Starting phenix.real_space_refine on Mon Aug 25 20:55:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_37546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_37546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_37546.map" model { file = "/net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_37546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whs_37546/08_2025/8whs_37546.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.45, 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.28 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: 6.91 Time building geometry restraints manager: 3.58 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: 4.120 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.140 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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 aren 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 covalent geometry : bond 0.00563 (31374) covalent geometry : angle 0.87295 (42687) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.24277 ( 84) hydrogen bonds : bond 0.20573 ( 1097) hydrogen bonds : angle 7.70821 ( 3093) metal coordination : bond 0.00080 ( 2) link_BETA1-4 : bond 0.00425 ( 17) link_BETA1-4 : angle 2.41990 ( 51) link_NAG-ASN : bond 0.00859 ( 51) link_NAG-ASN : angle 5.50871 ( 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 : 1.068 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: 0.1521 time to fit residues: 64.5598 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 : 0.905 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 207 HIS C 564 GLN C 836 GLN D 96 GLN D 139 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.226780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147464 restraints weight = 49120.753| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 5.27 r_work: 0.3429 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31486 Z= 0.219 Angle : 0.849 17.936 42975 Z= 0.406 Chirality : 0.054 0.678 4963 Planarity : 0.006 0.082 5424 Dihedral : 11.457 101.156 5486 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 4.49 % Allowed : 19.83 % Favored : 75.68 % 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 aren not related in a simple way. whole: -1.64 (0.13), residues: 3736 helix: 0.70 (0.16), residues: 1084 sheet: -1.24 (0.20), residues: 628 loop : -2.13 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 983 TYR 0.028 0.002 TYR C 266 PHE 0.023 0.002 PHE C1089 TRP 0.020 0.002 TRP D 477 HIS 0.009 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00488 (31374) covalent geometry : angle 0.78018 (42687) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.36419 ( 84) hydrogen bonds : bond 0.06279 ( 1097) hydrogen bonds : angle 5.54613 ( 3093) metal coordination : bond 0.00097 ( 2) link_BETA1-4 : bond 0.00565 ( 17) link_BETA1-4 : angle 4.27838 ( 51) link_NAG-ASN : bond 0.00840 ( 51) link_NAG-ASN : angle 5.03457 ( 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 362 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 214 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.5112 (t80) cc_final: 0.3674 (m-80) REVERT: A 773 GLU cc_start: 0.8212 (tt0) cc_final: 0.7775 (tt0) REVERT: A 790 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8518 (mttt) REVERT: A 820 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: A 984 LEU cc_start: 0.7517 (tp) cc_final: 0.7015 (tp) REVERT: B 64 TRP cc_start: 0.5672 (t60) cc_final: 0.5266 (t60) REVERT: B 336 CYS cc_start: 0.4490 (OUTLIER) cc_final: 0.4267 (t) REVERT: B 873 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: B 992 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6753 (mm-40) REVERT: B 1073 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: C 565 PHE cc_start: 0.5475 (m-80) cc_final: 0.4930 (m-10) REVERT: C 646 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: C 904 TYR cc_start: 0.8241 (m-10) cc_final: 0.7791 (m-10) REVERT: D 435 GLU cc_start: 0.0340 (OUTLIER) cc_final: -0.0561 (pt0) REVERT: D 579 MET cc_start: 0.0640 (mtm) cc_final: -0.1082 (ptp) outliers start: 148 outliers final: 85 residues processed: 344 average time/residue: 0.1453 time to fit residues: 85.4903 Evaluate side-chains 263 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 171 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 461 LEU 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 571 ASP 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 790 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 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 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 723 THR Chi-restraints excluded: chain B residue 736 VAL 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 976 VAL 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 133 PHE 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 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 791 THR 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 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 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 366 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 359 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 275 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 278 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 125 ASN B 506 GLN B 644 GLN C 66 HIS C 239 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.226168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.145643 restraints weight = 48752.111| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.90 r_work: 0.3422 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 31486 Z= 0.145 Angle : 0.703 17.641 42975 Z= 0.335 Chirality : 0.048 0.553 4963 Planarity : 0.005 0.052 5424 Dihedral : 8.738 91.350 5472 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 3.77 % Allowed : 21.23 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.14), residues: 3736 helix: 1.05 (0.16), residues: 1080 sheet: -1.01 (0.20), residues: 638 loop : -1.99 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 577 TYR 0.016 0.001 TYR A1067 PHE 0.028 0.001 PHE A 86 TRP 0.026 0.002 TRP D 275 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (31374) covalent geometry : angle 0.63553 (42687) SS BOND : bond 0.00433 ( 42) SS BOND : angle 1.16721 ( 84) hydrogen bonds : bond 0.05546 ( 1097) hydrogen bonds : angle 5.17241 ( 3093) metal coordination : bond 0.00071 ( 2) link_BETA1-4 : bond 0.00476 ( 17) link_BETA1-4 : angle 3.20561 ( 51) link_NAG-ASN : bond 0.00824 ( 51) link_NAG-ASN : angle 4.66717 ( 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 332 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 208 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.5122 (t80) cc_final: 0.4076 (m-80) REVERT: A 237 ARG cc_start: 0.4193 (ttp-170) cc_final: 0.3891 (ttp-170) REVERT: A 265 TYR cc_start: 0.7148 (m-10) cc_final: 0.6677 (m-10) REVERT: A 571 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (t70) REVERT: A 630 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8065 (m) REVERT: A 773 GLU cc_start: 0.7995 (tt0) cc_final: 0.7522 (tt0) REVERT: A 790 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8541 (mttt) REVERT: A 820 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 984 LEU cc_start: 0.7702 (tp) cc_final: 0.7297 (tp) REVERT: B 64 TRP cc_start: 0.5710 (t60) cc_final: 0.5353 (t60) REVERT: B 336 CYS cc_start: 0.5009 (OUTLIER) cc_final: 0.4726 (t) REVERT: B 492 LEU cc_start: 0.0304 (OUTLIER) cc_final: -0.0069 (mt) REVERT: B 1036 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8767 (tt0) REVERT: C 216 PHE cc_start: 0.4275 (OUTLIER) cc_final: 0.2495 (t80) REVERT: C 265 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5707 (m-80) REVERT: C 359 SER cc_start: -0.1755 (OUTLIER) cc_final: -0.2115 (p) REVERT: C 434 ILE cc_start: 0.1094 (OUTLIER) cc_final: 0.0669 (pt) REVERT: C 559 PHE cc_start: 0.3432 (OUTLIER) cc_final: 0.3003 (t80) REVERT: C 565 PHE cc_start: 0.5554 (m-80) cc_final: 0.4971 (m-10) REVERT: C 624 ILE cc_start: 0.8124 (mm) cc_final: 0.7899 (mm) REVERT: C 646 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8346 (mmm-85) REVERT: C 904 TYR cc_start: 0.8224 (m-10) cc_final: 0.7778 (m-10) REVERT: C 1001 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (tt) REVERT: C 1125 ASN cc_start: 0.7597 (t0) cc_final: 0.6659 (t0) REVERT: D 94 LYS cc_start: 0.2526 (OUTLIER) cc_final: 0.2087 (ptpt) REVERT: D 435 GLU cc_start: 0.0523 (OUTLIER) cc_final: -0.0269 (pt0) REVERT: D 579 MET cc_start: 0.0919 (mtm) cc_final: -0.0806 (ptp) outliers start: 124 outliers final: 60 residues processed: 314 average time/residue: 0.1415 time to fit residues: 76.3365 Evaluate side-chains 254 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 179 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 790 LYS 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 33 THR 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 133 PHE Chi-restraints excluded: chain B residue 159 VAL 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 565 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE 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 60 SER Chi-restraints excluded: chain C residue 133 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 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 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 637 SER Chi-restraints excluded: chain C residue 856 ASN 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 94 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 150 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 370 optimal weight: 30.0000 chunk 252 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** 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** A 907 ASN A1048 HIS B 121 ASN B 644 GLN B 914 ASN C 81 ASN C 239 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 101 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.218978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131724 restraints weight = 47544.017| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.96 r_work: 0.3299 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 31486 Z= 0.215 Angle : 0.769 16.524 42975 Z= 0.374 Chirality : 0.051 0.587 4963 Planarity : 0.005 0.062 5424 Dihedral : 8.218 85.625 5470 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.82 % Favored : 92.13 % Rotamer: Outliers : 5.80 % Allowed : 20.38 % Favored : 73.82 % 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 aren not related in a simple way. whole: -1.41 (0.13), residues: 3736 helix: 0.95 (0.16), residues: 1085 sheet: -1.06 (0.21), residues: 610 loop : -2.04 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 577 TYR 0.018 0.002 TYR B1067 PHE 0.021 0.002 PHE C 55 TRP 0.018 0.002 TRP C 886 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00520 (31374) covalent geometry : angle 0.70944 (42687) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.24132 ( 84) hydrogen bonds : bond 0.06511 ( 1097) hydrogen bonds : angle 5.17370 ( 3093) metal coordination : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00413 ( 17) link_BETA1-4 : angle 2.57859 ( 51) link_NAG-ASN : bond 0.00822 ( 51) link_NAG-ASN : angle 4.75962 ( 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 396 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 205 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: A 104 TRP cc_start: 0.4365 (OUTLIER) cc_final: 0.3591 (m-10) REVERT: A 127 PHE cc_start: 0.5943 (t80) cc_final: 0.5347 (m-80) REVERT: A 176 LEU cc_start: 0.5313 (pt) cc_final: 0.4486 (tt) REVERT: A 223 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 264 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5948 (p0) REVERT: A 314 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: A 568 ASP cc_start: 0.6552 (t0) cc_final: 0.6334 (t0) REVERT: A 571 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8337 (t70) REVERT: A 773 GLU cc_start: 0.8316 (tt0) cc_final: 0.7862 (tt0) REVERT: A 820 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: A 907 ASN cc_start: 0.9360 (OUTLIER) cc_final: 0.9047 (t0) REVERT: A 984 LEU cc_start: 0.7550 (tp) cc_final: 0.6963 (tp) REVERT: A 985 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6416 (p0) REVERT: B 64 TRP cc_start: 0.5990 (t60) cc_final: 0.5637 (t60) REVERT: B 167 THR cc_start: 0.6240 (OUTLIER) cc_final: 0.6015 (t) REVERT: B 271 GLN cc_start: 0.7360 (mt0) cc_final: 0.7147 (mt0) REVERT: B 309 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 336 CYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3936 (t) REVERT: B 492 LEU cc_start: 0.0063 (OUTLIER) cc_final: -0.0295 (mt) REVERT: B 873 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: B 1036 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: C 216 PHE cc_start: 0.4400 (OUTLIER) cc_final: 0.2658 (t80) REVERT: C 265 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: C 359 SER cc_start: -0.1808 (OUTLIER) cc_final: -0.2156 (p) REVERT: C 396 TYR cc_start: 0.1999 (OUTLIER) cc_final: 0.1052 (m-10) REVERT: C 625 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7068 (t-90) REVERT: C 759 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7440 (t80) REVERT: C 904 TYR cc_start: 0.8189 (m-10) cc_final: 0.7771 (m-10) REVERT: C 1001 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8832 (tt) REVERT: C 1125 ASN cc_start: 0.8206 (t0) cc_final: 0.7375 (t0) REVERT: D 323 MET cc_start: 0.2746 (tpp) cc_final: 0.2333 (mmm) REVERT: D 435 GLU cc_start: 0.0490 (OUTLIER) cc_final: -0.0385 (pt0) REVERT: D 579 MET cc_start: 0.0667 (mtm) cc_final: -0.1064 (ptp) outliers start: 191 outliers final: 113 residues processed: 373 average time/residue: 0.1494 time to fit residues: 96.2320 Evaluate side-chains 313 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 177 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 PHE 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 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 511 VAL 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 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 878 LEU Chi-restraints excluded: chain A residue 907 ASN 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 1116 THR 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 47 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 164 ASN Chi-restraints excluded: chain B residue 167 THR 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 309 GLU 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 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 649 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR 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 1106 GLN Chi-restraints excluded: chain B residue 1119 ASN 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 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 371 PHE 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 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 588 THR 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 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 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 107 VAL 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 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: 9.9990 chunk 192 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 326 optimal weight: 0.4980 chunk 155 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 914 ASN A 978 ASN B 30 ASN B 901 GLN C 99 ASN C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 429 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.214165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124482 restraints weight = 47336.851| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.44 r_work: 0.3220 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.186 31486 Z= 0.275 Angle : 0.836 15.456 42975 Z= 0.414 Chirality : 0.054 0.564 4963 Planarity : 0.005 0.060 5424 Dihedral : 8.421 84.041 5469 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.95 % Favored : 92.00 % Rotamer: Outliers : 6.26 % Allowed : 21.08 % Favored : 72.67 % 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 aren not related in a simple way. whole: -1.62 (0.13), residues: 3736 helix: 0.86 (0.16), residues: 1081 sheet: -1.36 (0.20), residues: 662 loop : -2.16 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.022 0.002 TYR A 837 PHE 0.031 0.002 PHE C 55 TRP 0.025 0.002 TRP A 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00674 (31374) covalent geometry : angle 0.77716 (42687) SS BOND : bond 0.00508 ( 42) SS BOND : angle 2.35035 ( 84) hydrogen bonds : bond 0.07145 ( 1097) hydrogen bonds : angle 5.30294 ( 3093) metal coordination : bond 0.00114 ( 2) link_BETA1-4 : bond 0.00460 ( 17) link_BETA1-4 : angle 2.20286 ( 51) link_NAG-ASN : bond 0.00882 ( 51) link_NAG-ASN : angle 4.82500 ( 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 418 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 212 time to evaluate : 1.066 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 104 TRP cc_start: 0.3783 (OUTLIER) cc_final: 0.3341 (m-10) REVERT: A 127 PHE cc_start: 0.6975 (t80) cc_final: 0.6394 (m-80) REVERT: A 176 LEU cc_start: 0.5746 (pt) cc_final: 0.5276 (mp) REVERT: A 264 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.5972 (p0) REVERT: A 287 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: A 314 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 472 ILE cc_start: -0.1190 (OUTLIER) cc_final: -0.1428 (tp) REVERT: A 534 VAL cc_start: 0.7158 (t) cc_final: 0.6937 (m) REVERT: A 571 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8012 (t70) REVERT: A 574 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7307 (t70) REVERT: A 773 GLU cc_start: 0.8448 (tt0) cc_final: 0.7971 (tt0) REVERT: A 820 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: B 167 THR cc_start: 0.6264 (OUTLIER) cc_final: 0.6048 (t) REVERT: B 309 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: B 492 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.0812 (mt) REVERT: B 549 THR cc_start: 0.7913 (p) cc_final: 0.7563 (p) REVERT: B 873 TYR cc_start: 0.9079 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: B 1142 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 190 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6549 (mtt-85) REVERT: C 216 PHE cc_start: 0.4679 (OUTLIER) cc_final: 0.3005 (t80) REVERT: C 265 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: C 276 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8487 (tp) REVERT: C 359 SER cc_start: -0.2032 (OUTLIER) cc_final: -0.2307 (p) REVERT: C 396 TYR cc_start: 0.2256 (OUTLIER) cc_final: 0.1192 (m-10) REVERT: C 625 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7185 (t-90) REVERT: C 759 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7618 (t80) REVERT: C 856 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8381 (p0) REVERT: C 934 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 977 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 1001 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 1038 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8495 (mptt) REVERT: C 1039 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8703 (mtp180) REVERT: D 123 MET cc_start: -0.0781 (ppp) cc_final: -0.1418 (tmm) REVERT: D 323 MET cc_start: 0.2433 (tpp) cc_final: 0.1976 (mmm) REVERT: D 435 GLU cc_start: 0.0451 (OUTLIER) cc_final: -0.0544 (pt0) REVERT: D 585 LEU cc_start: 0.1831 (mt) cc_final: 0.1457 (pp) outliers start: 206 outliers final: 119 residues processed: 389 average time/residue: 0.1460 time to fit residues: 97.7161 Evaluate side-chains 329 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 185 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 31 SER Chi-restraints excluded: chain A residue 40 ASP 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 270 LEU 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 505 HIS Chi-restraints excluded: chain A residue 523 THR 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 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 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 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 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 1116 THR 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 33 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 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 285 ILE Chi-restraints excluded: chain B residue 309 GLU 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 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 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 994 ASP 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 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 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 200 TYR 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 276 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 335 LEU Chi-restraints excluded: chain C residue 359 SER 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 586 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 637 SER Chi-restraints excluded: chain C residue 649 CYS 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 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 1039 ARG 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 1119 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 295 ASP 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: 30.0000 chunk 256 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 349 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 334 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 290 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS B 30 ASN B 544 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 101 GLN D 221 GLN D 374 HIS D 378 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.217088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131302 restraints weight = 47245.660| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.48 r_work: 0.3261 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.600 31486 Z= 0.200 Angle : 0.718 15.166 42975 Z= 0.349 Chirality : 0.049 0.566 4963 Planarity : 0.005 0.050 5424 Dihedral : 7.743 76.022 5466 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.95 % Allowed : 22.41 % Favored : 72.64 % 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 aren not related in a simple way. whole: -1.40 (0.13), residues: 3736 helix: 1.07 (0.16), residues: 1079 sheet: -1.30 (0.19), residues: 684 loop : -2.01 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.021 0.001 TYR A 396 PHE 0.017 0.001 PHE C1121 TRP 0.014 0.001 TRP A 64 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00364 (31374) covalent geometry : angle 0.65859 (42687) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.74072 ( 84) hydrogen bonds : bond 0.05636 ( 1097) hydrogen bonds : angle 5.03855 ( 3093) metal coordination : bond 0.47042 ( 2) link_BETA1-4 : bond 0.00387 ( 17) link_BETA1-4 : angle 2.20453 ( 51) link_NAG-ASN : bond 0.00737 ( 51) link_NAG-ASN : angle 4.51698 ( 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 371 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 208 time to evaluate : 0.770 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 31 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 127 PHE cc_start: 0.6929 (t80) cc_final: 0.6285 (m-80) REVERT: A 176 LEU cc_start: 0.5878 (pt) cc_final: 0.5441 (mp) REVERT: A 237 ARG cc_start: 0.7017 (ttt180) cc_final: 0.6769 (ttt-90) REVERT: A 264 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6067 (p0) REVERT: A 314 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: A 472 ILE cc_start: -0.0068 (OUTLIER) cc_final: -0.0333 (tp) REVERT: A 559 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 571 ASP cc_start: 0.8503 (m-30) cc_final: 0.7912 (t70) REVERT: A 773 GLU cc_start: 0.8212 (tt0) cc_final: 0.7736 (tt0) REVERT: A 820 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: B 41 LYS cc_start: 0.7358 (mmmt) cc_final: 0.7142 (mtpt) REVERT: B 167 THR cc_start: 0.6233 (OUTLIER) cc_final: 0.6020 (t) REVERT: B 492 LEU cc_start: -0.0531 (OUTLIER) cc_final: -0.0881 (mt) REVERT: B 549 THR cc_start: 0.7958 (p) cc_final: 0.7556 (p) REVERT: B 873 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: C 190 ARG cc_start: 0.7583 (mtp-110) cc_final: 0.6772 (mtt-85) REVERT: C 216 PHE cc_start: 0.4275 (OUTLIER) cc_final: 0.2739 (t80) REVERT: C 265 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: C 386 LYS cc_start: 0.3975 (OUTLIER) cc_final: 0.3748 (mtmt) REVERT: C 396 TYR cc_start: 0.2153 (OUTLIER) cc_final: 0.1119 (m-80) REVERT: C 625 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7042 (t-90) REVERT: C 759 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7229 (t80) REVERT: C 904 TYR cc_start: 0.7997 (m-10) cc_final: 0.7460 (m-10) REVERT: C 977 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7951 (mp) REVERT: C 1038 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8395 (mptt) REVERT: D 81 GLN cc_start: 0.5746 (pm20) cc_final: 0.5331 (mm-40) REVERT: D 123 MET cc_start: -0.0743 (ppp) cc_final: -0.1407 (tmm) REVERT: D 323 MET cc_start: 0.2687 (tpp) cc_final: 0.2085 (mmm) REVERT: D 435 GLU cc_start: 0.0446 (OUTLIER) cc_final: -0.0566 (pt0) REVERT: D 585 LEU cc_start: 0.1893 (mt) cc_final: 0.1449 (pp) outliers start: 163 outliers final: 103 residues processed: 353 average time/residue: 0.1442 time to fit residues: 86.7471 Evaluate side-chains 305 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 185 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER 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 194 PHE 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 436 TRP Chi-restraints excluded: chain A residue 472 ILE 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 630 THR Chi-restraints excluded: chain A residue 645 THR 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 820 ASP 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 1116 THR 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 33 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 94 SER 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 168 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE 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 544 ASN 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 693 ILE 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 976 VAL Chi-restraints excluded: chain B residue 994 ASP 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 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 200 TYR 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 335 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 386 LYS 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 553 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 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 720 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 813 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 937 SER Chi-restraints excluded: chain C residue 941 THR 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 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 1127 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 295 ASP 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 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: 0.6980 chunk 172 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 340 optimal weight: 7.9990 chunk 318 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 chunk 341 optimal weight: 40.0000 chunk 324 optimal weight: 40.0000 chunk 91 optimal weight: 1.9990 chunk 333 optimal weight: 30.0000 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 271 GLN B 914 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN D 378 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.214663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126866 restraints weight = 47306.473| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.79 r_work: 0.3233 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 31486 Z= 0.169 Angle : 0.715 14.345 42975 Z= 0.347 Chirality : 0.049 0.560 4963 Planarity : 0.005 0.055 5424 Dihedral : 7.497 73.082 5464 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.83 % Rotamer: Outliers : 4.80 % Allowed : 22.81 % Favored : 72.40 % 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 aren not related in a simple way. whole: -1.34 (0.14), residues: 3736 helix: 1.10 (0.16), residues: 1079 sheet: -1.23 (0.20), residues: 645 loop : -1.97 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1039 TYR 0.017 0.001 TYR B 265 PHE 0.019 0.002 PHE C 86 TRP 0.034 0.002 TRP A 104 HIS 0.013 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00396 (31374) covalent geometry : angle 0.65797 (42687) SS BOND : bond 0.00337 ( 42) SS BOND : angle 1.64567 ( 84) hydrogen bonds : bond 0.05652 ( 1097) hydrogen bonds : angle 4.96606 ( 3093) metal coordination : bond 0.08789 ( 2) link_BETA1-4 : bond 0.00383 ( 17) link_BETA1-4 : angle 2.13263 ( 51) link_NAG-ASN : bond 0.00696 ( 51) link_NAG-ASN : angle 4.46039 ( 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 351 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 193 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.9084 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 127 PHE cc_start: 0.7096 (t80) cc_final: 0.6550 (m-80) REVERT: A 176 LEU cc_start: 0.5882 (pt) cc_final: 0.5455 (mp) REVERT: A 237 ARG cc_start: 0.7214 (ttt180) cc_final: 0.6779 (ttt-90) REVERT: A 287 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8176 (m-30) REVERT: A 314 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: A 488 CYS cc_start: 0.5569 (OUTLIER) cc_final: 0.4581 (t) REVERT: A 559 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 571 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7863 (t70) REVERT: A 773 GLU cc_start: 0.8252 (tt0) cc_final: 0.7768 (tt0) REVERT: A 820 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8131 (m-30) REVERT: A 984 LEU cc_start: 0.7633 (tp) cc_final: 0.7386 (tp) REVERT: B 167 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.6069 (t) REVERT: B 492 LEU cc_start: -0.0448 (OUTLIER) cc_final: -0.0796 (mt) REVERT: C 190 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.6988 (mtt-85) REVERT: C 216 PHE cc_start: 0.3890 (OUTLIER) cc_final: 0.2360 (t80) REVERT: C 265 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.5446 (m-80) REVERT: C 346 ARG cc_start: 0.3441 (OUTLIER) cc_final: 0.3198 (tmt-80) REVERT: C 396 TYR cc_start: 0.2186 (OUTLIER) cc_final: 0.1152 (m-10) REVERT: C 574 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7942 (t0) REVERT: C 625 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: C 759 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 904 TYR cc_start: 0.8004 (m-10) cc_final: 0.7368 (m-10) REVERT: C 977 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7937 (mp) REVERT: C 1038 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8399 (mptt) REVERT: D 81 GLN cc_start: 0.5829 (pm20) cc_final: 0.5399 (mm-40) REVERT: D 123 MET cc_start: -0.0811 (ppp) cc_final: -0.1448 (tmm) REVERT: D 323 MET cc_start: 0.2836 (tpp) cc_final: 0.2088 (mmm) REVERT: D 435 GLU cc_start: 0.0400 (OUTLIER) cc_final: -0.0562 (pt0) REVERT: D 585 LEU cc_start: 0.2622 (mt) cc_final: 0.2154 (pp) outliers start: 158 outliers final: 114 residues processed: 333 average time/residue: 0.1421 time to fit residues: 81.1956 Evaluate side-chains 311 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 179 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER 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 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 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 505 HIS 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 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 574 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 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 794 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 1040 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1116 THR 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 33 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 LEU 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 216 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL 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 598 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 734 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 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP 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 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 278 LYS 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 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 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 645 THR Chi-restraints excluded: chain C residue 649 CYS 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 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 941 THR 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 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 1127 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 295 ASP 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 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: 6.9990 chunk 109 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 347 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.214221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129843 restraints weight = 47167.182| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.55 r_work: 0.3255 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5501 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= 0.133 Angle : 0.681 13.709 42975 Z= 0.329 Chirality : 0.048 0.562 4963 Planarity : 0.005 0.057 5424 Dihedral : 7.057 66.155 5462 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.07 % Allowed : 23.84 % Favored : 72.09 % 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 aren not related in a simple way. whole: -1.16 (0.14), residues: 3736 helix: 1.24 (0.16), residues: 1085 sheet: -1.09 (0.20), residues: 640 loop : -1.87 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.015 0.001 TYR C1067 PHE 0.023 0.001 PHE A 592 TRP 0.024 0.001 TRP A 104 HIS 0.012 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00305 (31374) covalent geometry : angle 0.62610 (42687) SS BOND : bond 0.00221 ( 42) SS BOND : angle 1.36192 ( 84) hydrogen bonds : bond 0.04916 ( 1097) hydrogen bonds : angle 4.83578 ( 3093) metal coordination : bond 0.02187 ( 2) link_BETA1-4 : bond 0.00443 ( 17) link_BETA1-4 : angle 2.09989 ( 51) link_NAG-ASN : bond 0.00681 ( 51) link_NAG-ASN : angle 4.28997 ( 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 333 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 199 time to evaluate : 0.880 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: 0.9097 (m) cc_final: 0.8828 (p) REVERT: A 127 PHE cc_start: 0.7270 (t80) cc_final: 0.6669 (m-80) REVERT: A 176 LEU cc_start: 0.5877 (pt) cc_final: 0.5449 (mp) REVERT: A 237 ARG cc_start: 0.7235 (ttt180) cc_final: 0.6630 (ttm110) REVERT: A 287 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: A 559 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 571 ASP cc_start: 0.8483 (m-30) cc_final: 0.7811 (t70) REVERT: A 773 GLU cc_start: 0.8150 (tt0) cc_final: 0.7700 (tt0) REVERT: A 816 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 820 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: A 984 LEU cc_start: 0.7653 (tp) cc_final: 0.7398 (tp) REVERT: B 492 LEU cc_start: -0.0690 (OUTLIER) cc_final: -0.0957 (mt) REVERT: B 992 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.6658 (mm-40) REVERT: C 190 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7275 (mtt-85) REVERT: C 216 PHE cc_start: 0.3879 (OUTLIER) cc_final: 0.2430 (t80) REVERT: C 265 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.5430 (m-80) REVERT: C 346 ARG cc_start: 0.3805 (OUTLIER) cc_final: 0.3457 (tmt-80) REVERT: C 396 TYR cc_start: 0.2186 (OUTLIER) cc_final: 0.1142 (m-10) REVERT: C 574 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 759 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 904 TYR cc_start: 0.8048 (m-10) cc_final: 0.7494 (m-10) REVERT: C 1125 ASN cc_start: 0.8439 (t0) cc_final: 0.7986 (t0) REVERT: D 81 GLN cc_start: 0.5888 (pm20) cc_final: 0.5341 (mm-40) REVERT: D 123 MET cc_start: -0.0601 (ppp) cc_final: -0.1587 (tmm) REVERT: D 309 LYS cc_start: 0.5367 (tppt) cc_final: 0.5009 (mmtt) REVERT: D 323 MET cc_start: 0.2483 (tpp) cc_final: 0.2172 (mmm) REVERT: D 435 GLU cc_start: 0.0419 (OUTLIER) cc_final: -0.0603 (pt0) REVERT: D 455 MET cc_start: 0.2647 (tpp) cc_final: 0.1768 (tpt) REVERT: D 585 LEU cc_start: 0.2954 (mt) cc_final: 0.2487 (pp) outliers start: 134 outliers final: 95 residues processed: 321 average time/residue: 0.1492 time to fit residues: 81.7937 Evaluate side-chains 289 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 181 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL 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 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 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR 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 962 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1116 THR 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 50 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 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 308 VAL 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 654 GLU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 720 ILE 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 992 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL 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 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 278 LYS 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 371 PHE Chi-restraints excluded: chain C residue 396 TYR 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 553 THR Chi-restraints excluded: chain C residue 574 ASP 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 645 THR 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 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 941 THR 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 1076 THR 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 373 HIS 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 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: 0.8980 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 0.0060 chunk 50 optimal weight: 0.4980 chunk 296 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 137 optimal weight: 7.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 63 ASN D 373 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.214191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131937 restraints weight = 47277.210| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.41 r_work: 0.3275 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31486 Z= 0.124 Angle : 0.676 15.546 42975 Z= 0.325 Chirality : 0.047 0.559 4963 Planarity : 0.004 0.054 5424 Dihedral : 6.849 62.456 5462 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.92 % Allowed : 23.99 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.14), residues: 3736 helix: 1.28 (0.16), residues: 1084 sheet: -1.03 (0.21), residues: 639 loop : -1.83 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.015 0.001 TYR A1067 PHE 0.023 0.001 PHE C 86 TRP 0.023 0.001 TRP A 104 HIS 0.030 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00278 (31374) covalent geometry : angle 0.62165 (42687) SS BOND : bond 0.00240 ( 42) SS BOND : angle 1.50552 ( 84) hydrogen bonds : bond 0.04815 ( 1097) hydrogen bonds : angle 4.81466 ( 3093) metal coordination : bond 0.01235 ( 2) link_BETA1-4 : bond 0.00444 ( 17) link_BETA1-4 : angle 2.09888 ( 51) link_NAG-ASN : bond 0.00656 ( 51) link_NAG-ASN : angle 4.23416 ( 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 318 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 189 time to evaluate : 0.767 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: 0.9019 (m) cc_final: 0.8799 (p) REVERT: A 127 PHE cc_start: 0.7269 (t80) cc_final: 0.6838 (t80) REVERT: A 176 LEU cc_start: 0.5973 (pt) cc_final: 0.5573 (mp) REVERT: A 287 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: A 559 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 571 ASP cc_start: 0.8461 (m-30) cc_final: 0.7784 (t70) REVERT: A 773 GLU cc_start: 0.8091 (tt0) cc_final: 0.7631 (tt0) REVERT: A 816 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 820 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: A 984 LEU cc_start: 0.7743 (tp) cc_final: 0.7377 (tp) REVERT: A 1128 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 492 LEU cc_start: -0.0670 (OUTLIER) cc_final: -0.0917 (mt) REVERT: C 190 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7284 (mtt-85) REVERT: C 216 PHE cc_start: 0.3878 (OUTLIER) cc_final: 0.2457 (t80) REVERT: C 265 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.5402 (m-80) REVERT: C 346 ARG cc_start: 0.3830 (OUTLIER) cc_final: 0.3530 (tmt-80) REVERT: C 396 TYR cc_start: 0.2132 (OUTLIER) cc_final: 0.1082 (m-10) REVERT: C 759 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7240 (t80) REVERT: C 904 TYR cc_start: 0.8037 (m-10) cc_final: 0.7469 (m-10) REVERT: C 977 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7870 (mp) REVERT: C 1125 ASN cc_start: 0.8388 (t0) cc_final: 0.7922 (t0) REVERT: C 1135 ASN cc_start: 0.7871 (t0) cc_final: 0.7657 (t0) REVERT: D 81 GLN cc_start: 0.5886 (pm20) cc_final: 0.5350 (mm-40) REVERT: D 123 MET cc_start: -0.0620 (ppp) cc_final: -0.1590 (tmm) REVERT: D 309 LYS cc_start: 0.5381 (tppt) cc_final: 0.5051 (mmtt) REVERT: D 323 MET cc_start: 0.2599 (tpp) cc_final: 0.2193 (mmm) REVERT: D 435 GLU cc_start: 0.0471 (OUTLIER) cc_final: -0.0545 (pt0) REVERT: D 455 MET cc_start: 0.2746 (tpp) cc_final: 0.2451 (tpt) REVERT: D 585 LEU cc_start: 0.2917 (mt) cc_final: 0.2536 (pp) outliers start: 129 outliers final: 98 residues processed: 305 average time/residue: 0.1473 time to fit residues: 76.8290 Evaluate side-chains 291 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 180 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 287 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 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 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE 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 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1071 GLN 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 54 LEU Chi-restraints excluded: chain B residue 90 VAL 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 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 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 598 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 720 ILE 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 994 ASP Chi-restraints excluded: chain B residue 1040 VAL 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 31 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 LEU 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 200 TYR Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 278 LYS 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 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 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 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 941 THR 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 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL 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 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: 0.6980 chunk 133 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 166 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 277 ASN D 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.213823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128244 restraints weight = 46923.895| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.04 r_work: 0.3203 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31486 Z= 0.149 Angle : 0.693 13.944 42975 Z= 0.334 Chirality : 0.048 0.549 4963 Planarity : 0.004 0.053 5424 Dihedral : 6.719 57.292 5462 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.70 % Allowed : 24.08 % Favored : 72.21 % 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 aren not related in a simple way. whole: -1.07 (0.14), residues: 3736 helix: 1.28 (0.16), residues: 1084 sheet: -0.93 (0.21), residues: 650 loop : -1.84 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.025 0.001 TYR A 396 PHE 0.024 0.001 PHE C 86 TRP 0.023 0.001 TRP A 104 HIS 0.010 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00351 (31374) covalent geometry : angle 0.63958 (42687) SS BOND : bond 0.00286 ( 42) SS BOND : angle 1.51103 ( 84) hydrogen bonds : bond 0.05169 ( 1097) hydrogen bonds : angle 4.84540 ( 3093) metal coordination : bond 0.03046 ( 2) link_BETA1-4 : bond 0.00372 ( 17) link_BETA1-4 : angle 2.04468 ( 51) link_NAG-ASN : bond 0.00633 ( 51) link_NAG-ASN : angle 4.23342 ( 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 303 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 181 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.7423 (t80) cc_final: 0.7125 (t80) REVERT: A 176 LEU cc_start: 0.6008 (pt) cc_final: 0.5622 (mp) REVERT: A 287 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: A 559 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8171 (t80) REVERT: A 571 ASP cc_start: 0.8477 (m-30) cc_final: 0.7852 (t70) REVERT: A 773 GLU cc_start: 0.8245 (tt0) cc_final: 0.7840 (tt0) REVERT: A 816 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8776 (m) REVERT: A 820 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: A 984 LEU cc_start: 0.7894 (tp) cc_final: 0.7440 (tp) REVERT: A 1128 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8355 (p) REVERT: B 492 LEU cc_start: -0.0663 (OUTLIER) cc_final: -0.0958 (mt) REVERT: C 190 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7477 (mtt-85) REVERT: C 216 PHE cc_start: 0.3995 (OUTLIER) cc_final: 0.2572 (t80) REVERT: C 265 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: C 346 ARG cc_start: 0.3850 (OUTLIER) cc_final: 0.3543 (tmt-80) REVERT: C 396 TYR cc_start: 0.2222 (OUTLIER) cc_final: 0.1164 (m-10) REVERT: C 759 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7373 (t80) REVERT: C 904 TYR cc_start: 0.8106 (m-10) cc_final: 0.7547 (m-10) REVERT: C 977 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7999 (mp) REVERT: D 81 GLN cc_start: 0.5890 (pm20) cc_final: 0.5370 (mm-40) REVERT: D 123 MET cc_start: -0.0666 (ppp) cc_final: -0.1312 (tmm) REVERT: D 198 ASP cc_start: 0.1804 (OUTLIER) cc_final: 0.1276 (m-30) REVERT: D 309 LYS cc_start: 0.5470 (tppt) cc_final: 0.5208 (mmtt) REVERT: D 323 MET cc_start: 0.2552 (tpp) cc_final: 0.2131 (mmm) REVERT: D 435 GLU cc_start: 0.0455 (OUTLIER) cc_final: -0.0533 (pt0) REVERT: D 455 MET cc_start: 0.2664 (tpp) cc_final: 0.2374 (tpt) REVERT: D 585 LEU cc_start: 0.3256 (mt) cc_final: 0.2870 (pp) outliers start: 122 outliers final: 97 residues processed: 290 average time/residue: 0.1363 time to fit residues: 68.6276 Evaluate side-chains 281 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 170 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 287 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 VAL 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 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 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE 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 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1071 GLN 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 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 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 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 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 598 ILE Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 720 ILE 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 994 ASP Chi-restraints excluded: chain B residue 1040 VAL 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 31 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 278 LYS 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 492 LEU 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 617 CYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 662 CYS 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 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 941 THR 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 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 280 SER 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 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: 1.9990 chunk 183 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 0.5980 chunk 351 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 232 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 356 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.213229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128464 restraints weight = 47071.312| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.48 r_work: 0.3273 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31486 Z= 0.124 Angle : 0.667 13.916 42975 Z= 0.320 Chirality : 0.047 0.549 4963 Planarity : 0.004 0.052 5424 Dihedral : 6.473 57.373 5462 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.49 % Allowed : 24.20 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3736 helix: 1.34 (0.16), residues: 1089 sheet: -0.85 (0.21), residues: 646 loop : -1.80 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.025 0.001 TYR B 265 PHE 0.016 0.001 PHE C1121 TRP 0.021 0.001 TRP A 104 HIS 0.015 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00281 (31374) covalent geometry : angle 0.61431 (42687) SS BOND : bond 0.00228 ( 42) SS BOND : angle 1.48617 ( 84) hydrogen bonds : bond 0.04680 ( 1097) hydrogen bonds : angle 4.73494 ( 3093) metal coordination : bond 0.02710 ( 2) link_BETA1-4 : bond 0.00433 ( 17) link_BETA1-4 : angle 2.03103 ( 51) link_NAG-ASN : bond 0.00639 ( 51) link_NAG-ASN : angle 4.11258 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8191.79 seconds wall clock time: 140 minutes 34.58 seconds (8434.58 seconds total)