Starting phenix.real_space_refine on Thu Jun 26 16:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whs_37546/06_2025/8whs_37546.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whs_37546/06_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_37546/06_2025/8whs_37546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whs_37546/06_2025/8whs_37546.map" model { file = "/net/cci-nas-00/data/ceres_data/8whs_37546/06_2025/8whs_37546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whs_37546/06_2025/8whs_37546.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.55, per 1000 atoms: 0.57 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: 7.58 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7070 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 57 sheets defined 31.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 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: 12.53 Time building geometry restraints manager: 9.01 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 1144 or resid 1301 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: 2.260 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: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 72.650 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.170 ------------------------------------------------------------------------------- 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 : 12.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP C1102 HIS 0.004 0.001 HIS A 49 PHE 0.025 0.002 PHE B 86 TYR 0.020 0.001 TYR D 237 ARG 0.013 0.001 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 51) link_NAG-ASN : angle 5.50871 ( 153) link_BETA1-4 : bond 0.00425 ( 17) link_BETA1-4 : angle 2.41990 ( 51) hydrogen bonds : bond 0.20573 ( 1097) hydrogen bonds : angle 7.70821 ( 3093) metal coordination : bond 0.00080 ( 2) SS BOND : bond 0.00318 ( 42) SS BOND : angle 1.24277 ( 84) covalent geometry : bond 0.00563 (31374) covalent geometry : angle 0.87295 (42687) *********************** 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 : 2.961 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 984 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7831 (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: 0.3264 (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: 0.0431 (t80) outliers start: 33 outliers final: 11 residues processed: 252 average time/residue: 0.4092 time to fit residues: 173.9367 Evaluate side-chains 189 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 315 optimal weight: 6.9990 chunk 283 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 628 GLN C 836 GLN D 139 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.231831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149735 restraints weight = 48905.489| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.89 r_work: 0.3464 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 31486 Z= 0.188 Angle : 0.809 17.912 42975 Z= 0.382 Chirality : 0.053 0.669 4963 Planarity : 0.005 0.059 5424 Dihedral : 12.522 102.748 5486 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.75 % Rotamer: Outliers : 4.22 % Allowed : 19.68 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3736 helix: 0.83 (0.16), residues: 1079 sheet: -1.18 (0.20), residues: 618 loop : -2.10 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 477 HIS 0.010 0.001 HIS C 519 PHE 0.024 0.002 PHE C 192 TYR 0.025 0.002 TYR C1067 ARG 0.018 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 51) link_NAG-ASN : angle 4.94457 ( 153) link_BETA1-4 : bond 0.00538 ( 17) link_BETA1-4 : angle 3.92816 ( 51) hydrogen bonds : bond 0.05967 ( 1097) hydrogen bonds : angle 5.49845 ( 3093) metal coordination : bond 0.00059 ( 2) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.28160 ( 84) covalent geometry : bond 0.00429 (31374) covalent geometry : angle 0.74123 (42687) *********************** 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 349 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 210 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.4714 (t80) cc_final: 0.3440 (m-80) REVERT: A 773 GLU cc_start: 0.8046 (tt0) cc_final: 0.7562 (tt0) REVERT: A 820 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: A 984 LEU cc_start: 0.7427 (tp) cc_final: 0.6960 (tp) REVERT: B 64 TRP cc_start: 0.5669 (t60) cc_final: 0.5233 (t60) REVERT: B 675 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: B 740 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8671 (tpp) REVERT: B 873 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: B 992 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6603 (mm-40) REVERT: B 1111 GLU cc_start: 0.8458 (tp30) cc_final: 0.8242 (tt0) REVERT: C 359 SER cc_start: -0.1571 (OUTLIER) cc_final: -0.1919 (p) REVERT: C 559 PHE cc_start: 0.3571 (OUTLIER) cc_final: 0.2910 (t80) REVERT: C 904 TYR cc_start: 0.8251 (m-10) cc_final: 0.7744 (m-10) REVERT: D 376 MET cc_start: -0.1095 (mmm) cc_final: -0.1407 (mtp) REVERT: D 435 GLU cc_start: 0.0342 (OUTLIER) cc_final: -0.0432 (pt0) REVERT: D 579 MET cc_start: 0.0986 (mtm) cc_final: -0.0891 (ptp) REVERT: D 592 PHE cc_start: 0.2063 (t80) cc_final: 0.1678 (t80) outliers start: 139 outliers final: 73 residues processed: 329 average time/residue: 0.3574 time to fit residues: 201.8415 Evaluate side-chains 251 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 170 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 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 524 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 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 630 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 261 optimal weight: 0.3980 chunk 309 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 343 optimal weight: 50.0000 chunk 181 optimal weight: 0.6980 chunk 346 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 506 GLN B 644 GLN C 239 GLN C 613 GLN C1010 GLN D 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.225459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147180 restraints weight = 47617.303| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 4.55 r_work: 0.3453 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31486 Z= 0.155 Angle : 0.717 17.865 42975 Z= 0.344 Chirality : 0.049 0.542 4963 Planarity : 0.005 0.053 5424 Dihedral : 8.528 92.805 5472 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.90 % Rotamer: Outliers : 4.19 % Allowed : 20.22 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3736 helix: 1.10 (0.16), residues: 1068 sheet: -1.08 (0.20), residues: 660 loop : -1.98 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 275 HIS 0.008 0.001 HIS A 207 PHE 0.020 0.002 PHE C 515 TYR 0.016 0.001 TYR B1067 ARG 0.014 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 51) link_NAG-ASN : angle 4.59725 ( 153) link_BETA1-4 : bond 0.00546 ( 17) link_BETA1-4 : angle 2.99389 ( 51) hydrogen bonds : bond 0.05676 ( 1097) hydrogen bonds : angle 5.15650 ( 3093) metal coordination : bond 0.00066 ( 2) SS BOND : bond 0.00279 ( 42) SS BOND : angle 1.14267 ( 84) covalent geometry : bond 0.00344 (31374) covalent geometry : angle 0.65415 (42687) *********************** 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 364 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 226 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8876 (m) cc_final: 0.8428 (p) REVERT: A 127 PHE cc_start: 0.5275 (t80) cc_final: 0.4181 (m-80) REVERT: A 568 ASP cc_start: 0.6589 (t0) cc_final: 0.6370 (t0) REVERT: A 571 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8068 (t70) REVERT: A 630 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 773 GLU cc_start: 0.8005 (tt0) cc_final: 0.7561 (tt0) REVERT: A 820 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: A 984 LEU cc_start: 0.7803 (tp) cc_final: 0.7443 (tp) REVERT: B 64 TRP cc_start: 0.5828 (t60) cc_final: 0.5474 (t60) REVERT: B 492 LEU cc_start: 0.0211 (OUTLIER) cc_final: -0.0162 (mt) REVERT: B 740 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8778 (tpp) REVERT: B 1036 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8787 (pt0) REVERT: C 189 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5609 (mm) REVERT: C 216 PHE cc_start: 0.4177 (OUTLIER) cc_final: 0.2434 (t80) REVERT: C 265 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5736 (m-80) REVERT: C 565 PHE cc_start: 0.5545 (m-80) cc_final: 0.5053 (m-10) REVERT: C 624 ILE cc_start: 0.8124 (mm) cc_final: 0.7835 (mm) REVERT: C 646 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.8289 (mmm-85) REVERT: C 759 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7011 (t80) REVERT: C 868 GLU cc_start: 0.8287 (tt0) cc_final: 0.8011 (mt-10) REVERT: C 904 TYR cc_start: 0.8147 (m-10) cc_final: 0.7724 (m-10) REVERT: C 1001 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8726 (tt) REVERT: D 94 LYS cc_start: 0.2630 (OUTLIER) cc_final: 0.2191 (ptpt) REVERT: D 323 MET cc_start: 0.2793 (tpp) cc_final: 0.2506 (mmm) REVERT: D 376 MET cc_start: -0.0867 (mmm) cc_final: -0.1642 (mtp) REVERT: D 435 GLU cc_start: 0.0452 (OUTLIER) cc_final: -0.0373 (pt0) REVERT: D 579 MET cc_start: 0.0798 (mtm) cc_final: -0.1005 (ptp) outliers start: 138 outliers final: 67 residues processed: 343 average time/residue: 0.3614 time to fit residues: 212.9681 Evaluate side-chains 264 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 189 LEU 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 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 649 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 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 177 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1115 ILE 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 47 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 524 VAL 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 642 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 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 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 557 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 302 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 324 optimal weight: 40.0000 chunk 26 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 341 optimal weight: 0.2980 chunk 270 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 644 GLN B 914 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 98 GLN D 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.224258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145376 restraints weight = 47189.201| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.87 r_work: 0.3410 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31486 Z= 0.134 Angle : 0.680 17.018 42975 Z= 0.324 Chirality : 0.048 0.569 4963 Planarity : 0.004 0.053 5424 Dihedral : 7.870 83.592 5472 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.56 % Favored : 93.42 % Rotamer: Outliers : 4.01 % Allowed : 21.08 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3736 helix: 1.22 (0.16), residues: 1078 sheet: -0.99 (0.20), residues: 671 loop : -1.93 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 165 HIS 0.005 0.001 HIS A 207 PHE 0.033 0.001 PHE A 86 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG D 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 51) link_NAG-ASN : angle 4.54634 ( 153) link_BETA1-4 : bond 0.00371 ( 17) link_BETA1-4 : angle 2.74515 ( 51) hydrogen bonds : bond 0.04967 ( 1097) hydrogen bonds : angle 4.94778 ( 3093) metal coordination : bond 0.00060 ( 2) SS BOND : bond 0.00258 ( 42) SS BOND : angle 0.96659 ( 84) covalent geometry : bond 0.00302 (31374) covalent geometry : angle 0.61747 (42687) *********************** 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 336 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 204 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 127 PHE cc_start: 0.5324 (t80) cc_final: 0.4245 (m-80) REVERT: A 264 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5244 (p0) REVERT: A 314 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: A 546 LEU cc_start: 0.7951 (mm) cc_final: 0.7743 (pp) REVERT: A 568 ASP cc_start: 0.6627 (t0) cc_final: 0.6378 (t0) REVERT: A 571 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8198 (t70) REVERT: A 773 GLU cc_start: 0.7978 (tt0) cc_final: 0.7568 (tt0) REVERT: A 820 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: A 984 LEU cc_start: 0.7799 (tp) cc_final: 0.7326 (tp) REVERT: A 985 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6400 (p0) REVERT: B 64 TRP cc_start: 0.5828 (t60) cc_final: 0.5496 (t60) REVERT: B 167 THR cc_start: 0.6203 (OUTLIER) cc_final: 0.5985 (t) REVERT: B 280 ASN cc_start: 0.8418 (t0) cc_final: 0.7254 (t0) REVERT: B 281 GLU cc_start: 0.9044 (pt0) cc_final: 0.8813 (pm20) REVERT: B 492 LEU cc_start: 0.0091 (OUTLIER) cc_final: -0.0266 (mt) REVERT: B 740 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8866 (tpp) REVERT: B 873 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: C 216 PHE cc_start: 0.4225 (OUTLIER) cc_final: 0.2572 (t80) REVERT: C 265 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: C 396 TYR cc_start: 0.1966 (OUTLIER) cc_final: 0.1025 (m-10) REVERT: C 559 PHE cc_start: 0.3941 (OUTLIER) cc_final: 0.3670 (t80) REVERT: C 565 PHE cc_start: 0.5440 (m-80) cc_final: 0.4818 (m-10) REVERT: C 591 SER cc_start: 0.8265 (m) cc_final: 0.7971 (m) REVERT: C 625 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.6959 (t-90) REVERT: C 646 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8298 (mmm-85) REVERT: C 868 GLU cc_start: 0.8286 (tt0) cc_final: 0.8040 (mt-10) REVERT: C 904 TYR cc_start: 0.8154 (m-10) cc_final: 0.7758 (m-10) REVERT: C 1125 ASN cc_start: 0.7802 (t0) cc_final: 0.6965 (t0) REVERT: D 229 THR cc_start: 0.1022 (p) cc_final: 0.0584 (p) REVERT: D 270 MET cc_start: -0.3094 (tpp) cc_final: -0.3574 (tpp) REVERT: D 275 TRP cc_start: 0.0525 (m-10) cc_final: -0.0702 (m-90) REVERT: D 323 MET cc_start: 0.2875 (tpp) cc_final: 0.2446 (mmm) REVERT: D 376 MET cc_start: -0.1013 (mmm) cc_final: -0.1545 (mtp) REVERT: D 435 GLU cc_start: 0.0487 (OUTLIER) cc_final: -0.0374 (pt0) REVERT: D 579 MET cc_start: 0.0603 (mtm) cc_final: -0.1163 (ptp) outliers start: 132 outliers final: 87 residues processed: 314 average time/residue: 0.3638 time to fit residues: 196.4658 Evaluate side-chains 287 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 184 time to evaluate : 3.181 ------------------------------------------------------------------------------- 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 42 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR 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 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 592 PHE 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 794 ILE 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 985 ASP Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 740 MET 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 994 ASP Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 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 368 LEU Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 THR 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 859 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1077 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 23 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 123 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 339 optimal weight: 40.0000 chunk 134 optimal weight: 2.9990 chunk 311 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 914 ASN B1005 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.224334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144282 restraints weight = 48140.831| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 5.44 r_work: 0.3401 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 31486 Z= 0.125 Angle : 0.658 16.369 42975 Z= 0.315 Chirality : 0.048 0.551 4963 Planarity : 0.004 0.054 5424 Dihedral : 7.402 78.714 5469 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.43 % Allowed : 20.89 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3736 helix: 1.33 (0.16), residues: 1078 sheet: -0.91 (0.20), residues: 658 loop : -1.86 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 271 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.001 PHE B 643 TYR 0.015 0.001 TYR C1067 ARG 0.007 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 51) link_NAG-ASN : angle 4.45175 ( 153) link_BETA1-4 : bond 0.00444 ( 17) link_BETA1-4 : angle 2.35511 ( 51) hydrogen bonds : bond 0.04802 ( 1097) hydrogen bonds : angle 4.85561 ( 3093) metal coordination : bond 0.00031 ( 2) SS BOND : bond 0.00265 ( 42) SS BOND : angle 1.36838 ( 84) covalent geometry : bond 0.00276 (31374) covalent geometry : angle 0.59499 (42687) *********************** 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 356 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 210 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 104 TRP cc_start: 0.4134 (OUTLIER) cc_final: 0.3507 (m-10) REVERT: A 127 PHE cc_start: 0.5701 (t80) cc_final: 0.5144 (m-80) REVERT: A 176 LEU cc_start: 0.4731 (pt) cc_final: 0.3911 (tt) REVERT: A 237 ARG cc_start: 0.4512 (ttt180) cc_final: 0.3450 (ttt-90) REVERT: A 314 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: A 472 ILE cc_start: -0.0502 (OUTLIER) cc_final: -0.0745 (tp) REVERT: A 546 LEU cc_start: 0.7853 (mm) cc_final: 0.7587 (pp) REVERT: A 568 ASP cc_start: 0.6544 (t0) cc_final: 0.6268 (t0) REVERT: A 571 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7934 (t70) REVERT: A 773 GLU cc_start: 0.8017 (tt0) cc_final: 0.7551 (tt0) REVERT: B 64 TRP cc_start: 0.6011 (t60) cc_final: 0.5481 (t60) REVERT: B 167 THR cc_start: 0.6212 (OUTLIER) cc_final: 0.5993 (t) REVERT: B 280 ASN cc_start: 0.8362 (t0) cc_final: 0.8042 (t0) REVERT: B 281 GLU cc_start: 0.9058 (pt0) cc_final: 0.8797 (pp20) REVERT: B 492 LEU cc_start: -0.0160 (OUTLIER) cc_final: -0.0505 (mt) REVERT: B 740 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8863 (tpp) REVERT: B 873 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: B 1036 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8673 (tt0) REVERT: C 216 PHE cc_start: 0.4409 (OUTLIER) cc_final: 0.2735 (t80) REVERT: C 265 TYR cc_start: 0.6643 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: C 359 SER cc_start: -0.1869 (OUTLIER) cc_final: -0.2303 (p) REVERT: C 396 TYR cc_start: 0.1921 (OUTLIER) cc_final: 0.0853 (m-10) REVERT: C 565 PHE cc_start: 0.5519 (m-80) cc_final: 0.5078 (m-10) REVERT: C 591 SER cc_start: 0.8275 (m) cc_final: 0.8005 (m) REVERT: C 646 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8253 (mmm-85) REVERT: C 759 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 868 GLU cc_start: 0.8357 (tt0) cc_final: 0.8140 (mp0) REVERT: C 904 TYR cc_start: 0.8151 (m-10) cc_final: 0.7802 (m-10) REVERT: C 1125 ASN cc_start: 0.8093 (t0) cc_final: 0.7413 (t0) REVERT: D 81 GLN cc_start: 0.5870 (pm20) cc_final: 0.5624 (pt0) REVERT: D 275 TRP cc_start: 0.0286 (m-10) cc_final: -0.1183 (m-90) REVERT: D 309 LYS cc_start: 0.5298 (tppt) cc_final: 0.4973 (mmtt) REVERT: D 323 MET cc_start: 0.2702 (tpp) cc_final: 0.2215 (mmm) REVERT: D 376 MET cc_start: -0.0958 (mmm) cc_final: -0.1515 (mtp) REVERT: D 435 GLU cc_start: 0.0419 (OUTLIER) cc_final: -0.0529 (pt0) REVERT: D 579 MET cc_start: 0.0474 (mtm) cc_final: -0.1026 (ptp) outliers start: 146 outliers final: 91 residues processed: 333 average time/residue: 0.3641 time to fit residues: 208.8110 Evaluate side-chains 298 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 191 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 314 GLN 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 472 ILE 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 539 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 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 317 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1036 GLN 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 45 SER Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 223 LEU 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 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL 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 949 GLN Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL 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 C residue 1128 VAL 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 557 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 72 optimal weight: 4.9990 chunk 324 optimal weight: 40.0000 chunk 364 optimal weight: 40.0000 chunk 133 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 327 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 A1005 GLN B 121 ASN B 914 ASN C 239 GLN C 613 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.215789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129131 restraints weight = 47441.371| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.52 r_work: 0.3244 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 31486 Z= 0.240 Angle : 0.782 14.713 42975 Z= 0.383 Chirality : 0.051 0.564 4963 Planarity : 0.005 0.054 5424 Dihedral : 7.703 76.447 5468 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.62 % Allowed : 20.35 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3736 helix: 1.05 (0.16), residues: 1082 sheet: -1.06 (0.20), residues: 630 loop : -2.00 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 886 HIS 0.010 0.001 HIS A 207 PHE 0.030 0.002 PHE B 643 TYR 0.018 0.002 TYR A1067 ARG 0.015 0.001 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 51) link_NAG-ASN : angle 4.59221 ( 153) link_BETA1-4 : bond 0.00512 ( 17) link_BETA1-4 : angle 2.32441 ( 51) hydrogen bonds : bond 0.06781 ( 1097) hydrogen bonds : angle 5.13742 ( 3093) metal coordination : bond 0.00090 ( 2) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.92688 ( 84) covalent geometry : bond 0.00581 (31374) covalent geometry : angle 0.72598 (42687) *********************** 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 392 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 207 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.9089 (m) cc_final: 0.8740 (p) REVERT: A 104 TRP cc_start: 0.3771 (OUTLIER) cc_final: 0.3174 (m-10) REVERT: A 127 PHE cc_start: 0.6479 (t80) cc_final: 0.5847 (m-80) REVERT: A 176 LEU cc_start: 0.5759 (pt) cc_final: 0.5276 (mp) REVERT: A 264 ASP cc_start: 0.6272 (OUTLIER) cc_final: 0.5842 (p0) REVERT: A 314 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 472 ILE cc_start: 0.0917 (OUTLIER) cc_final: 0.0626 (tp) REVERT: A 571 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8081 (t70) REVERT: A 773 GLU cc_start: 0.8389 (tt0) cc_final: 0.7944 (tt0) REVERT: B 64 TRP cc_start: 0.6426 (t60) cc_final: 0.6203 (t60) REVERT: B 167 THR cc_start: 0.6292 (OUTLIER) cc_final: 0.6075 (t) REVERT: B 271 GLN cc_start: 0.7809 (mt0) cc_final: 0.7597 (mt0) REVERT: B 280 ASN cc_start: 0.8534 (t0) cc_final: 0.8331 (t0) REVERT: B 309 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: B 492 LEU cc_start: 0.0065 (OUTLIER) cc_final: -0.0261 (mt) REVERT: B 549 THR cc_start: 0.7901 (p) cc_final: 0.7592 (p) REVERT: B 873 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: B 1036 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8885 (tt0) REVERT: C 190 ARG cc_start: 0.7974 (ptm160) cc_final: 0.6324 (mtt-85) REVERT: C 216 PHE cc_start: 0.4657 (OUTLIER) cc_final: 0.3051 (t80) REVERT: C 265 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: C 277 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 346 ARG cc_start: 0.3405 (OUTLIER) cc_final: 0.3195 (tmt-80) REVERT: C 359 SER cc_start: -0.1761 (OUTLIER) cc_final: -0.2061 (p) REVERT: C 396 TYR cc_start: 0.2004 (OUTLIER) cc_final: 0.1154 (m-10) REVERT: C 591 SER cc_start: 0.8591 (m) cc_final: 0.8373 (m) REVERT: C 625 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7259 (t-90) REVERT: C 759 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7344 (t80) REVERT: C 904 TYR cc_start: 0.8224 (m-10) cc_final: 0.7512 (m-10) REVERT: C 977 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 1001 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8856 (tt) REVERT: D 123 MET cc_start: -0.1310 (ppp) cc_final: -0.1953 (tmm) REVERT: D 275 TRP cc_start: 0.0303 (m-10) cc_final: -0.0672 (m-10) REVERT: D 309 LYS cc_start: 0.5177 (tppt) cc_final: 0.4899 (mmtt) REVERT: D 323 MET cc_start: 0.3003 (tpp) cc_final: 0.2289 (mmm) REVERT: D 376 MET cc_start: -0.1068 (mmm) cc_final: -0.1541 (mtp) REVERT: D 435 GLU cc_start: 0.0405 (OUTLIER) cc_final: -0.0363 (pt0) REVERT: D 581 VAL cc_start: 0.1800 (m) cc_final: 0.1455 (m) REVERT: D 592 PHE cc_start: 0.1998 (t80) cc_final: 0.1555 (t80) outliers start: 185 outliers final: 116 residues processed: 366 average time/residue: 0.3835 time to fit residues: 240.9800 Evaluate side-chains 315 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 178 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL 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 265 TYR Chi-restraints excluded: chain A residue 276 LEU 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 495 TYR Chi-restraints excluded: chain A residue 511 VAL 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 640 SER Chi-restraints excluded: chain A residue 645 THR 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 794 ILE 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 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 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 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 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 778 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 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 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 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 346 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 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 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 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 C residue 1128 VAL 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 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 Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 40 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 0.0980 chunk 369 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 293 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 978 ASN B 121 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.217834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133712 restraints weight = 47705.891| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.79 r_work: 0.3281 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.550 31486 Z= 0.169 Angle : 0.686 15.013 42975 Z= 0.330 Chirality : 0.048 0.553 4963 Planarity : 0.005 0.054 5424 Dihedral : 7.141 68.859 5465 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.22 % Allowed : 22.05 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.14), residues: 3736 helix: 1.21 (0.16), residues: 1086 sheet: -0.90 (0.20), residues: 641 loop : -1.90 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 633 HIS 0.014 0.001 HIS D 374 PHE 0.034 0.001 PHE B 329 TYR 0.016 0.001 TYR C1067 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 51) link_NAG-ASN : angle 4.41897 ( 153) link_BETA1-4 : bond 0.00424 ( 17) link_BETA1-4 : angle 2.11374 ( 51) hydrogen bonds : bond 0.05126 ( 1097) hydrogen bonds : angle 4.90280 ( 3093) metal coordination : bond 0.38900 ( 2) SS BOND : bond 0.00265 ( 42) SS BOND : angle 1.44890 ( 84) covalent geometry : bond 0.00303 (31374) covalent geometry : angle 0.62755 (42687) *********************** 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 347 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 208 time to evaluate : 3.299 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: 0.9045 (m) cc_final: 0.8780 (p) REVERT: A 90 VAL cc_start: 0.7810 (p) cc_final: 0.7604 (p) REVERT: A 127 PHE cc_start: 0.6882 (t80) cc_final: 0.6308 (m-80) REVERT: A 176 LEU cc_start: 0.5562 (pt) cc_final: 0.5135 (mp) REVERT: A 264 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5694 (p0) REVERT: A 314 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: A 472 ILE cc_start: -0.0522 (OUTLIER) cc_final: -0.0759 (tp) REVERT: A 571 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7964 (t70) REVERT: A 773 GLU cc_start: 0.8105 (tt0) cc_final: 0.7704 (tt0) REVERT: A 1142 GLN cc_start: 0.6065 (tm-30) cc_final: 0.5800 (tt0) REVERT: B 167 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.6084 (t) REVERT: B 271 GLN cc_start: 0.7791 (mt0) cc_final: 0.7473 (mt0) REVERT: B 280 ASN cc_start: 0.8429 (t0) cc_final: 0.8155 (t0) REVERT: B 492 LEU cc_start: -0.0517 (OUTLIER) cc_final: -0.0868 (mt) REVERT: B 549 THR cc_start: 0.7776 (p) cc_final: 0.7392 (p) REVERT: B 873 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8906 (m-80) REVERT: B 1076 THR cc_start: 0.7249 (OUTLIER) cc_final: 0.6969 (m) REVERT: C 190 ARG cc_start: 0.7669 (ptm160) cc_final: 0.6374 (mtt-85) REVERT: C 216 PHE cc_start: 0.4552 (OUTLIER) cc_final: 0.2994 (t80) REVERT: C 265 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: C 277 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 346 ARG cc_start: 0.3603 (OUTLIER) cc_final: 0.3350 (tmt-80) REVERT: C 359 SER cc_start: -0.2209 (OUTLIER) cc_final: -0.2443 (p) REVERT: C 396 TYR cc_start: 0.2112 (OUTLIER) cc_final: 0.1058 (m-10) REVERT: C 591 SER cc_start: 0.8519 (m) cc_final: 0.8290 (m) REVERT: C 759 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 904 TYR cc_start: 0.8065 (m-10) cc_final: 0.7509 (m-10) REVERT: C 977 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7980 (mp) REVERT: D 123 MET cc_start: -0.0768 (ppp) cc_final: -0.1376 (tmm) REVERT: D 275 TRP cc_start: -0.0111 (m-10) cc_final: -0.1182 (m-10) REVERT: D 309 LYS cc_start: 0.5399 (tppt) cc_final: 0.5071 (mmtt) REVERT: D 323 MET cc_start: 0.2649 (tpp) cc_final: 0.2429 (mmp) REVERT: D 333 LEU cc_start: 0.3870 (mt) cc_final: 0.3512 (pp) REVERT: D 376 MET cc_start: -0.1330 (mmm) cc_final: -0.1588 (mtp) REVERT: D 435 GLU cc_start: 0.0402 (OUTLIER) cc_final: -0.0594 (pt0) REVERT: D 585 LEU cc_start: 0.1995 (mt) cc_final: 0.1456 (pp) REVERT: D 592 PHE cc_start: 0.2032 (t80) cc_final: 0.1382 (t80) outliers start: 139 outliers final: 95 residues processed: 332 average time/residue: 0.3598 time to fit residues: 206.2112 Evaluate side-chains 303 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 191 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR 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 314 GLN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 ILE 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 523 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU 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 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 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 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 616 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 752 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 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 1076 THR 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 47 VAL 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 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU 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 346 ARG 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 386 LYS 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 574 ASP Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 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 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 290 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 284 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 580 GLN C 644 GLN C1010 GLN D 63 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.219176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133312 restraints weight = 47757.793| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.79 r_work: 0.3299 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31486 Z= 0.126 Angle : 0.668 14.468 42975 Z= 0.320 Chirality : 0.047 0.547 4963 Planarity : 0.004 0.056 5424 Dihedral : 6.805 65.324 5465 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.98 % Allowed : 22.65 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3736 helix: 1.34 (0.16), residues: 1081 sheet: -0.88 (0.21), residues: 643 loop : -1.84 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.018 0.001 HIS D 378 PHE 0.026 0.001 PHE B 329 TYR 0.016 0.001 TYR C 660 ARG 0.010 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 51) link_NAG-ASN : angle 4.28154 ( 153) link_BETA1-4 : bond 0.00422 ( 17) link_BETA1-4 : angle 2.10843 ( 51) hydrogen bonds : bond 0.04750 ( 1097) hydrogen bonds : angle 4.77432 ( 3093) metal coordination : bond 0.03689 ( 2) SS BOND : bond 0.00249 ( 42) SS BOND : angle 1.34239 ( 84) covalent geometry : bond 0.00280 (31374) covalent geometry : angle 0.61198 (42687) *********************** 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 339 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 208 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8958 (m) cc_final: 0.8749 (p) REVERT: A 127 PHE cc_start: 0.6978 (t80) cc_final: 0.6360 (m-80) REVERT: A 176 LEU cc_start: 0.5802 (pt) cc_final: 0.5410 (mp) REVERT: A 472 ILE cc_start: -0.0532 (OUTLIER) cc_final: -0.0746 (tp) REVERT: A 571 ASP cc_start: 0.8534 (m-30) cc_final: 0.7906 (t70) REVERT: A 574 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6888 (p0) REVERT: A 773 GLU cc_start: 0.8049 (tt0) cc_final: 0.7657 (tt0) REVERT: A 816 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8711 (m) REVERT: A 834 ILE cc_start: 0.3434 (OUTLIER) cc_final: 0.2881 (tp) REVERT: A 1128 VAL cc_start: 0.8390 (m) cc_final: 0.8165 (p) REVERT: B 167 THR cc_start: 0.6281 (OUTLIER) cc_final: 0.6062 (t) REVERT: B 271 GLN cc_start: 0.7728 (mt0) cc_final: 0.7462 (mt0) REVERT: B 280 ASN cc_start: 0.8436 (t0) cc_final: 0.8188 (t0) REVERT: B 492 LEU cc_start: -0.0624 (OUTLIER) cc_final: -0.0931 (mt) REVERT: B 549 THR cc_start: 0.7769 (p) cc_final: 0.7337 (p) REVERT: B 1076 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6815 (m) REVERT: C 190 ARG cc_start: 0.7781 (ptm160) cc_final: 0.6584 (mtt-85) REVERT: C 216 PHE cc_start: 0.4170 (OUTLIER) cc_final: 0.2656 (t80) REVERT: C 265 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5501 (m-80) REVERT: C 277 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 346 ARG cc_start: 0.3775 (OUTLIER) cc_final: 0.3448 (tmt-80) REVERT: C 359 SER cc_start: -0.2417 (OUTLIER) cc_final: -0.2636 (p) REVERT: C 396 TYR cc_start: 0.2083 (OUTLIER) cc_final: 0.1007 (m-10) REVERT: C 591 SER cc_start: 0.8404 (m) cc_final: 0.8145 (m) REVERT: C 625 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: C 759 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7225 (t80) REVERT: C 904 TYR cc_start: 0.8020 (m-10) cc_final: 0.7485 (m-10) REVERT: C 977 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7907 (mp) REVERT: D 123 MET cc_start: -0.0723 (ppp) cc_final: -0.1348 (tmm) REVERT: D 152 MET cc_start: 0.0923 (tmm) cc_final: 0.0580 (tmm) REVERT: D 270 MET cc_start: -0.3141 (tpp) cc_final: -0.3494 (tpt) REVERT: D 275 TRP cc_start: -0.0377 (m-10) cc_final: -0.1310 (m-10) REVERT: D 309 LYS cc_start: 0.5442 (tppt) cc_final: 0.5095 (mmtt) REVERT: D 323 MET cc_start: 0.2535 (tpp) cc_final: 0.1977 (mmm) REVERT: D 333 LEU cc_start: 0.3837 (mt) cc_final: 0.3504 (pp) REVERT: D 435 GLU cc_start: 0.0411 (OUTLIER) cc_final: -0.0587 (pt0) REVERT: D 455 MET cc_start: 0.2672 (tpp) cc_final: 0.2342 (tpt) REVERT: D 585 LEU cc_start: 0.2446 (mt) cc_final: 0.1915 (pp) outliers start: 131 outliers final: 94 residues processed: 324 average time/residue: 0.3803 time to fit residues: 211.4255 Evaluate side-chains 301 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 190 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 ILE 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 560 LEU Chi-restraints excluded: chain A residue 574 ASP 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 816 SER Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1040 VAL 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 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 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 242 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 784 GLN 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 1076 THR 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 45 SER Chi-restraints excluded: chain C residue 47 VAL 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 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU 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 346 ARG 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 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 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 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 878 LEU 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 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 100 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 370 optimal weight: 20.0000 chunk 304 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 311 optimal weight: 0.0070 chunk 237 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN C1010 GLN C1106 GLN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.218377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134938 restraints weight = 47573.314| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.58 r_work: 0.3329 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31486 Z= 0.117 Angle : 0.661 14.196 42975 Z= 0.317 Chirality : 0.047 0.552 4963 Planarity : 0.004 0.055 5424 Dihedral : 6.471 59.904 5463 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.46 % Allowed : 23.14 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3736 helix: 1.40 (0.16), residues: 1081 sheet: -0.75 (0.20), residues: 657 loop : -1.81 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.009 0.001 HIS D 378 PHE 0.030 0.001 PHE B 643 TYR 0.015 0.001 TYR B 265 ARG 0.007 0.000 ARG C 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 51) link_NAG-ASN : angle 4.18524 ( 153) link_BETA1-4 : bond 0.00445 ( 17) link_BETA1-4 : angle 2.07413 ( 51) hydrogen bonds : bond 0.04409 ( 1097) hydrogen bonds : angle 4.72346 ( 3093) metal coordination : bond 0.02406 ( 2) SS BOND : bond 0.00208 ( 42) SS BOND : angle 1.28628 ( 84) covalent geometry : bond 0.00258 (31374) covalent geometry : angle 0.60672 (42687) *********************** 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 314 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 200 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8938 (m) cc_final: 0.8732 (p) REVERT: A 127 PHE cc_start: 0.6913 (t80) cc_final: 0.6361 (m-80) REVERT: A 176 LEU cc_start: 0.5714 (pt) cc_final: 0.5330 (mp) REVERT: A 287 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: A 472 ILE cc_start: -0.0585 (OUTLIER) cc_final: -0.0811 (tp) REVERT: A 571 ASP cc_start: 0.8409 (m-30) cc_final: 0.7809 (t70) REVERT: A 574 ASP cc_start: 0.7105 (t70) cc_final: 0.6893 (p0) REVERT: A 773 GLU cc_start: 0.7932 (tt0) cc_final: 0.7452 (tt0) REVERT: A 816 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8683 (m) REVERT: A 834 ILE cc_start: 0.3561 (OUTLIER) cc_final: 0.2977 (tp) REVERT: B 167 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.6061 (t) REVERT: B 271 GLN cc_start: 0.7699 (mt0) cc_final: 0.7424 (mt0) REVERT: B 280 ASN cc_start: 0.8446 (t0) cc_final: 0.8208 (t0) REVERT: B 492 LEU cc_start: -0.0410 (OUTLIER) cc_final: -0.0676 (mt) REVERT: B 549 THR cc_start: 0.7789 (p) cc_final: 0.7372 (p) REVERT: B 992 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6519 (mm-40) REVERT: C 127 PHE cc_start: 0.6054 (t80) cc_final: 0.5406 (t80) REVERT: C 190 ARG cc_start: 0.7753 (ptm160) cc_final: 0.6557 (mtt-85) REVERT: C 216 PHE cc_start: 0.3903 (OUTLIER) cc_final: 0.2440 (t80) REVERT: C 265 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: C 277 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 346 ARG cc_start: 0.3827 (OUTLIER) cc_final: 0.3502 (tmt-80) REVERT: C 359 SER cc_start: -0.2812 (OUTLIER) cc_final: -0.3036 (p) REVERT: C 396 TYR cc_start: 0.2063 (OUTLIER) cc_final: 0.1000 (m-10) REVERT: C 591 SER cc_start: 0.8300 (m) cc_final: 0.8015 (m) REVERT: C 759 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7204 (t80) REVERT: C 904 TYR cc_start: 0.7954 (m-10) cc_final: 0.7437 (m-10) REVERT: C 1125 ASN cc_start: 0.8490 (t0) cc_final: 0.8141 (t0) REVERT: D 81 GLN cc_start: 0.5939 (pm20) cc_final: 0.5487 (pt0) REVERT: D 123 MET cc_start: -0.0670 (ppp) cc_final: -0.1565 (tmm) REVERT: D 270 MET cc_start: -0.3126 (tpp) cc_final: -0.3401 (mmt) REVERT: D 275 TRP cc_start: -0.0668 (m-10) cc_final: -0.1623 (m-10) REVERT: D 309 LYS cc_start: 0.5428 (tppt) cc_final: 0.5108 (mmtt) REVERT: D 323 MET cc_start: 0.2634 (tpp) cc_final: 0.2054 (mmm) REVERT: D 333 LEU cc_start: 0.4087 (mt) cc_final: 0.3810 (pp) REVERT: D 435 GLU cc_start: 0.0397 (OUTLIER) cc_final: -0.0572 (pt0) REVERT: D 455 MET cc_start: 0.2741 (tpp) cc_final: 0.2457 (tpt) REVERT: D 585 LEU cc_start: 0.2644 (mt) cc_final: 0.2299 (pp) REVERT: D 592 PHE cc_start: 0.1801 (t80) cc_final: 0.1194 (m-80) outliers start: 114 outliers final: 80 residues processed: 302 average time/residue: 0.3406 time to fit residues: 176.6316 Evaluate side-chains 286 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 191 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 ILE 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 560 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 962 LEU 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 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 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 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 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 643 PHE Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 849 LEU 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 31 SER Chi-restraints excluded: chain C residue 45 SER 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 277 LEU 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 346 ARG 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 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR 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 1040 VAL Chi-restraints excluded: chain C residue 1071 GLN Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 271 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 179 optimal weight: 0.0870 chunk 211 optimal weight: 5.9990 chunk 143 optimal weight: 50.0000 chunk 54 optimal weight: 0.0470 chunk 249 optimal weight: 0.0980 chunk 319 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A1048 HIS C1010 GLN D 277 ASN ** D 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.220465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135679 restraints weight = 47929.033| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 4.14 r_work: 0.3335 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31486 Z= 0.109 Angle : 0.638 13.892 42975 Z= 0.305 Chirality : 0.046 0.540 4963 Planarity : 0.004 0.057 5424 Dihedral : 6.160 55.130 5462 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.73 % Allowed : 24.08 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3736 helix: 1.56 (0.16), residues: 1072 sheet: -0.71 (0.20), residues: 656 loop : -1.74 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 104 HIS 0.012 0.001 HIS D 378 PHE 0.015 0.001 PHE B 643 TYR 0.024 0.001 TYR B 265 ARG 0.003 0.000 ARG C 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 51) link_NAG-ASN : angle 4.07654 ( 153) link_BETA1-4 : bond 0.00463 ( 17) link_BETA1-4 : angle 2.05646 ( 51) hydrogen bonds : bond 0.04032 ( 1097) hydrogen bonds : angle 4.61158 ( 3093) metal coordination : bond 0.02150 ( 2) SS BOND : bond 0.00219 ( 42) SS BOND : angle 1.09953 ( 84) covalent geometry : bond 0.00237 (31374) covalent geometry : angle 0.58523 (42687) ********************** 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 299 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.6749 (t80) cc_final: 0.6215 (m-80) REVERT: A 176 LEU cc_start: 0.5655 (pt) cc_final: 0.5263 (mp) REVERT: A 472 ILE cc_start: -0.0378 (OUTLIER) cc_final: -0.0627 (tp) REVERT: A 559 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8221 (t80) REVERT: A 571 ASP cc_start: 0.8364 (m-30) cc_final: 0.7689 (t70) REVERT: A 773 GLU cc_start: 0.7867 (tt0) cc_final: 0.7381 (tt0) REVERT: A 816 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8652 (m) REVERT: A 1051 SER cc_start: 0.9003 (p) cc_final: 0.8732 (m) REVERT: B 167 THR cc_start: 0.6272 (OUTLIER) cc_final: 0.6066 (t) REVERT: B 271 GLN cc_start: 0.7555 (mt0) cc_final: 0.7270 (mt0) REVERT: B 280 ASN cc_start: 0.8387 (t0) cc_final: 0.8135 (t0) REVERT: B 492 LEU cc_start: -0.0027 (OUTLIER) cc_final: -0.0342 (mt) REVERT: B 549 THR cc_start: 0.7828 (p) cc_final: 0.7399 (p) REVERT: B 992 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6218 (mm-40) REVERT: C 127 PHE cc_start: 0.5859 (t80) cc_final: 0.5292 (t80) REVERT: C 190 ARG cc_start: 0.7742 (ptm160) cc_final: 0.6592 (mtt-85) REVERT: C 216 PHE cc_start: 0.4026 (OUTLIER) cc_final: 0.2555 (t80) REVERT: C 265 TYR cc_start: 0.6572 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: C 346 ARG cc_start: 0.3833 (OUTLIER) cc_final: 0.3536 (tmt-80) REVERT: C 359 SER cc_start: -0.2800 (OUTLIER) cc_final: -0.3021 (p) REVERT: C 396 TYR cc_start: 0.2210 (OUTLIER) cc_final: 0.1073 (m-10) REVERT: C 591 SER cc_start: 0.8215 (m) cc_final: 0.7888 (m) REVERT: C 759 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7223 (t80) REVERT: C 856 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8005 (p0) REVERT: C 904 TYR cc_start: 0.7956 (m-10) cc_final: 0.7434 (m-10) REVERT: C 1125 ASN cc_start: 0.8362 (t0) cc_final: 0.8064 (t0) REVERT: D 81 GLN cc_start: 0.6046 (pm20) cc_final: 0.5689 (pt0) REVERT: D 123 MET cc_start: -0.0829 (ppp) cc_final: -0.1680 (tmm) REVERT: D 152 MET cc_start: 0.0760 (tmm) cc_final: 0.0360 (tmm) REVERT: D 162 LEU cc_start: -0.0289 (tp) cc_final: -0.0526 (pp) REVERT: D 270 MET cc_start: -0.3118 (tpp) cc_final: -0.3513 (mmt) REVERT: D 275 TRP cc_start: -0.0728 (m-10) cc_final: -0.1604 (m-10) REVERT: D 309 LYS cc_start: 0.5415 (tppt) cc_final: 0.5118 (mmtt) REVERT: D 323 MET cc_start: 0.2817 (tpp) cc_final: 0.2370 (mmm) REVERT: D 333 LEU cc_start: 0.4430 (mt) cc_final: 0.4217 (pp) REVERT: D 435 GLU cc_start: 0.0648 (OUTLIER) cc_final: -0.0286 (pt0) REVERT: D 455 MET cc_start: 0.2536 (tpp) cc_final: 0.2271 (tpt) REVERT: D 585 LEU cc_start: 0.3117 (mt) cc_final: 0.2761 (pp) outliers start: 90 outliers final: 70 residues processed: 291 average time/residue: 0.3678 time to fit residues: 185.0898 Evaluate side-chains 277 residues out of total 3302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 193 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 ILE 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 512 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU 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 859 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 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 177 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 524 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 720 ILE Chi-restraints excluded: chain B residue 849 LEU 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 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 45 SER 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 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 335 LEU Chi-restraints excluded: chain C residue 346 ARG 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 492 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR 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 941 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1127 ASP 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 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 26 optimal weight: 0.9980 chunk 351 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 252 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 907 ASN B 121 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN D 277 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.211162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122817 restraints weight = 47021.121| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.88 r_work: 0.3162 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 31486 Z= 0.274 Angle : 0.824 15.132 42975 Z= 0.407 Chirality : 0.052 0.565 4963 Planarity : 0.005 0.050 5424 Dihedral : 6.949 55.957 5462 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.70 % Allowed : 23.57 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3736 helix: 1.04 (0.16), residues: 1068 sheet: -1.03 (0.20), residues: 654 loop : -1.94 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.010 0.002 HIS A 49 PHE 0.039 0.003 PHE B 643 TYR 0.029 0.002 TYR A 265 ARG 0.015 0.001 ARG C1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 51) link_NAG-ASN : angle 4.51030 ( 153) link_BETA1-4 : bond 0.00408 ( 17) link_BETA1-4 : angle 2.11549 ( 51) hydrogen bonds : bond 0.07370 ( 1097) hydrogen bonds : angle 5.10549 ( 3093) metal coordination : bond 0.01508 ( 2) SS BOND : bond 0.00380 ( 42) SS BOND : angle 2.04289 ( 84) covalent geometry : bond 0.00673 (31374) covalent geometry : angle 0.77314 (42687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20044.38 seconds wall clock time: 345 minutes 51.54 seconds (20751.54 seconds total)