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 969 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.8946 (mtpp) REVERT: C 977 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8458 (mm) REVERT: C 1019 ARG cc_start: 0.8725 (tpp80) cc_final: 0.8525 (tpp80) REVERT: C 1029 MET cc_start: 0.9026 (tpp) cc_final: 0.8702 (tpp) outliers start: 149 outliers final: 83 residues processed: 380 average time/residue: 0.1361 time to fit residues: 86.1866 Evaluate side-chains 315 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 217 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 186 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 262 optimal weight: 0.1980 chunk 177 optimal weight: 0.0170 chunk 156 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 777 ASN A1002 GLN B 360 ASN B 978 ASN C 394 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073010 restraints weight = 101463.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.075200 restraints weight = 55920.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076639 restraints weight = 37520.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.077587 restraints weight = 28634.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.078240 restraints weight = 23926.033| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26493 Z= 0.134 Angle : 0.772 16.009 36185 Z= 0.365 Chirality : 0.051 0.602 4237 Planarity : 0.005 0.067 4559 Dihedral : 7.986 104.363 4727 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.44 % Favored : 92.47 % Rotamer: Outliers : 4.58 % Allowed : 27.35 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3159 helix: 1.17 (0.20), residues: 694 sheet: -0.94 (0.20), residues: 608 loop : -2.11 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.042 0.001 TYR B 495 PHE 0.045 0.001 PHE C 133 TRP 0.021 0.001 TRP B 452 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (26392) covalent geometry : angle 0.69982 / 0.35 (35921) SS BOND : bond 0.00516 / 0.29 ( 39) SS BOND : angle 1.99121 / 1.31 ( 78) hydrogen bonds : bond 0.04696 / 3.07 ( 874) hydrogen bonds : angle 5.53429 / 3.77 ( 2412) link_BETA1-4 : bond 0.00335 / 0.22 ( 14) link_BETA1-4 : angle 2.67171 / 1.66 ( 42) link_NAG-ASN : bond 0.00789 / 0.53 ( 48) link_NAG-ASN : angle 4.84415 / 3.03 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 232 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9493 (tp) cc_final: 0.9159 (tt) REVERT: A 173 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: A 177 MET cc_start: 0.6449 (pmm) cc_final: 0.5741 (mmt) REVERT: A 223 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 369 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 402 ILE cc_start: 0.6622 (tp) cc_final: 0.6049 (tp) REVERT: A 453 TYR cc_start: 0.8033 (p90) cc_final: 0.7394 (p90) REVERT: A 464 PHE cc_start: 0.5668 (p90) cc_final: 0.5289 (p90) REVERT: A 495 TYR cc_start: 0.5517 (OUTLIER) cc_final: 0.5020 (t80) REVERT: A 759 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7436 (t80) REVERT: A 786 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8452 (ptpp) REVERT: A 950 ASP cc_start: 0.8659 (t0) cc_final: 0.8453 (t0) REVERT: A 981 LEU cc_start: 0.9159 (tp) cc_final: 0.8647 (pp) REVERT: A 1005 GLN cc_start: 0.9000 (mm110) cc_final: 0.8725 (mm-40) REVERT: A 1128 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8081 (t) REVERT: B 104 TRP cc_start: 0.5688 (m-90) cc_final: 0.4579 (m-90) REVERT: B 126 VAL cc_start: 0.4539 (t) cc_final: 0.4105 (t) REVERT: B 170 TYR cc_start: 0.7291 (t80) cc_final: 0.6805 (t80) REVERT: B 177 MET cc_start: 0.2489 (ppp) cc_final: 0.1896 (pmm) REVERT: B 200 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.4510 (t80) REVERT: B 214 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6561 (mmt180) REVERT: B 456 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: B 586 ASP cc_start: 0.7904 (p0) cc_final: 0.7458 (p0) REVERT: B 643 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: B 909 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7906 (tp) REVERT: B 1002 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8685 (tm-30) REVERT: C 104 TRP cc_start: 0.8742 (OUTLIER) cc_final: 0.7916 (m100) REVERT: C 133 PHE cc_start: 0.5414 (m-80) cc_final: 0.4762 (m-80) REVERT: C 177 MET cc_start: 0.1447 (mmp) cc_final: 0.0478 (mtm) REVERT: C 271 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 387 LEU cc_start: 0.9402 (mt) cc_final: 0.9093 (mt) REVERT: C 515 PHE cc_start: 0.8677 (m-80) cc_final: 0.8207 (m-80) REVERT: C 559 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: C 582 LEU cc_start: 0.8537 (mt) cc_final: 0.7580 (tp) REVERT: C 940 SER cc_start: 0.8995 (m) cc_final: 0.8669 (p) REVERT: C 977 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8348 (mm) REVERT: C 996 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9362 (mp) REVERT: C 1029 MET cc_start: 0.9068 (tpp) cc_final: 0.8727 (tpp) REVERT: C 1105 THR cc_start: 0.8324 (m) cc_final: 0.8067 (m) outliers start: 127 outliers final: 79 residues processed: 330 average time/residue: 0.1589 time to fit residues: 87.7653 Evaluate side-chains 310 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 216 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 chunk 278 optimal weight: 0.0670 chunk 288 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 180 optimal weight: 0.0980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 49 HIS B 487 ASN C 394 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.097724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074657 restraints weight = 101523.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076797 restraints weight = 57004.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.078216 restraints weight = 38738.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.079138 restraints weight = 29793.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.079736 restraints weight = 25020.646| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26493 Z= 0.127 Angle : 0.758 15.742 36185 Z= 0.356 Chirality : 0.050 0.594 4237 Planarity : 0.005 0.066 4559 Dihedral : 7.515 101.816 4722 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 4.47 % Allowed : 26.99 % Favored : 68.54 % 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: -1.47 (0.15), residues: 3159 helix: 1.36 (0.20), residues: 682 sheet: -0.92 (0.21), residues: 589 loop : -1.99 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.033 0.001 TYR B 495 PHE 0.031 0.001 PHE C 133 TRP 0.019 0.001 TRP B 452 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (26392) covalent geometry : angle 0.68923 / 0.34 (35921) SS BOND : bond 0.00364 / 0.22 ( 39) SS BOND : angle 1.60023 / 1.09 ( 78) hydrogen bonds : bond 0.04430 / 2.89 ( 874) hydrogen bonds : angle 5.36698 / 3.66 ( 2412) link_BETA1-4 : bond 0.00227 / 0.15 ( 14) link_BETA1-4 : angle 2.47319 / 1.52 ( 42) link_NAG-ASN : bond 0.00773 / 0.52 ( 48) link_NAG-ASN : angle 4.76553 / 2.99 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 227 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: A 177 MET cc_start: 0.6418 (pmm) cc_final: 0.5993 (mmt) REVERT: A 369 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8129 (t80) REVERT: A 453 TYR cc_start: 0.8100 (p90) cc_final: 0.7651 (p90) REVERT: A 759 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 981 LEU cc_start: 0.9174 (tp) cc_final: 0.8675 (pp) REVERT: A 1005 GLN cc_start: 0.8906 (mm110) cc_final: 0.8699 (mm-40) REVERT: A 1122 VAL cc_start: 0.5428 (OUTLIER) cc_final: 0.5128 (p) REVERT: A 1128 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8099 (t) REVERT: B 104 TRP cc_start: 0.5804 (m-90) cc_final: 0.4600 (m-90) REVERT: B 126 VAL cc_start: 0.4644 (t) cc_final: 0.4226 (t) REVERT: B 170 TYR cc_start: 0.7220 (t80) cc_final: 0.6737 (t80) REVERT: B 177 MET cc_start: 0.2229 (ppp) cc_final: 0.1569 (pmm) REVERT: B 200 TYR cc_start: 0.5534 (OUTLIER) cc_final: 0.4690 (t80) REVERT: B 214 ARG cc_start: 0.7810 (mtt180) cc_final: 0.6863 (mmt180) REVERT: B 270 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7922 (tp) REVERT: B 643 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: B 909 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 1002 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 104 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.7860 (m100) REVERT: C 133 PHE cc_start: 0.5343 (m-80) cc_final: 0.4935 (m-80) REVERT: C 177 MET cc_start: 0.1374 (mmp) cc_final: 0.0422 (mtm) REVERT: C 387 LEU cc_start: 0.9419 (mt) cc_final: 0.9093 (mt) REVERT: C 515 PHE cc_start: 0.8726 (m-80) cc_final: 0.8393 (m-80) REVERT: C 559 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: C 582 LEU cc_start: 0.8483 (mt) cc_final: 0.7486 (tp) REVERT: C 940 SER cc_start: 0.8895 (m) cc_final: 0.8563 (p) REVERT: C 969 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.8973 (mtpp) REVERT: C 977 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8339 (mm) REVERT: C 1029 MET cc_start: 0.9010 (tpp) cc_final: 0.8596 (tpp) REVERT: C 1105 THR cc_start: 0.8251 (m) cc_final: 0.8039 (m) outliers start: 124 outliers final: 79 residues processed: 323 average time/residue: 0.1541 time to fit residues: 83.7314 Evaluate side-chains 294 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 202 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 314 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 394 ASN A 439 ASN A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 957 GLN A1002 GLN A1036 GLN A1135 ASN B 115 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 506 GLN B 580 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065255 restraints weight = 103427.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067139 restraints weight = 59252.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068383 restraints weight = 41156.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069220 restraints weight = 32259.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069774 restraints weight = 27361.082| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 26493 Z= 0.291 Angle : 0.948 14.875 36185 Z= 0.468 Chirality : 0.055 0.692 4237 Planarity : 0.006 0.093 4559 Dihedral : 8.404 108.424 4721 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.35 % Rotamer: Outliers : 5.80 % Allowed : 26.74 % Favored : 67.46 % Cbeta Deviations : 0.03 % 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: -1.88 (0.14), residues: 3159 helix: 0.81 (0.20), residues: 686 sheet: -0.95 (0.22), residues: 533 loop : -2.24 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 273 TYR 0.030 0.003 TYR A 451 PHE 0.033 0.003 PHE A 592 TRP 0.016 0.002 TRP B 104 HIS 0.007 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.29 (26392) covalent geometry : angle 0.88811 / 0.45 (35921) SS BOND : bond 0.00670 / 0.40 ( 39) SS BOND : angle 2.01123 / 1.32 ( 78) hydrogen bonds : bond 0.06506 / 4.26 ( 874) hydrogen bonds : angle 6.04600 / 4.12 ( 2412) link_BETA1-4 : bond 0.00569 / 0.38 ( 14) link_BETA1-4 : angle 2.80142 / 1.81 ( 42) link_NAG-ASN : bond 0.00881 / 0.55 ( 48) link_NAG-ASN : angle 4.94588 / 3.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 205 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7580 (t80) cc_final: 0.7378 (t80) REVERT: A 173 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: A 177 MET cc_start: 0.6481 (pmm) cc_final: 0.6198 (mmt) REVERT: A 369 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 451 TYR cc_start: 0.6313 (m-10) cc_final: 0.5508 (m-80) REVERT: A 453 TYR cc_start: 0.8299 (p90) cc_final: 0.7494 (p90) REVERT: A 484 LYS cc_start: 0.2462 (OUTLIER) cc_final: 0.1810 (mttt) REVERT: A 556 ASN cc_start: 0.8062 (t0) cc_final: 0.7244 (t0) REVERT: A 564 GLN cc_start: 0.6707 (tp-100) cc_final: 0.6443 (mm110) REVERT: A 731 MET cc_start: 0.8335 (ptm) cc_final: 0.7975 (ptm) REVERT: A 759 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 878 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8998 (mt) REVERT: A 896 ILE cc_start: 0.8363 (tp) cc_final: 0.8129 (mm) REVERT: A 981 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9020 (pp) REVERT: A 1005 GLN cc_start: 0.8877 (mm110) cc_final: 0.8623 (mm-40) REVERT: A 1034 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 1128 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8475 (t) REVERT: B 104 TRP cc_start: 0.6120 (m-90) cc_final: 0.5550 (m-90) REVERT: B 170 TYR cc_start: 0.7439 (t80) cc_final: 0.7238 (t80) REVERT: B 177 MET cc_start: 0.2452 (ppp) cc_final: 0.1549 (pmm) REVERT: B 200 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.4701 (t80) REVERT: B 270 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 425 LEU cc_start: 0.6377 (mt) cc_final: 0.5845 (mt) REVERT: B 456 PHE cc_start: 0.5139 (OUTLIER) cc_final: 0.4870 (m-80) REVERT: B 909 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8389 (tp) REVERT: B 984 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6756 (mm) REVERT: C 104 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7969 (m100) REVERT: C 133 PHE cc_start: 0.5599 (m-80) cc_final: 0.5195 (m-80) REVERT: C 159 VAL cc_start: 0.5911 (OUTLIER) cc_final: 0.5582 (t) REVERT: C 177 MET cc_start: 0.2852 (mmp) cc_final: 0.1518 (mtm) REVERT: C 329 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8304 (t80) REVERT: C 515 PHE cc_start: 0.8864 (m-80) cc_final: 0.8590 (m-80) REVERT: C 556 ASN cc_start: 0.8346 (t0) cc_final: 0.7307 (p0) REVERT: C 773 GLU cc_start: 0.8708 (tp30) cc_final: 0.8391 (tp30) REVERT: C 969 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9006 (mtpp) REVERT: C 1029 MET cc_start: 0.9187 (tpp) cc_final: 0.8970 (tpp) REVERT: C 1041 ASP cc_start: 0.8298 (t0) cc_final: 0.7789 (t0) REVERT: C 1111 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8045 (tm-30) outliers start: 161 outliers final: 101 residues processed: 336 average time/residue: 0.1504 time to fit residues: 83.9542 Evaluate side-chains 294 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 176 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 66 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 302 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 439 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 207 HIS B 405 ASN B 487 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.091042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068148 restraints weight = 102188.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070183 restraints weight = 56926.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071492 restraints weight = 38745.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072396 restraints weight = 29987.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073008 restraints weight = 25244.118| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.8966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26493 Z= 0.137 Angle : 0.797 14.095 36185 Z= 0.379 Chirality : 0.051 0.581 4237 Planarity : 0.005 0.065 4559 Dihedral : 7.657 103.422 4721 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.04 % Rotamer: Outliers : 3.46 % Allowed : 28.83 % Favored : 67.71 % 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: -1.52 (0.15), residues: 3159 helix: 1.34 (0.20), residues: 672 sheet: -0.86 (0.21), residues: 607 loop : -2.06 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 577 TYR 0.027 0.001 TYR B 495 PHE 0.027 0.002 PHE C 133 TRP 0.017 0.002 TRP B 452 HIS 0.010 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (26392) covalent geometry : angle 0.73614 / 0.37 (35921) SS BOND : bond 0.00421 / 0.29 ( 39) SS BOND : angle 1.76142 / 1.09 ( 78) hydrogen bonds : bond 0.04999 / 3.27 ( 874) hydrogen bonds : angle 5.42615 / 3.71 ( 2412) link_BETA1-4 : bond 0.00379 / 0.25 ( 14) link_BETA1-4 : angle 2.36025 / 1.47 ( 42) link_NAG-ASN : bond 0.00754 / 0.49 ( 48) link_NAG-ASN : angle 4.58649 / 2.88 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 212 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 177 MET cc_start: 0.6308 (pmm) cc_final: 0.5597 (mmt) REVERT: A 369 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 451 TYR cc_start: 0.6387 (m-10) cc_final: 0.5646 (m-80) REVERT: A 453 TYR cc_start: 0.8278 (p90) cc_final: 0.7508 (p90) REVERT: A 556 ASN cc_start: 0.7984 (t0) cc_final: 0.7129 (t0) REVERT: A 731 MET cc_start: 0.8515 (ptm) cc_final: 0.7683 (ptm) REVERT: A 759 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 869 MET cc_start: 0.9145 (mpp) cc_final: 0.8846 (ptp) REVERT: A 878 LEU cc_start: 0.9285 (tp) cc_final: 0.8906 (mt) REVERT: A 906 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 981 LEU cc_start: 0.9183 (tp) cc_final: 0.8969 (pp) REVERT: A 1005 GLN cc_start: 0.8922 (mm110) cc_final: 0.8678 (mm-40) REVERT: A 1034 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 1128 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8393 (t) REVERT: B 104 TRP cc_start: 0.6188 (m-90) cc_final: 0.5556 (m-90) REVERT: B 177 MET cc_start: 0.2276 (ppp) cc_final: 0.1945 (pmm) REVERT: B 200 TYR cc_start: 0.5432 (OUTLIER) cc_final: 0.4722 (t80) REVERT: B 214 ARG cc_start: 0.7483 (mtt180) cc_final: 0.6715 (mmt180) REVERT: B 456 PHE cc_start: 0.5174 (OUTLIER) cc_final: 0.4827 (m-80) REVERT: B 909 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 1031 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8104 (tm-30) REVERT: C 66 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7931 (t70) REVERT: C 104 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8096 (m100) REVERT: C 159 VAL cc_start: 0.6182 (OUTLIER) cc_final: 0.5821 (t) REVERT: C 177 MET cc_start: 0.2373 (mmp) cc_final: 0.1044 (mtt) REVERT: C 265 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: C 329 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (t80) REVERT: C 556 ASN cc_start: 0.8245 (t0) cc_final: 0.7538 (p0) REVERT: C 745 ASP cc_start: 0.8428 (t0) cc_final: 0.8029 (t0) REVERT: C 773 GLU cc_start: 0.8614 (tp30) cc_final: 0.8394 (tp30) REVERT: C 969 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.8997 (mtpp) REVERT: C 1041 ASP cc_start: 0.8213 (t0) cc_final: 0.7818 (t0) REVERT: C 1111 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7982 (tm-30) outliers start: 96 outliers final: 67 residues processed: 289 average time/residue: 0.1490 time to fit residues: 71.9141 Evaluate side-chains 263 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 181 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 54 optimal weight: 1.9990 chunk 317 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 316 optimal weight: 0.0060 chunk 179 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1036 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067131 restraints weight = 101970.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069088 restraints weight = 57586.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070386 restraints weight = 39430.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071264 restraints weight = 30574.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.071849 restraints weight = 25739.653| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.9325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26493 Z= 0.154 Angle : 0.789 15.652 36185 Z= 0.377 Chirality : 0.051 0.598 4237 Planarity : 0.005 0.064 4559 Dihedral : 7.486 102.717 4721 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 3.32 % Allowed : 29.44 % Favored : 67.24 % 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: -1.49 (0.15), residues: 3159 helix: 1.35 (0.20), residues: 682 sheet: -0.87 (0.21), residues: 616 loop : -2.05 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 355 TYR 0.024 0.001 TYR B 495 PHE 0.040 0.002 PHE C 133 TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (26392) covalent geometry : angle 0.72939 / 0.36 (35921) SS BOND : bond 0.00372 / 0.24 ( 39) SS BOND : angle 1.60924 / 1.03 ( 78) hydrogen bonds : bond 0.04881 / 3.20 ( 874) hydrogen bonds : angle 5.31129 / 3.62 ( 2412) link_BETA1-4 : bond 0.00316 / 0.21 ( 14) link_BETA1-4 : angle 2.41930 / 1.52 ( 42) link_NAG-ASN : bond 0.00720 / 0.46 ( 48) link_NAG-ASN : angle 4.55728 / 2.87 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 197 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: A 369 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.8067 (t80) REVERT: A 453 TYR cc_start: 0.8405 (p90) cc_final: 0.7981 (p90) REVERT: A 549 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9167 (m) REVERT: A 556 ASN cc_start: 0.8087 (t0) cc_final: 0.7279 (t0) REVERT: A 877 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9393 (mp) REVERT: A 878 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8917 (mt) REVERT: A 906 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8011 (t80) REVERT: A 981 LEU cc_start: 0.9257 (tp) cc_final: 0.9051 (pp) REVERT: A 1034 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8492 (tt) REVERT: A 1128 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8647 (t) REVERT: B 55 PHE cc_start: 0.7649 (m-10) cc_final: 0.7372 (m-10) REVERT: B 104 TRP cc_start: 0.6234 (m-90) cc_final: 0.5693 (m-90) REVERT: B 177 MET cc_start: 0.2420 (ppp) cc_final: 0.1758 (mmt) REVERT: B 200 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.4585 (t80) REVERT: B 214 ARG cc_start: 0.7219 (mtt180) cc_final: 0.6698 (mmt180) REVERT: B 270 LEU cc_start: 0.8728 (mm) cc_final: 0.8069 (mm) REVERT: B 425 LEU cc_start: 0.6267 (mt) cc_final: 0.6043 (mt) REVERT: B 456 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4955 (m-80) REVERT: B 909 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8427 (tp) REVERT: B 984 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6880 (mm) REVERT: C 66 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7962 (t70) REVERT: C 104 TRP cc_start: 0.8834 (OUTLIER) cc_final: 0.8023 (m100) REVERT: C 177 MET cc_start: 0.2642 (mmp) cc_final: 0.1353 (mtt) REVERT: C 265 TYR cc_start: 0.7062 (t80) cc_final: 0.6769 (m-80) REVERT: C 329 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8341 (t80) REVERT: C 556 ASN cc_start: 0.8384 (t0) cc_final: 0.7801 (p0) REVERT: C 740 MET cc_start: 0.8657 (tpp) cc_final: 0.8346 (tpp) REVERT: C 745 ASP cc_start: 0.8373 (t0) cc_final: 0.8090 (t0) REVERT: C 969 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.8996 (mtpp) REVERT: C 1041 ASP cc_start: 0.8348 (t0) cc_final: 0.7800 (t0) REVERT: C 1111 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8072 (tm-30) outliers start: 92 outliers final: 62 residues processed: 272 average time/residue: 0.1591 time to fit residues: 71.8022 Evaluate side-chains 259 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 221 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.087347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065000 restraints weight = 101401.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066903 restraints weight = 56927.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.068166 restraints weight = 38921.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068990 restraints weight = 30110.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069591 restraints weight = 25408.453| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.9851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26493 Z= 0.202 Angle : 0.825 15.021 36185 Z= 0.400 Chirality : 0.051 0.613 4237 Planarity : 0.005 0.091 4559 Dihedral : 7.725 103.524 4720 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 3.42 % Allowed : 29.41 % Favored : 67.17 % 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: -1.60 (0.15), residues: 3159 helix: 1.24 (0.20), residues: 686 sheet: -0.95 (0.21), residues: 596 loop : -2.10 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1107 TYR 0.028 0.002 TYR C 904 PHE 0.042 0.002 PHE A 175 TRP 0.019 0.002 TRP A 353 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (26392) covalent geometry : angle 0.76883 / 0.39 (35921) SS BOND : bond 0.00417 / 0.25 ( 39) SS BOND : angle 1.71928 / 1.11 ( 78) hydrogen bonds : bond 0.05289 / 3.45 ( 874) hydrogen bonds : angle 5.47775 / 3.74 ( 2412) link_BETA1-4 : bond 0.00340 / 0.22 ( 14) link_BETA1-4 : angle 2.41040 / 1.51 ( 42) link_NAG-ASN : bond 0.00693 / 0.44 ( 48) link_NAG-ASN : angle 4.50991 / 2.85 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 183 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: A 453 TYR cc_start: 0.8332 (p90) cc_final: 0.7561 (p90) REVERT: A 556 ASN cc_start: 0.7985 (t0) cc_final: 0.7269 (t0) REVERT: A 759 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7846 (t80) REVERT: A 877 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9429 (mp) REVERT: A 878 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 906 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8066 (t80) REVERT: A 1005 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8378 (mp10) REVERT: A 1034 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 1128 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8897 (t) REVERT: B 104 TRP cc_start: 0.6314 (m-90) cc_final: 0.5975 (m-90) REVERT: B 214 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6994 (mmt180) REVERT: B 270 LEU cc_start: 0.8578 (mm) cc_final: 0.7898 (mm) REVERT: B 425 LEU cc_start: 0.6654 (mt) cc_final: 0.6166 (mt) REVERT: B 456 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.5174 (m-80) REVERT: B 661 GLU cc_start: 0.7691 (pm20) cc_final: 0.7485 (pm20) REVERT: B 909 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8578 (tp) REVERT: B 984 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6932 (mm) REVERT: B 1031 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 104 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.8075 (m100) REVERT: C 177 MET cc_start: 0.3088 (mmp) cc_final: 0.1439 (mtm) REVERT: C 265 TYR cc_start: 0.7007 (t80) cc_final: 0.6751 (m-80) REVERT: C 329 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8362 (t80) REVERT: C 556 ASN cc_start: 0.8394 (t0) cc_final: 0.7904 (p0) REVERT: C 745 ASP cc_start: 0.8337 (t0) cc_final: 0.7982 (t0) REVERT: C 969 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9024 (mtpp) REVERT: C 1041 ASP cc_start: 0.8347 (t0) cc_final: 0.7972 (t0) outliers start: 95 outliers final: 67 residues processed: 262 average time/residue: 0.1553 time to fit residues: 68.5234 Evaluate side-chains 255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 175 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 108 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 255 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 305 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 26 GLN B 487 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.087811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065384 restraints weight = 100959.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067314 restraints weight = 56745.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068597 restraints weight = 38849.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069421 restraints weight = 30074.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.070002 restraints weight = 25434.330| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 1.0082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26493 Z= 0.154 Angle : 0.801 15.075 36185 Z= 0.381 Chirality : 0.051 0.585 4237 Planarity : 0.005 0.095 4559 Dihedral : 7.564 102.728 4720 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 3.10 % Allowed : 29.91 % Favored : 66.99 % 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: -1.53 (0.15), residues: 3159 helix: 1.33 (0.20), residues: 681 sheet: -0.82 (0.21), residues: 628 loop : -2.11 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.024 0.001 TYR B 495 PHE 0.028 0.002 PHE A 175 TRP 0.017 0.001 TRP A 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26392) covalent geometry : angle 0.74479 / 0.37 (35921) SS BOND : bond 0.00346 / 0.22 ( 39) SS BOND : angle 1.58431 / 1.02 ( 78) hydrogen bonds : bond 0.04938 / 3.23 ( 874) hydrogen bonds : angle 5.33002 / 3.64 ( 2412) link_BETA1-4 : bond 0.00330 / 0.20 ( 14) link_BETA1-4 : angle 2.34181 / 1.46 ( 42) link_NAG-ASN : bond 0.00700 / 0.45 ( 48) link_NAG-ASN : angle 4.44856 / 2.81 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.17 seconds wall clock time: 80 minutes 45.92 seconds (4845.92 seconds total)