Starting phenix.real_space_refine on Sun Jul 5 22:10:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whs_37546/07_2026/8whs_37546.map" } resolution = 3.33 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= 0.075 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 143 5.16 5 Cl 1 4.86 5 C 19539 2.51 5 N 4986 2.21 5 O 5972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30642 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8285 Classifications: {'peptide': 1059} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1003} Chain breaks: 5 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: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} 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: "R" 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: "S" 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: "T" 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: "U" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 30642 At special positions: 0 Unit cell: (140.17, 151.94, 243.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 143 16.00 O 5972 8.00 N 4986 7.00 C 19539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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=2.03 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 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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 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 R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " " NAG U 1 " - " BMA U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 354 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 331 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 331 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG D 905 " - " ASN D 322 " " NAG D 906 " - " ASN D 53 " " NAG E 1 " - " ASN A 354 " " NAG G 1 " - " ASN A1134 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 354 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7070 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 57 sheets defined 31.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.696A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.761A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 627 removed outlier: 3.659A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.598A 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: 4.090A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.556A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.335A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.858A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.279A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.832A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.974A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.753A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 616 through 627 removed outlier: 3.981A 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 removed outlier: 3.506A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 881 removed outlier: 3.642A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (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 912 through 919 removed outlier: 4.399A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.917A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.860A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.626A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.491A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.827A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.770A 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 618 through 627 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.692A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) 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: 4.508A 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 885 removed outlier: 3.919A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.835A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.859A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.980A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.556A pdb=" N LEU C1004 " --> pdb=" O ARG C1000 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.983A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.807A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.533A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.959A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.234A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.781A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.654A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.983A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.677A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.905A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.801A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.596A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.094A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.620A pdb=" N ASN D 508 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 509' Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.467A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.663A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.659A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.748A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (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: 3.612A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.893A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.602A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.613A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 5.300A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.560A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.947A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.725A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.025A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.696A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 575 through 577 removed outlier: 3.647A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.363A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.545A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 713 through 715 removed outlier: 3.656A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.740A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.511A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.666A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.706A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.557A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.620A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.979A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.834A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.054A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.563A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.248A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.597A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.730A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.669A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.178A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.246A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.525A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.907A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.248A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 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: 4.270A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.452A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.725A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF9, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AG1, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AG2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.899A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'D' and resid 347 through 352 removed outlier: 4.024A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3093 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: 6.75 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4958 1.32 - 1.44: 8927 1.44 - 1.57: 17296 1.57 - 1.70: 2 1.70 - 1.83: 191 Bond restraints: 31374 Sorted by residual: bond pdb=" C VAL C 991 " pdb=" O VAL C 991 " ideal model delta sigma weight residual 1.237 1.299 -0.062 1.14e-02 7.69e+03 3.00e+01 bond pdb=" C ARG B 995 " pdb=" O ARG B 995 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.16e-02 7.43e+03 2.76e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" C GLU C 988 " pdb=" O GLU C 988 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.22e-02 6.72e+03 2.06e+01 bond pdb=" C ASP C 985 " pdb=" O ASP C 985 " ideal model delta sigma weight residual 1.238 1.294 -0.056 1.28e-02 6.10e+03 1.94e+01 ... (remaining 31369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 41617 2.52 - 5.05: 951 5.05 - 7.57: 110 7.57 - 10.10: 7 10.10 - 12.62: 2 Bond angle restraints: 42687 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 122.48 -11.78 1.22e+00 6.72e-01 9.33e+01 angle pdb=" C THR B 998 " pdb=" N GLY B 999 " pdb=" CA GLY B 999 " ideal model delta sigma weight residual 119.98 112.48 7.50 1.11e+00 8.12e-01 4.57e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 114.39 106.67 7.72 1.45e+00 4.76e-01 2.84e+01 angle pdb=" C THR C 998 " pdb=" N GLY C 999 " pdb=" CA GLY C 999 " ideal model delta sigma weight residual 119.98 114.23 5.75 1.11e+00 8.12e-01 2.68e+01 ... (remaining 42682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 17457 23.50 - 47.00: 1590 47.00 - 70.50: 211 70.50 - 93.99: 149 93.99 - 117.49: 114 Dihedral angle restraints: 19521 sinusoidal: 8524 harmonic: 10997 Sorted by residual: dihedral pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " pdb=" CZ ARG A 983 " pdb=" NH1 ARG A 983 " ideal model delta sinusoidal sigma weight residual 0.00 -87.19 87.19 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CD ARG A 995 " pdb=" NE ARG A 995 " pdb=" CZ ARG A 995 " pdb=" NH1 ARG A 995 " ideal model delta sinusoidal sigma weight residual 0.00 84.84 -84.84 1 1.00e+01 1.00e-02 8.74e+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 33.81 59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 19518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 4904 0.176 - 0.351: 50 0.351 - 0.527: 5 0.527 - 0.702: 1 0.702 - 0.878: 3 Chirality restraints: 4963 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 4960 not shown) Planarity restraints: 5475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " -0.231 2.00e-02 2.50e+03 1.93e-01 4.64e+02 pdb=" C7 NAG B1306 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.318 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.204 2.00e-02 2.50e+03 1.72e-01 3.71e+02 pdb=" C7 NAG C1310 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.139 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.292 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -1.102 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG A 983 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.016 2.00e-02 2.50e+03 ... (remaining 5472 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1351 2.71 - 3.26: 30505 3.26 - 3.80: 48666 3.80 - 4.35: 59700 4.35 - 4.90: 100203 Nonbonded interactions: 240425 Sorted by model distance: nonbonded pdb=" O PHE C1075 " pdb=" OG1 THR C1076 " model vdw 2.161 3.040 nonbonded pdb=" O PHE B1075 " pdb=" OG1 THR B1076 " model vdw 2.171 3.040 nonbonded pdb=" O SER A 982 " pdb=" CG ARG A 983 " model vdw 2.173 3.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 124 " pdb=" O7 NAG B1301 " model vdw 2.204 3.040 ... (remaining 240420 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' and resid 23 through 1310) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 31.470 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 0.112 31486 Z= 0.339 Angle : 0.935 20.539 42975 Z= 0.525 Chirality : 0.061 0.878 4963 Planarity : 0.014 0.494 5424 Dihedral : 20.670 117.492 12325 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.47 % Favored : 92.29 % Rotamer: Outliers : 1.00 % Allowed : 21.71 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.71 (0.13), residues: 3736 helix: 0.71 (0.16), residues: 1047 sheet: -1.11 (0.21), residues: 593 loop : -2.21 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 34 TYR 0.020 0.001 TYR D 237 PHE 0.025 0.002 PHE B 86 TRP 0.033 0.002 TRP C1102 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.34 (31374) covalent geometry : angle 0.87295 / 0.51 (42687) SS BOND : bond 0.00318 / 0.22 ( 42) SS BOND : angle 1.24277 / 0.82 ( 84) hydrogen bonds : bond 0.20573 / 13.42 ( 1097) hydrogen bonds : angle 7.70821 / 5.28 ( 3093) metal coordination : bond 0.00080 / 0.04 ( 2) link_BETA1-4 : bond 0.00425 / 0.28 ( 17) link_BETA1-4 : angle 2.41990 / 1.53 ( 51) link_NAG-ASN : bond 0.00859 / 0.62 ( 51) link_NAG-ASN : angle 5.50871 / 3.75 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 1.078 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 984 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7830 (tp) REVERT: A 996 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 332 VAL cc_start: 0.3578 (OUTLIER) cc_final: 0.3265 (t) REVERT: B 531 THR cc_start: 0.7597 (p) cc_final: 0.7327 (p) REVERT: C 565 PHE cc_start: 0.4896 (m-80) cc_final: 0.4487 (m-10) REVERT: C 992 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7846 (mm110) REVERT: D 592 PHE cc_start: 0.1574 (t80) cc_final: 0.0432 (t80) outliers start: 33 outliers final: 11 residues processed: 252 average time/residue: 0.1579 time to fit residues: 67.5212 Evaluate side-chains 191 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 992 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN C 81 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 540 ASN C 564 GLN C 836 GLN D 96 GLN D 139 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.227175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146600 restraints weight = 49146.923| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.84 r_work: 0.3460 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31486 Z= 0.204 Angle : 0.834 17.735 42975 Z= 0.395 Chirality : 0.054 0.665 4963 Planarity : 0.005 0.091 5424 Dihedral : 11.814 100.765 5486 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 4.43 % Allowed : 19.83 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.62 (0.13), residues: 3736 helix: 0.72 (0.16), residues: 1086 sheet: -1.19 (0.20), residues: 618 loop : -2.13 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 983 TYR 0.024 0.002 TYR B1067 PHE 0.022 0.002 PHE C1089 TRP 0.021 0.002 TRP D 477 HIS 0.010 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (31374) covalent geometry : angle 0.76619 / 0.38 (42687) SS BOND : bond 0.00330 / 0.22 ( 42) SS BOND : angle 1.31765 / 0.88 ( 84) hydrogen bonds : bond 0.06089 / 3.96 ( 1097) hydrogen bonds : angle 5.49994 / 3.78 ( 3093) metal coordination : bond 0.00107 / 0.05 ( 2) link_BETA1-4 : bond 0.00483 / 0.31 ( 17) link_BETA1-4 : angle 4.09623 / 2.61 ( 51) link_NAG-ASN : bond 0.00932 / 0.65 ( 51) link_NAG-ASN : angle 5.02376 / 3.47 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 214 time to evaluate : 0.930 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 127 PHE cc_start: 0.4708 (t80) cc_final: 0.3427 (m-80) REVERT: A 773 GLU cc_start: 0.8053 (tt0) cc_final: 0.7563 (tt0) REVERT: A 820 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: A 984 LEU cc_start: 0.7371 (tp) cc_final: 0.6880 (tp) REVERT: B 64 TRP cc_start: 0.5482 (t60) cc_final: 0.5069 (t60) REVERT: B 336 CYS cc_start: 0.4667 (OUTLIER) cc_final: 0.4454 (t) REVERT: B 675 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7289 (tp40) REVERT: B 873 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: B 992 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6589 (mm-40) REVERT: B 1073 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8328 (mtpp) REVERT: B 1111 GLU cc_start: 0.8560 (tp30) cc_final: 0.8312 (tt0) REVERT: C 359 SER cc_start: -0.1641 (OUTLIER) cc_final: -0.2011 (p) REVERT: C 565 PHE cc_start: 0.5567 (m-80) cc_final: 0.5001 (m-10) REVERT: C 646 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8306 (mmm-85) REVERT: C 904 TYR cc_start: 0.8176 (m-10) cc_final: 0.7680 (m-10) REVERT: D 435 GLU cc_start: 0.0336 (OUTLIER) cc_final: -0.0496 (pt0) REVERT: D 579 MET cc_start: 0.0804 (mtm) cc_final: -0.1002 (ptp) REVERT: D 592 PHE cc_start: 0.1961 (t80) cc_final: 0.1523 (t80) outliers start: 146 outliers final: 82 residues processed: 341 average time/residue: 0.1562 time to fit residues: 91.8744 Evaluate side-chains 266 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 176 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1073 LYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 366 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 213 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 275 optimal weight: 0.3980 chunk 225 optimal weight: 0.0030 chunk 278 optimal weight: 0.8980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A1106 GLN B 125 ASN B 506 GLN B 644 GLN C 66 HIS C 81 ASN C 239 GLN C1010 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.226601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144333 restraints weight = 48703.452| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.11 r_work: 0.3432 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31486 Z= 0.143 Angle : 0.707 17.705 42975 Z= 0.337 Chirality : 0.048 0.567 4963 Planarity : 0.005 0.052 5424 Dihedral : 8.907 91.589 5470 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 3.61 % Allowed : 21.35 % Favored : 75.04 % 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: -1.34 (0.13), residues: 3736 helix: 1.06 (0.16), residues: 1078 sheet: -1.11 (0.20), residues: 644 loop : -1.99 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 190 TYR 0.016 0.001 TYR B1067 PHE 0.041 0.001 PHE C 192 TRP 0.024 0.001 TRP D 275 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (31374) covalent geometry : angle 0.64064 / 0.32 (42687) SS BOND : bond 0.00240 / 0.15 ( 42) SS BOND : angle 1.07750 / 0.70 ( 84) hydrogen bonds : bond 0.05499 / 3.58 ( 1097) hydrogen bonds : angle 5.18120 / 3.54 ( 3093) metal coordination : bond 0.00117 / 0.06 ( 2) link_BETA1-4 : bond 0.00465 / 0.28 ( 17) link_BETA1-4 : angle 3.25080 / 2.06 ( 51) link_NAG-ASN : bond 0.00808 / 0.58 ( 51) link_NAG-ASN : angle 4.67198 / 3.25 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 210 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.5186 (t80) cc_final: 0.4068 (m-80) REVERT: A 237 ARG cc_start: 0.4141 (ttp-170) cc_final: 0.3779 (ttp-170) REVERT: A 630 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (m) REVERT: A 773 GLU cc_start: 0.8001 (tt0) cc_final: 0.7533 (tt0) REVERT: A 820 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: A 984 LEU cc_start: 0.7807 (tp) cc_final: 0.7397 (tp) REVERT: B 64 TRP cc_start: 0.5742 (t60) cc_final: 0.5379 (t60) REVERT: B 336 CYS cc_start: 0.5032 (OUTLIER) cc_final: 0.4680 (t) REVERT: B 492 LEU cc_start: 0.0058 (OUTLIER) cc_final: -0.0333 (mt) REVERT: B 1036 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: C 190 ARG cc_start: 0.6912 (ptm160) cc_final: 0.6653 (ptm160) REVERT: C 216 PHE cc_start: 0.4203 (OUTLIER) cc_final: 0.2410 (t80) REVERT: C 434 ILE cc_start: 0.1256 (OUTLIER) cc_final: 0.0843 (pt) REVERT: C 559 PHE cc_start: 0.3473 (OUTLIER) cc_final: 0.2998 (t80) REVERT: C 565 PHE cc_start: 0.5525 (m-80) cc_final: 0.4921 (m-10) REVERT: C 646 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: C 904 TYR cc_start: 0.8211 (m-10) cc_final: 0.7761 (m-10) REVERT: C 1001 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8775 (tt) REVERT: D 323 MET cc_start: 0.2883 (mmm) cc_final: 0.2632 (mmm) REVERT: D 435 GLU cc_start: 0.0548 (OUTLIER) cc_final: -0.0360 (pt0) REVERT: D 579 MET cc_start: 0.0638 (mtm) cc_final: -0.1109 (ptp) outliers start: 119 outliers final: 68 residues processed: 311 average time/residue: 0.1502 time to fit residues: 80.7871 Evaluate side-chains 259 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 150 optimal weight: 0.0870 chunk 226 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 249 optimal weight: 20.0000 chunk 152 optimal weight: 1.9990 chunk 370 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 914 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.224462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.145972 restraints weight = 48321.425| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 5.28 r_work: 0.3391 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31486 Z= 0.141 Angle : 0.687 17.057 42975 Z= 0.328 Chirality : 0.048 0.566 4963 Planarity : 0.004 0.056 5424 Dihedral : 7.836 84.553 5470 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.66 % Rotamer: Outliers : 4.89 % Allowed : 20.44 % Favored : 74.67 % 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: -1.19 (0.14), residues: 3736 helix: 1.21 (0.16), residues: 1079 sheet: -0.98 (0.20), residues: 640 loop : -1.93 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.016 0.001 TYR B1067 PHE 0.018 0.001 PHE C 32 TRP 0.014 0.001 TRP D 165 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31374) covalent geometry : angle 0.62306 / 0.31 (42687) SS BOND : bond 0.00232 / 0.15 ( 42) SS BOND : angle 1.00297 / 0.68 ( 84) hydrogen bonds : bond 0.05143 / 3.36 ( 1097) hydrogen bonds : angle 4.96112 / 3.39 ( 3093) metal coordination : bond 0.00055 / 0.03 ( 2) link_BETA1-4 : bond 0.00368 / 0.22 ( 17) link_BETA1-4 : angle 2.79380 / 1.74 ( 51) link_NAG-ASN : bond 0.00808 / 0.57 ( 51) link_NAG-ASN : angle 4.60740 / 3.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 207 time to evaluate : 1.023 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 127 PHE cc_start: 0.5377 (t80) cc_final: 0.4277 (m-80) REVERT: A 176 LEU cc_start: 0.4637 (pt) cc_final: 0.3846 (tt) REVERT: A 223 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7015 (mp) REVERT: A 264 ASP cc_start: 0.5620 (OUTLIER) cc_final: 0.5362 (p0) REVERT: A 314 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: A 773 GLU cc_start: 0.8049 (tt0) cc_final: 0.7644 (tt0) REVERT: A 820 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: A 984 LEU cc_start: 0.7833 (tp) cc_final: 0.7359 (tp) REVERT: A 985 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6253 (p0) REVERT: A 1092 GLU cc_start: 0.8407 (pm20) cc_final: 0.8172 (pp20) REVERT: B 64 TRP cc_start: 0.5952 (t60) cc_final: 0.5628 (t60) REVERT: B 167 THR cc_start: 0.6250 (OUTLIER) cc_final: 0.6037 (t) REVERT: B 280 ASN cc_start: 0.8408 (t0) cc_final: 0.8187 (t0) REVERT: B 281 GLU cc_start: 0.9038 (pt0) cc_final: 0.8768 (pp20) REVERT: B 336 CYS cc_start: 0.4423 (OUTLIER) cc_final: 0.4101 (t) REVERT: B 492 LEU cc_start: 0.0007 (OUTLIER) cc_final: -0.0360 (mt) REVERT: B 675 GLN cc_start: 0.7783 (pp30) cc_final: 0.7551 (tp40) REVERT: B 873 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: B 1036 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: C 216 PHE cc_start: 0.4386 (OUTLIER) cc_final: 0.2709 (t80) REVERT: C 265 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5944 (m-80) REVERT: C 359 SER cc_start: -0.1772 (OUTLIER) cc_final: -0.2187 (p) REVERT: C 396 TYR cc_start: 0.1987 (OUTLIER) cc_final: 0.1031 (m-10) REVERT: C 559 PHE cc_start: 0.3919 (OUTLIER) cc_final: 0.3637 (t80) REVERT: C 565 PHE cc_start: 0.5484 (m-80) cc_final: 0.4960 (m-10) REVERT: C 591 SER cc_start: 0.8358 (m) cc_final: 0.8106 (m) REVERT: C 759 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7585 (t80) REVERT: C 904 TYR cc_start: 0.8180 (m-10) cc_final: 0.7799 (m-10) REVERT: C 1125 ASN cc_start: 0.7836 (t0) cc_final: 0.6799 (t0) REVERT: D 67 ASP cc_start: 0.7745 (m-30) cc_final: 0.7409 (p0) REVERT: D 229 THR cc_start: 0.1043 (p) cc_final: 0.0595 (p) REVERT: D 435 GLU cc_start: 0.0496 (OUTLIER) cc_final: -0.0406 (pt0) REVERT: D 579 MET cc_start: 0.0447 (mtm) cc_final: -0.1288 (ptp) outliers start: 161 outliers final: 99 residues processed: 350 average time/residue: 0.1459 time to fit residues: 87.9006 Evaluate side-chains 304 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 188 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 358 optimal weight: 40.0000 chunk 192 optimal weight: 0.9980 chunk 317 optimal weight: 20.0000 chunk 273 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 326 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 762 GLN A 907 ASN A 914 ASN A1048 HIS B 30 ASN B 49 HIS B 121 ASN B 914 ASN C 99 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN D 277 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN D 429 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.212123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125173 restraints weight = 47184.498| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.69 r_work: 0.3178 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 31486 Z= 0.349 Angle : 0.931 15.605 42975 Z= 0.463 Chirality : 0.057 0.595 4963 Planarity : 0.006 0.056 5424 Dihedral : 8.764 87.532 5467 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.73 % Favored : 91.19 % Rotamer: Outliers : 6.50 % Allowed : 20.68 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.78 (0.13), residues: 3736 helix: 0.65 (0.16), residues: 1078 sheet: -1.35 (0.19), residues: 660 loop : -2.25 (0.12), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 646 TYR 0.023 0.002 TYR A 837 PHE 0.042 0.003 PHE C 55 TRP 0.031 0.002 TRP C 886 HIS 0.014 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.35 (31374) covalent geometry : angle 0.87301 / 0.45 (42687) SS BOND : bond 0.00983 / 0.62 ( 42) SS BOND : angle 2.59275 / 1.72 ( 84) hydrogen bonds : bond 0.08477 / 5.43 ( 1097) hydrogen bonds : angle 5.52152 / 3.80 ( 3093) metal coordination : bond 0.00177 / 0.09 ( 2) link_BETA1-4 : bond 0.00510 / 0.28 ( 17) link_BETA1-4 : angle 2.43702 / 1.62 ( 51) link_NAG-ASN : bond 0.00894 / 0.59 ( 51) link_NAG-ASN : angle 5.02925 / 3.58 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 225 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.9138 (m) cc_final: 0.8571 (p) REVERT: A 127 PHE cc_start: 0.6575 (t80) cc_final: 0.6343 (t80) REVERT: A 176 LEU cc_start: 0.5895 (pt) cc_final: 0.5271 (tt) REVERT: A 237 ARG cc_start: 0.6895 (ttp-170) cc_final: 0.6485 (ttp-170) REVERT: A 264 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.6124 (p0) REVERT: A 287 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8186 (m-30) REVERT: A 314 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 472 ILE cc_start: -0.0776 (OUTLIER) cc_final: -0.1136 (tp) REVERT: A 534 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6757 (m) REVERT: A 559 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 568 ASP cc_start: 0.6434 (t0) cc_final: 0.6128 (t0) REVERT: A 773 GLU cc_start: 0.8700 (tt0) cc_final: 0.8153 (tt0) REVERT: A 816 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8720 (m) REVERT: A 820 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: A 907 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.9071 (t0) REVERT: B 280 ASN cc_start: 0.8609 (t0) cc_final: 0.8326 (t0) REVERT: B 309 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 492 LEU cc_start: -0.0003 (OUTLIER) cc_final: -0.0345 (mt) REVERT: B 549 THR cc_start: 0.7928 (p) cc_final: 0.7663 (p) REVERT: B 675 GLN cc_start: 0.8178 (pp30) cc_final: 0.7910 (tp40) REVERT: B 873 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 990 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: C 190 ARG cc_start: 0.7890 (ptm160) cc_final: 0.6383 (mtt-85) REVERT: C 216 PHE cc_start: 0.4516 (OUTLIER) cc_final: 0.2841 (t80) REVERT: C 265 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.5948 (m-80) REVERT: C 277 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 359 SER cc_start: -0.1831 (OUTLIER) cc_final: -0.2079 (p) REVERT: C 396 TYR cc_start: 0.2209 (OUTLIER) cc_final: 0.1196 (m-10) REVERT: C 625 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7247 (t-90) REVERT: C 759 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7705 (t80) REVERT: C 856 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8354 (p0) REVERT: C 934 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8555 (tp) REVERT: C 977 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 1001 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 1038 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8437 (mptt) REVERT: D 123 MET cc_start: -0.0984 (ppp) cc_final: -0.1873 (tmm) REVERT: D 435 GLU cc_start: 0.0432 (OUTLIER) cc_final: -0.0416 (pt0) outliers start: 214 outliers final: 120 residues processed: 407 average time/residue: 0.1539 time to fit residues: 107.8116 Evaluate side-chains 327 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 182 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 350 optimal weight: 50.0000 chunk 256 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 349 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 978 ASN C 81 ASN C 239 GLN C 540 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN D 98 GLN D 101 GLN D 221 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.214481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126610 restraints weight = 47200.475| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.43 r_work: 0.3231 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31486 Z= 0.210 Angle : 0.766 14.853 42975 Z= 0.375 Chirality : 0.051 0.572 4963 Planarity : 0.005 0.058 5424 Dihedral : 8.028 79.208 5464 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.47 % Allowed : 22.05 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.13), residues: 3736 helix: 0.88 (0.16), residues: 1086 sheet: -1.43 (0.19), residues: 690 loop : -2.13 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 190 TYR 0.019 0.001 TYR B1067 PHE 0.023 0.002 PHE B 329 TRP 0.018 0.002 TRP A 104 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (31374) covalent geometry : angle 0.70772 / 0.36 (42687) SS BOND : bond 0.00614 / 0.40 ( 42) SS BOND : angle 1.91892 / 1.24 ( 84) hydrogen bonds : bond 0.06255 / 4.06 ( 1097) hydrogen bonds : angle 5.12242 / 3.52 ( 3093) metal coordination : bond 0.00145 / 0.07 ( 2) link_BETA1-4 : bond 0.00364 / 0.22 ( 17) link_BETA1-4 : angle 2.19474 / 1.43 ( 51) link_NAG-ASN : bond 0.00767 / 0.55 ( 51) link_NAG-ASN : angle 4.64858 / 3.26 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 209 time to evaluate : 0.759 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 31 SER cc_start: 0.9106 (m) cc_final: 0.8588 (p) REVERT: A 32 PHE cc_start: 0.8643 (m-10) cc_final: 0.8368 (m-80) REVERT: A 127 PHE cc_start: 0.6991 (t80) cc_final: 0.6347 (m-80) REVERT: A 176 LEU cc_start: 0.6039 (pt) cc_final: 0.5599 (mp) REVERT: A 237 ARG cc_start: 0.6816 (ttp-170) cc_final: 0.5685 (ttm110) REVERT: A 314 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: A 472 ILE cc_start: -0.0309 (OUTLIER) cc_final: -0.0559 (tp) REVERT: A 559 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 773 GLU cc_start: 0.8263 (tt0) cc_final: 0.7789 (tt0) REVERT: A 820 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: B 167 THR cc_start: 0.6252 (OUTLIER) cc_final: 0.6031 (t) REVERT: B 269 TYR cc_start: 0.7626 (m-80) cc_final: 0.7342 (m-80) REVERT: B 271 GLN cc_start: 0.8112 (mt0) cc_final: 0.7714 (mt0) REVERT: B 280 ASN cc_start: 0.8504 (t0) cc_final: 0.8257 (t0) REVERT: B 492 LEU cc_start: -0.0472 (OUTLIER) cc_final: -0.0822 (mt) REVERT: B 549 THR cc_start: 0.7943 (p) cc_final: 0.7578 (p) REVERT: B 873 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: C 190 ARG cc_start: 0.8201 (ptm160) cc_final: 0.6779 (mtt-85) REVERT: C 216 PHE cc_start: 0.4730 (OUTLIER) cc_final: 0.3120 (t80) REVERT: C 265 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.5545 (m-80) REVERT: C 359 SER cc_start: -0.2300 (OUTLIER) cc_final: -0.2507 (p) REVERT: C 396 TYR cc_start: 0.2270 (OUTLIER) cc_final: 0.1201 (m-10) REVERT: C 574 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 625 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7067 (t-90) REVERT: C 759 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7376 (t80) REVERT: C 904 TYR cc_start: 0.8056 (m-10) cc_final: 0.7448 (m-10) REVERT: C 977 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 1038 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8366 (mptt) REVERT: D 123 MET cc_start: -0.0827 (ppp) cc_final: -0.1472 (tmm) REVERT: D 435 GLU cc_start: 0.0473 (OUTLIER) cc_final: -0.0544 (pt0) REVERT: D 581 VAL cc_start: 0.1652 (OUTLIER) cc_final: 0.1425 (m) outliers start: 180 outliers final: 107 residues processed: 367 average time/residue: 0.1508 time to fit residues: 95.2771 Evaluate side-chains 309 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 185 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 181 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 340 optimal weight: 40.0000 chunk 318 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 341 optimal weight: 20.0000 chunk 324 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 333 optimal weight: 40.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.208340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122087 restraints weight = 47298.717| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.42 r_work: 0.3146 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 31486 Z= 0.295 Angle : 0.865 16.465 42975 Z= 0.430 Chirality : 0.054 0.586 4963 Planarity : 0.006 0.061 5424 Dihedral : 8.322 80.027 5464 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.93 % Rotamer: Outliers : 5.86 % Allowed : 22.29 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3736 helix: 0.77 (0.16), residues: 1073 sheet: -1.52 (0.19), residues: 680 loop : -2.24 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 328 TYR 0.025 0.002 TYR A 837 PHE 0.035 0.003 PHE A 392 TRP 0.034 0.002 TRP D 271 HIS 0.010 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.30 (31374) covalent geometry : angle 0.80925 / 0.42 (42687) SS BOND : bond 0.00468 / 0.30 ( 42) SS BOND : angle 2.39343 / 1.55 ( 84) hydrogen bonds : bond 0.07581 / 4.88 ( 1097) hydrogen bonds : angle 5.29128 / 3.67 ( 3093) metal coordination : bond 0.00096 / 0.05 ( 2) link_BETA1-4 : bond 0.00456 / 0.25 ( 17) link_BETA1-4 : angle 2.31075 / 1.56 ( 51) link_NAG-ASN : bond 0.00718 / 0.49 ( 51) link_NAG-ASN : angle 4.76514 / 3.34 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 188 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.9195 (m) cc_final: 0.8787 (p) REVERT: A 62 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7463 (m) REVERT: A 127 PHE cc_start: 0.7393 (t80) cc_final: 0.6926 (t80) REVERT: A 176 LEU cc_start: 0.6168 (pt) cc_final: 0.5884 (mp) REVERT: A 202 LYS cc_start: 0.7789 (mttm) cc_final: 0.7144 (mptt) REVERT: A 237 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.6984 (ttm110) REVERT: A 287 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: A 314 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: A 488 CYS cc_start: 0.5723 (OUTLIER) cc_final: 0.5223 (m) REVERT: A 559 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 571 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8039 (t70) REVERT: A 742 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8716 (pt) REVERT: A 773 GLU cc_start: 0.8665 (tt0) cc_final: 0.8176 (tt0) REVERT: A 816 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8809 (m) REVERT: A 820 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: B 271 GLN cc_start: 0.8378 (mt0) cc_final: 0.8011 (mt0) REVERT: B 309 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: B 492 LEU cc_start: -0.0378 (OUTLIER) cc_final: -0.0727 (mt) REVERT: B 873 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: C 190 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7125 (mtt-85) REVERT: C 216 PHE cc_start: 0.4025 (OUTLIER) cc_final: 0.2497 (t80) REVERT: C 226 LEU cc_start: 0.6582 (tt) cc_final: 0.6193 (tp) REVERT: C 265 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: C 277 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 346 ARG cc_start: 0.3699 (OUTLIER) cc_final: 0.3354 (tmt-80) REVERT: C 396 TYR cc_start: 0.2394 (OUTLIER) cc_final: 0.1194 (m-10) REVERT: C 625 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7134 (t-90) REVERT: C 759 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7746 (t80) REVERT: C 850 ILE cc_start: 0.7018 (mm) cc_final: 0.6748 (mp) REVERT: C 977 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8287 (mp) REVERT: C 1001 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 1038 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8398 (mptt) REVERT: C 1118 ASP cc_start: 0.8272 (m-30) cc_final: 0.7795 (m-30) REVERT: D 123 MET cc_start: -0.0539 (ppp) cc_final: -0.1618 (tmm) REVERT: D 435 GLU cc_start: 0.0436 (OUTLIER) cc_final: -0.0557 (pt0) REVERT: D 585 LEU cc_start: 0.1801 (mt) cc_final: 0.1432 (pp) outliers start: 193 outliers final: 139 residues processed: 355 average time/residue: 0.1486 time to fit residues: 90.9280 Evaluate side-chains 331 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 170 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 352 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 223 optimal weight: 0.0270 chunk 266 optimal weight: 0.9990 chunk 131 optimal weight: 0.0020 chunk 53 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 347 optimal weight: 9.9990 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 960 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN ** D 378 HIS ** 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 = 0.4550 r_free = 0.4550 target = 0.212702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128969 restraints weight = 47239.901| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.43 r_work: 0.3266 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31486 Z= 0.130 Angle : 0.704 14.222 42975 Z= 0.344 Chirality : 0.048 0.569 4963 Planarity : 0.005 0.064 5424 Dihedral : 7.288 70.522 5464 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.28 % Allowed : 24.60 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.41 (0.13), residues: 3736 helix: 1.04 (0.16), residues: 1085 sheet: -1.18 (0.19), residues: 698 loop : -2.06 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 357 TYR 0.022 0.001 TYR A 396 PHE 0.022 0.001 PHE B 329 TRP 0.020 0.001 TRP D 271 HIS 0.014 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (31374) covalent geometry : angle 0.64751 / 0.33 (42687) SS BOND : bond 0.00272 / 0.17 ( 42) SS BOND : angle 1.45342 / 0.92 ( 84) hydrogen bonds : bond 0.04964 / 3.22 ( 1097) hydrogen bonds : angle 5.01127 / 3.45 ( 3093) metal coordination : bond 0.01239 / 0.65 ( 2) link_BETA1-4 : bond 0.00662 / 0.49 ( 17) link_BETA1-4 : angle 2.08902 / 1.37 ( 51) link_NAG-ASN : bond 0.00696 / 0.51 ( 51) link_NAG-ASN : angle 4.45162 / 3.12 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 196 time to evaluate : 1.121 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 31 SER cc_start: 0.9135 (m) cc_final: 0.8846 (p) REVERT: A 127 PHE cc_start: 0.7388 (t80) cc_final: 0.6920 (t80) REVERT: A 176 LEU cc_start: 0.6032 (pt) cc_final: 0.5770 (mp) REVERT: A 237 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7000 (ttm110) REVERT: A 265 TYR cc_start: 0.7282 (m-80) cc_final: 0.6884 (m-80) REVERT: A 559 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 571 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.7998 (t70) REVERT: A 773 GLU cc_start: 0.8094 (tt0) cc_final: 0.7632 (tt0) REVERT: B 167 THR cc_start: 0.6226 (OUTLIER) cc_final: 0.6023 (t) REVERT: B 190 ARG cc_start: 0.6710 (ptp90) cc_final: 0.5850 (mpt180) REVERT: B 265 TYR cc_start: 0.5484 (m-80) cc_final: 0.4990 (t80) REVERT: B 492 LEU cc_start: -0.0648 (OUTLIER) cc_final: -0.0909 (mt) REVERT: B 873 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: B 1115 ILE cc_start: 0.8766 (tt) cc_final: 0.8546 (mt) REVERT: C 190 ARG cc_start: 0.7792 (ptm160) cc_final: 0.7223 (mtt-85) REVERT: C 216 PHE cc_start: 0.3920 (OUTLIER) cc_final: 0.2420 (t80) REVERT: C 265 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.5640 (m-80) REVERT: C 346 ARG cc_start: 0.3821 (OUTLIER) cc_final: 0.3390 (tmt-80) REVERT: C 396 TYR cc_start: 0.2332 (OUTLIER) cc_final: 0.1232 (m-10) REVERT: C 759 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7331 (t80) REVERT: C 904 TYR cc_start: 0.8056 (m-10) cc_final: 0.7485 (m-10) REVERT: C 977 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8042 (mp) REVERT: C 1038 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8374 (mptt) REVERT: C 1118 ASP cc_start: 0.8201 (m-30) cc_final: 0.7633 (m-30) REVERT: D 81 GLN cc_start: 0.5985 (pm20) cc_final: 0.5535 (mm110) REVERT: D 123 MET cc_start: -0.0660 (ppp) cc_final: -0.1313 (tmm) REVERT: D 435 GLU cc_start: 0.0443 (OUTLIER) cc_final: -0.0598 (pt0) REVERT: D 585 LEU cc_start: 0.2350 (mt) cc_final: 0.1798 (pp) outliers start: 108 outliers final: 75 residues processed: 292 average time/residue: 0.1597 time to fit residues: 79.3495 Evaluate side-chains 256 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 169 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 557 MET Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 182 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.211284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125753 restraints weight = 47221.699| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.57 r_work: 0.3214 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31486 Z= 0.153 Angle : 0.713 14.942 42975 Z= 0.345 Chirality : 0.048 0.550 4963 Planarity : 0.005 0.058 5424 Dihedral : 7.036 68.847 5462 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.19 % Allowed : 24.60 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.32 (0.14), residues: 3736 helix: 1.11 (0.16), residues: 1088 sheet: -1.17 (0.20), residues: 687 loop : -1.99 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 34 TYR 0.021 0.001 TYR A 396 PHE 0.018 0.002 PHE B 133 TRP 0.015 0.001 TRP D 271 HIS 0.012 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (31374) covalent geometry : angle 0.65872 / 0.33 (42687) SS BOND : bond 0.00316 / 0.20 ( 42) SS BOND : angle 1.55627 / 1.01 ( 84) hydrogen bonds : bond 0.05469 / 3.54 ( 1097) hydrogen bonds : angle 4.90059 / 3.38 ( 3093) metal coordination : bond 0.06158 / 3.10 ( 2) link_BETA1-4 : bond 0.00444 / 0.27 ( 17) link_BETA1-4 : angle 2.08144 / 1.38 ( 51) link_NAG-ASN : bond 0.00663 / 0.47 ( 51) link_NAG-ASN : angle 4.35970 / 3.05 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 190 time to evaluate : 0.975 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 127 PHE cc_start: 0.7586 (t80) cc_final: 0.7304 (t80) REVERT: A 176 LEU cc_start: 0.6105 (pt) cc_final: 0.5884 (mp) REVERT: A 237 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7237 (ttm110) REVERT: A 265 TYR cc_start: 0.7226 (m-80) cc_final: 0.6909 (m-80) REVERT: A 559 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8193 (t80) REVERT: A 773 GLU cc_start: 0.8246 (tt0) cc_final: 0.7793 (tt0) REVERT: B 167 THR cc_start: 0.6277 (OUTLIER) cc_final: 0.6066 (t) REVERT: B 190 ARG cc_start: 0.6801 (ptp90) cc_final: 0.6021 (mpt180) REVERT: B 492 LEU cc_start: -0.0549 (OUTLIER) cc_final: -0.0803 (mt) REVERT: C 190 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7232 (mtt-85) REVERT: C 216 PHE cc_start: 0.4083 (OUTLIER) cc_final: 0.2603 (t80) REVERT: C 226 LEU cc_start: 0.6398 (tt) cc_final: 0.5973 (tp) REVERT: C 237 ARG cc_start: 0.5485 (mtp85) cc_final: 0.5173 (pmt-80) REVERT: C 346 ARG cc_start: 0.3857 (OUTLIER) cc_final: 0.3546 (tmt-80) REVERT: C 396 TYR cc_start: 0.2329 (OUTLIER) cc_final: 0.1225 (m-10) REVERT: C 759 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7450 (t80) REVERT: C 904 TYR cc_start: 0.8031 (m-10) cc_final: 0.7410 (m-10) REVERT: C 977 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8057 (mp) REVERT: C 1118 ASP cc_start: 0.8233 (m-30) cc_final: 0.7700 (m-30) REVERT: D 81 GLN cc_start: 0.5952 (pm20) cc_final: 0.5485 (mm110) REVERT: D 123 MET cc_start: -0.0655 (ppp) cc_final: -0.1305 (tmm) REVERT: D 435 GLU cc_start: 0.0422 (OUTLIER) cc_final: -0.0575 (pt0) REVERT: D 585 LEU cc_start: 0.2609 (mt) cc_final: 0.2074 (pp) outliers start: 105 outliers final: 86 residues processed: 283 average time/residue: 0.1581 time to fit residues: 76.2617 Evaluate side-chains 268 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 173 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 269 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 355 optimal weight: 0.0870 chunk 302 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 901 GLN B 914 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.211774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126919 restraints weight = 46853.555| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.48 r_work: 0.3238 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31486 Z= 0.136 Angle : 0.696 13.774 42975 Z= 0.336 Chirality : 0.047 0.557 4963 Planarity : 0.005 0.058 5424 Dihedral : 6.819 63.690 5462 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.13 % Allowed : 24.54 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.14), residues: 3736 helix: 1.19 (0.16), residues: 1089 sheet: -1.10 (0.19), residues: 696 loop : -1.93 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.028 0.001 TYR C 160 PHE 0.032 0.001 PHE C 133 TRP 0.018 0.001 TRP D 271 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (31374) covalent geometry : angle 0.64334 / 0.32 (42687) SS BOND : bond 0.00233 / 0.15 ( 42) SS BOND : angle 1.55830 / 1.00 ( 84) hydrogen bonds : bond 0.05017 / 3.26 ( 1097) hydrogen bonds : angle 4.81697 / 3.33 ( 3093) metal coordination : bond 0.01897 / 0.96 ( 2) link_BETA1-4 : bond 0.00512 / 0.34 ( 17) link_BETA1-4 : angle 1.97257 / 1.31 ( 51) link_NAG-ASN : bond 0.00643 / 0.47 ( 51) link_NAG-ASN : angle 4.22037 / 2.97 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 179 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7278 (ttm110) REVERT: A 265 TYR cc_start: 0.7143 (m-80) cc_final: 0.6795 (m-80) REVERT: A 357 ARG cc_start: 0.6676 (mmp-170) cc_final: 0.5930 (tpt170) REVERT: A 559 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 571 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.7921 (t70) REVERT: A 773 GLU cc_start: 0.8162 (tt0) cc_final: 0.7718 (tt0) REVERT: A 816 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8804 (m) REVERT: A 984 LEU cc_start: 0.7622 (tp) cc_final: 0.7375 (tp) REVERT: B 167 THR cc_start: 0.6265 (OUTLIER) cc_final: 0.6054 (t) REVERT: B 190 ARG cc_start: 0.6792 (ptp90) cc_final: 0.6065 (mpt180) REVERT: B 492 LEU cc_start: -0.0607 (OUTLIER) cc_final: -0.0899 (mt) REVERT: C 190 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7318 (mtt-85) REVERT: C 216 PHE cc_start: 0.4149 (OUTLIER) cc_final: 0.2704 (t80) REVERT: C 237 ARG cc_start: 0.5759 (mtp85) cc_final: 0.5349 (pmt-80) REVERT: C 265 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: C 346 ARG cc_start: 0.3861 (OUTLIER) cc_final: 0.3545 (tmt-80) REVERT: C 396 TYR cc_start: 0.2242 (OUTLIER) cc_final: 0.1165 (m-10) REVERT: C 559 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.4761 (m-80) REVERT: C 759 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7372 (t80) REVERT: C 904 TYR cc_start: 0.8056 (m-10) cc_final: 0.7475 (m-10) REVERT: C 977 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8022 (mp) REVERT: C 1118 ASP cc_start: 0.8240 (m-30) cc_final: 0.7729 (m-30) REVERT: D 81 GLN cc_start: 0.5873 (pm20) cc_final: 0.5451 (mm110) REVERT: D 123 MET cc_start: -0.0603 (ppp) cc_final: -0.1579 (tmm) REVERT: D 435 GLU cc_start: 0.0487 (OUTLIER) cc_final: -0.0556 (pt0) REVERT: D 585 LEU cc_start: 0.2733 (mt) cc_final: 0.2255 (pp) outliers start: 103 outliers final: 83 residues processed: 270 average time/residue: 0.1708 time to fit residues: 78.0068 Evaluate side-chains 268 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 172 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 79 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 232 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 356 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.210864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125906 restraints weight = 47023.993| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.63 r_work: 0.3216 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31486 Z= 0.143 Angle : 0.695 13.886 42975 Z= 0.337 Chirality : 0.047 0.552 4963 Planarity : 0.005 0.056 5424 Dihedral : 6.630 58.499 5462 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.31 % Allowed : 24.51 % Favored : 72.18 % 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: -1.18 (0.14), residues: 3736 helix: 1.20 (0.16), residues: 1087 sheet: -1.02 (0.20), residues: 700 loop : -1.92 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.016 0.001 TYR A1067 PHE 0.027 0.001 PHE C 133 TRP 0.018 0.001 TRP D 271 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (31374) covalent geometry : angle 0.64420 / 0.32 (42687) SS BOND : bond 0.00302 / 0.18 ( 42) SS BOND : angle 1.46718 / 0.95 ( 84) hydrogen bonds : bond 0.05154 / 3.34 ( 1097) hydrogen bonds : angle 4.78871 / 3.32 ( 3093) metal coordination : bond 0.02292 / 1.15 ( 2) link_BETA1-4 : bond 0.00489 / 0.32 ( 17) link_BETA1-4 : angle 1.94434 / 1.29 ( 51) link_NAG-ASN : bond 0.00614 / 0.45 ( 51) link_NAG-ASN : angle 4.19331 / 2.95 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8406.59 seconds wall clock time: 144 minutes 10.01 seconds (8650.01 seconds total)