Starting phenix.real_space_refine on Sun Jul 5 15:52:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.cif" model { file = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we8_32442/07_2026/7we8_32442.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 18217 2.51 5 N 4668 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28585 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.88, per 1000 atoms: 0.21 Number of scatterers: 28585 At special positions: 0 Unit cell: (147.66, 144.45, 236.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 5577 8.00 N 4668 7.00 C 18217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.02 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1301 " - " ASN A1155 " " NAG A1302 " - " ASN A 143 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 613 " " NAG A1308 " - " ASN A 706 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG C1301 " - " ASN C1155 " " NAG C1302 " - " ASN C 123 " " NAG C1303 " - " ASN C 143 " " NAG C1304 " - " ASN C 17 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 600 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 613 " " NAG C1309 " - " ASN C 706 " " NAG D 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 714 " " NAG G 1 " - " ASN A1071 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN B 328 " " NAG T 1 " - " ASN C 714 " " NAG V 1 " - " ASN C 798 " " NAG W 1 " - " ASN C1095 " " NAG X 1 " - " ASN C1131 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 57 sheets defined 24.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.528A pdb=" N LEU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.931A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 402 through 408 removed outlier: 5.157A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 741 removed outlier: 3.524A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 removed outlier: 3.575A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 756 through 780 removed outlier: 3.639A pdb=" N LYS A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 762 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.586A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.507A pdb=" N GLN A 850 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.523A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.678A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 removed outlier: 4.406A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.933A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.838A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 4.064A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 955 " --> pdb=" O HIS A 951 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 removed outlier: 4.076A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 975 through 980' Processing helix chain 'A' and resid 985 through 1030 removed outlier: 3.659A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1137 through 1157 removed outlier: 3.875A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS A1151 " --> pdb=" O GLU A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.166A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.169A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 382 through 386' Processing helix chain 'B' and resid 402 through 408 removed outlier: 5.150A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 406 " --> pdb=" O GLU B 403 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.870A pdb=" N SER B 634 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 635 " --> pdb=" O ARG B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 635' Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.620A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 751 removed outlier: 3.572A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.550A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.886A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 removed outlier: 3.557A pdb=" N TYR B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 880 " --> pdb=" O ALA B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 907 removed outlier: 3.879A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 4.046A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 928 removed outlier: 3.553A pdb=" N ILE B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 938 removed outlier: 3.777A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 4.194A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 980 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.006A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1138 through 1155 removed outlier: 4.124A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.879A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 408 removed outlier: 3.542A pdb=" N GLU C 403 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 404 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.550A pdb=" N ASN C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.846A pdb=" N TYR C 633 " --> pdb=" O TRP C 630 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 3.613A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 removed outlier: 3.774A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 754 No H-bonds generated for 'chain 'C' and resid 753 through 754' Processing helix chain 'C' and resid 755 through 756 No H-bonds generated for 'chain 'C' and resid 755 through 756' Processing helix chain 'C' and resid 757 through 775 removed outlier: 3.664A pdb=" N LYS C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 767 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.503A pdb=" N PHE C 779 " --> pdb=" O THR C 775 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 780' Processing helix chain 'C' and resid 813 through 822 removed outlier: 3.607A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 853 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.565A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 881 " --> pdb=" O GLY C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 907 removed outlier: 3.516A pdb=" N MET C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 902 " --> pdb=" O GLN C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.981A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.559A pdb=" N GLY C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 4.606A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN C 957 " --> pdb=" O ALA C 953 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 removed outlier: 4.313A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.187A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'C' and resid 1145 through 1158 Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.966A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.858A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 261 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.979A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.916A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.259A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.861A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.648A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 432 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.828A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.848A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 548 through 551 removed outlier: 3.517A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563 removed outlier: 3.520A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.803A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 668 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 712 removed outlier: 3.588A pdb=" N ILE A 711 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A1070 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.665A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 6.011A pdb=" N VAL A1119 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A1086 " --> pdb=" O VAL A1119 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY A1121 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.859A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.004A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.187A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.914A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 118 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 115 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 117 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.557A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 640 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.652A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.767A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.121A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.782A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 449 through 451 removed outlier: 3.534A pdb=" N TYR B 450 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.658A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 548 through 550 Processing sheet with id=AD5, first strand: chain 'B' and resid 651 through 656 removed outlier: 6.386A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 688 " --> pdb=" O GLN B 672 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 672 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AD7, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.752A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.577A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 3.626A pdb=" N VAL B1091 " --> pdb=" O THR B1102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.764A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.734A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.723A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 103 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 236 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 308 through 311 removed outlier: 3.622A pdb=" N THR C 596 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 609 " --> pdb=" O CYS C 646 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS C 646 " --> pdb=" O TYR C 609 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 321 through 325 removed outlier: 3.808A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.959A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 355 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 432 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR C 373 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.442A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF2, first strand: chain 'C' and resid 548 through 551 removed outlier: 3.681A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 550 " --> pdb=" O ASP C 583 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 573 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.090A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 708 through 712 removed outlier: 4.803A pdb=" N GLN C1103 " --> pdb=" O GLU C1108 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU C1108 " --> pdb=" O GLN C1103 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.268A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF7, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.776A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AF9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.498A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.682A pdb=" N TYR H 108 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.558A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP L 38 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 19 through 24 916 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8970 1.34 - 1.46: 7204 1.46 - 1.59: 12914 1.59 - 1.71: 0 1.71 - 1.83: 155 Bond restraints: 29243 Sorted by residual: bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.90e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.11e-02 8.12e+03 1.52e+01 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 29238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 38960 2.09 - 4.18: 732 4.18 - 6.27: 71 6.27 - 8.36: 13 8.36 - 10.45: 4 Bond angle restraints: 39780 Sorted by residual: angle pdb=" N PHE C 104 " pdb=" CA PHE C 104 " pdb=" C PHE C 104 " ideal model delta sigma weight residual 108.55 115.41 -6.86 1.62e+00 3.81e-01 1.79e+01 angle pdb=" N VAL B 207 " pdb=" CA VAL B 207 " pdb=" C VAL B 207 " ideal model delta sigma weight residual 106.21 110.72 -4.51 1.07e+00 8.73e-01 1.78e+01 angle pdb=" CA ILE A 329 " pdb=" C ILE A 329 " pdb=" O ILE A 329 " ideal model delta sigma weight residual 121.63 117.65 3.98 9.90e-01 1.02e+00 1.62e+01 angle pdb=" N PHE A 303 " pdb=" CA PHE A 303 " pdb=" C PHE A 303 " ideal model delta sigma weight residual 114.31 109.20 5.11 1.29e+00 6.01e-01 1.57e+01 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" O ASN A 328 " ideal model delta sigma weight residual 122.37 118.01 4.36 1.15e+00 7.56e-01 1.44e+01 ... (remaining 39775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 15338 17.78 - 35.56: 1288 35.56 - 53.34: 197 53.34 - 71.12: 36 71.12 - 88.90: 22 Dihedral angle restraints: 16881 sinusoidal: 6608 harmonic: 10273 Sorted by residual: dihedral pdb=" CB CYS A 735 " pdb=" SG CYS A 735 " pdb=" SG CYS A 757 " pdb=" CB CYS A 757 " ideal model delta sinusoidal sigma weight residual -86.00 -4.22 -81.78 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 23.80 69.20 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS A 740 " pdb=" SG CYS A 740 " pdb=" SG CYS A 746 " pdb=" CB CYS A 746 " ideal model delta sinusoidal sigma weight residual -86.00 -24.54 -61.46 1 1.00e+01 1.00e-02 5.01e+01 ... (remaining 16878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 4585 0.117 - 0.234: 99 0.234 - 0.351: 7 0.351 - 0.468: 0 0.468 - 0.585: 1 Chirality restraints: 4692 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A1071 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 4689 not shown) Planarity restraints: 5073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 321 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C GLU B 321 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU B 321 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 706 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.05e+00 pdb=" CG ASN B 706 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 706 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 706 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 558 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.027 5.00e-02 4.00e+02 ... (remaining 5070 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 15 2.26 - 2.92: 12490 2.92 - 3.58: 39725 3.58 - 4.24: 62145 4.24 - 4.90: 103968 Nonbonded interactions: 218343 Sorted by model distance: nonbonded pdb=" OG SER A 443 " pdb=" NE ARG H 60 " model vdw 1.600 3.120 nonbonded pdb=" CB SER A 443 " pdb=" NE ARG H 60 " model vdw 1.947 3.520 nonbonded pdb=" O ASN B 367 " pdb=" OH TYR C 486 " model vdw 2.065 3.040 nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.127 3.040 nonbonded pdb=" O PRO C1140 " pdb=" OG SER C1144 " model vdw 2.166 3.040 ... (remaining 218338 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 14 through 1308) selection = (chain 'C' and resid 14 through 1308) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.790 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.004 0.082 29352 Z= 0.231 Angle : 0.688 20.264 40057 Z= 0.355 Chirality : 0.048 0.585 4692 Planarity : 0.004 0.069 5032 Dihedral : 13.214 88.905 10146 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3488 helix: -0.08 (0.21), residues: 659 sheet: -0.37 (0.20), residues: 708 loop : -1.66 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 574 TYR 0.021 0.001 TYR C 450 PHE 0.018 0.001 PHE C 104 TRP 0.026 0.001 TRP H 109 HIS 0.011 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.23 (29243) covalent geometry : angle 0.66288 / 0.35 (39780) SS BOND : bond 0.00302 / 0.21 ( 41) SS BOND : angle 1.01161 / 0.67 ( 82) hydrogen bonds : bond 0.27070 / 17.65 ( 907) hydrogen bonds : angle 8.70942 / 5.98 ( 2418) Misc. bond : bond 0.00036 / 0.02 ( 3) link_BETA1-4 : bond 0.00496 / 0.31 ( 24) link_BETA1-4 : angle 1.62655 / 1.21 ( 72) link_NAG-ASN : bond 0.00599 / 0.47 ( 41) link_NAG-ASN : angle 3.13552 / 2.32 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 215 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7882 (mm-40) REVERT: A 742 ASP cc_start: 0.6922 (p0) cc_final: 0.6382 (t0) REVERT: B 377 TYR cc_start: 0.6299 (m-10) cc_final: 0.6090 (m-10) REVERT: B 448 TYR cc_start: 0.6210 (m-10) cc_final: 0.5312 (m-80) REVERT: B 1143 ASP cc_start: 0.9071 (m-30) cc_final: 0.8812 (p0) REVERT: L 52 TYR cc_start: 0.8169 (p90) cc_final: 0.7835 (p90) outliers start: 8 outliers final: 2 residues processed: 183 average time/residue: 0.1765 time to fit residues: 51.9437 Evaluate side-chains 116 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 533 ASN B 622 HIS ** B 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN C 119 ASN C 191 ASN C 406 GLN C 923 GLN C 962 GLN C1103 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.072130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048050 restraints weight = 143048.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049659 restraints weight = 68976.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050667 restraints weight = 44635.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051297 restraints weight = 34291.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.051674 restraints weight = 29263.091| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29352 Z= 0.217 Angle : 0.695 18.113 40057 Z= 0.351 Chirality : 0.047 0.485 4692 Planarity : 0.004 0.059 5032 Dihedral : 5.005 52.156 3785 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.84 % Allowed : 7.29 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3488 helix: -0.06 (0.20), residues: 697 sheet: -0.42 (0.19), residues: 757 loop : -1.75 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1104 TYR 0.019 0.002 TYR C 165 PHE 0.022 0.002 PHE H 27 TRP 0.025 0.002 TRP H 109 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (29243) covalent geometry : angle 0.67261 / 0.35 (39780) SS BOND : bond 0.00318 / 0.21 ( 41) SS BOND : angle 1.20587 / 0.79 ( 82) hydrogen bonds : bond 0.06927 / 4.54 ( 907) hydrogen bonds : angle 6.75349 / 4.65 ( 2418) Misc. bond : bond 0.00046 / 0.02 ( 3) link_BETA1-4 : bond 0.00651 / 0.41 ( 24) link_BETA1-4 : angle 1.59270 / 1.18 ( 72) link_NAG-ASN : bond 0.00431 / 0.31 ( 41) link_NAG-ASN : angle 2.91306 / 2.15 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: A 633 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6040 (t80) REVERT: A 742 ASP cc_start: 0.7030 (p0) cc_final: 0.6372 (t0) REVERT: B 84 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7416 (t80) REVERT: B 314 ASN cc_start: 0.7424 (t0) cc_final: 0.7154 (t0) REVERT: B 448 TYR cc_start: 0.6663 (m-10) cc_final: 0.5676 (m-80) REVERT: B 737 MET cc_start: 0.9284 (tpt) cc_final: 0.8844 (tpp) REVERT: C 119 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: C 424 ASP cc_start: 0.8787 (m-30) cc_final: 0.8515 (m-30) REVERT: C 516 HIS cc_start: 0.8228 (m90) cc_final: 0.7876 (m-70) REVERT: C 633 TYR cc_start: 0.8337 (t80) cc_final: 0.7889 (t80) REVERT: H 87 MET cc_start: 0.5384 (pmm) cc_final: 0.4604 (pmm) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.1524 time to fit residues: 39.3127 Evaluate side-chains 132 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 109 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 294 optimal weight: 0.4980 chunk 226 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 759 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C1007 GLN H 30 ASN H 86 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.071728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047518 restraints weight = 145589.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049132 restraints weight = 70185.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050146 restraints weight = 45527.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050775 restraints weight = 35015.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051149 restraints weight = 29933.949| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29352 Z= 0.199 Angle : 0.652 16.638 40057 Z= 0.326 Chirality : 0.046 0.468 4692 Planarity : 0.004 0.049 5032 Dihedral : 4.986 48.485 3785 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 1.39 % Allowed : 10.82 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3488 helix: -0.01 (0.20), residues: 700 sheet: -0.50 (0.19), residues: 716 loop : -1.73 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 45 TYR 0.017 0.001 TYR B1064 PHE 0.020 0.002 PHE B 133 TRP 0.018 0.001 TRP H 109 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (29243) covalent geometry : angle 0.63144 / 0.32 (39780) SS BOND : bond 0.00256 / 0.17 ( 41) SS BOND : angle 1.01218 / 0.68 ( 82) hydrogen bonds : bond 0.06083 / 3.96 ( 907) hydrogen bonds : angle 6.40136 / 4.40 ( 2418) Misc. bond : bond 0.00010 / 0.00 ( 3) link_BETA1-4 : bond 0.00453 / 0.29 ( 24) link_BETA1-4 : angle 1.40369 / 1.00 ( 72) link_NAG-ASN : bond 0.00426 / 0.33 ( 41) link_NAG-ASN : angle 2.79022 / 2.06 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: A 318 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: A 633 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 742 ASP cc_start: 0.7013 (p0) cc_final: 0.6425 (t0) REVERT: B 84 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7386 (t80) REVERT: B 314 ASN cc_start: 0.7491 (t0) cc_final: 0.7236 (t0) REVERT: B 448 TYR cc_start: 0.6880 (m-10) cc_final: 0.5809 (m-80) REVERT: B 737 MET cc_start: 0.9325 (tpt) cc_final: 0.8925 (tpp) REVERT: C 119 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7588 (m-40) REVERT: C 165 TYR cc_start: 0.8411 (t80) cc_final: 0.8164 (t80) REVERT: C 516 HIS cc_start: 0.8269 (m90) cc_final: 0.7797 (m90) REVERT: C 633 TYR cc_start: 0.8400 (t80) cc_final: 0.7806 (t80) REVERT: C 737 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8516 (ttp) REVERT: H 87 MET cc_start: 0.5241 (pmm) cc_final: 0.4735 (pmm) outliers start: 43 outliers final: 24 residues processed: 157 average time/residue: 0.1493 time to fit residues: 39.6283 Evaluate side-chains 143 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 46 optimal weight: 0.4980 chunk 215 optimal weight: 8.9990 chunk 120 optimal weight: 0.0770 chunk 106 optimal weight: 0.3980 chunk 277 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 541 ASN B 622 HIS B 759 GLN B1103 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN C 622 HIS C 898 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.072869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.048823 restraints weight = 142227.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050496 restraints weight = 67783.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051548 restraints weight = 43474.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052195 restraints weight = 33156.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052581 restraints weight = 28207.902| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29352 Z= 0.111 Angle : 0.590 15.975 40057 Z= 0.292 Chirality : 0.044 0.411 4692 Planarity : 0.004 0.075 5032 Dihedral : 4.653 47.348 3783 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.52 % Allowed : 12.15 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3488 helix: 0.14 (0.20), residues: 707 sheet: -0.22 (0.20), residues: 720 loop : -1.63 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 99 TYR 0.016 0.001 TYR A 393 PHE 0.021 0.001 PHE B 133 TRP 0.014 0.001 TRP H 109 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (29243) covalent geometry : angle 0.57007 / 0.29 (39780) SS BOND : bond 0.00267 / 0.18 ( 41) SS BOND : angle 0.83902 / 0.56 ( 82) hydrogen bonds : bond 0.04911 / 3.19 ( 907) hydrogen bonds : angle 5.95994 / 4.08 ( 2418) Misc. bond : bond 0.00019 / 0.01 ( 3) link_BETA1-4 : bond 0.00533 / 0.34 ( 24) link_BETA1-4 : angle 1.38441 / 1.00 ( 72) link_NAG-ASN : bond 0.00417 / 0.34 ( 41) link_NAG-ASN : angle 2.60346 / 1.93 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8488 (mm) REVERT: A 133 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: A 148 MET cc_start: 0.7376 (mmm) cc_final: 0.7122 (mmm) REVERT: A 633 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6173 (t80) REVERT: A 742 ASP cc_start: 0.6826 (p0) cc_final: 0.6177 (t0) REVERT: B 84 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 314 ASN cc_start: 0.7298 (t0) cc_final: 0.7068 (t0) REVERT: B 448 TYR cc_start: 0.6673 (m-10) cc_final: 0.5857 (m-80) REVERT: B 737 MET cc_start: 0.9269 (tpt) cc_final: 0.8883 (tpp) REVERT: B 777 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 999 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 116 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 165 TYR cc_start: 0.8191 (t80) cc_final: 0.7984 (t80) REVERT: C 335 PHE cc_start: 0.8842 (m-10) cc_final: 0.8618 (m-10) REVERT: C 516 HIS cc_start: 0.8344 (m90) cc_final: 0.7830 (m90) REVERT: C 633 TYR cc_start: 0.8227 (t80) cc_final: 0.7491 (t80) REVERT: C 952 ASN cc_start: 0.8680 (m-40) cc_final: 0.8196 (m110) REVERT: C 954 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8514 (tm-30) REVERT: H 87 MET cc_start: 0.5334 (pmm) cc_final: 0.4878 (pmm) REVERT: H 106 PHE cc_start: 0.7716 (m-80) cc_final: 0.7153 (m-80) REVERT: L 52 TYR cc_start: 0.8073 (p90) cc_final: 0.7770 (p90) outliers start: 47 outliers final: 20 residues processed: 174 average time/residue: 0.1483 time to fit residues: 44.0960 Evaluate side-chains 149 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 265 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 224 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 346 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 333 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 759 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.070842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.046821 restraints weight = 144031.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048422 restraints weight = 69277.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049413 restraints weight = 44772.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050022 restraints weight = 34351.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050406 restraints weight = 29384.298| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29352 Z= 0.238 Angle : 0.679 14.703 40057 Z= 0.339 Chirality : 0.046 0.466 4692 Planarity : 0.004 0.051 5032 Dihedral : 4.948 48.851 3783 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 1.98 % Allowed : 13.67 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3488 helix: 0.02 (0.20), residues: 718 sheet: -0.43 (0.19), residues: 731 loop : -1.72 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 99 TYR 0.020 0.001 TYR B1064 PHE 0.024 0.002 PHE C 756 TRP 0.017 0.002 TRP B 255 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (29243) covalent geometry : angle 0.66095 / 0.34 (39780) SS BOND : bond 0.00303 / 0.19 ( 41) SS BOND : angle 1.06019 / 0.70 ( 82) hydrogen bonds : bond 0.05645 / 3.65 ( 907) hydrogen bonds : angle 6.19303 / 4.25 ( 2418) Misc. bond : bond 0.00015 / 0.01 ( 3) link_BETA1-4 : bond 0.00465 / 0.31 ( 24) link_BETA1-4 : angle 1.40341 / 1.00 ( 72) link_NAG-ASN : bond 0.00472 / 0.34 ( 41) link_NAG-ASN : angle 2.67762 / 1.91 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 133 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: A 318 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: A 633 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 983 LYS cc_start: 0.7859 (pttt) cc_final: 0.6830 (mmtm) REVERT: B 84 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7423 (t80) REVERT: B 195 TYR cc_start: 0.8437 (m-80) cc_final: 0.8070 (t80) REVERT: B 314 ASN cc_start: 0.7538 (t0) cc_final: 0.7172 (t0) REVERT: B 448 TYR cc_start: 0.6601 (m-10) cc_final: 0.5573 (m-80) REVERT: B 737 MET cc_start: 0.9295 (tpt) cc_final: 0.8965 (tpp) REVERT: B 783 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8530 (mmmt) REVERT: B 999 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 126 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 165 TYR cc_start: 0.8318 (t80) cc_final: 0.8105 (t80) REVERT: C 516 HIS cc_start: 0.8238 (m90) cc_final: 0.7774 (m90) REVERT: C 633 TYR cc_start: 0.8462 (t80) cc_final: 0.8008 (t80) REVERT: C 737 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8456 (ttp) REVERT: C 954 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8564 (tm-30) REVERT: H 106 PHE cc_start: 0.7726 (m-80) cc_final: 0.7267 (m-80) outliers start: 61 outliers final: 39 residues processed: 169 average time/residue: 0.1400 time to fit residues: 40.8984 Evaluate side-chains 159 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 814 PHE Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 60 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 chunk 300 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 312 optimal weight: 0.0670 chunk 343 optimal weight: 9.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.072030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048034 restraints weight = 143488.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049684 restraints weight = 68787.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050708 restraints weight = 44348.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051348 restraints weight = 34063.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051732 restraints weight = 29039.967| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29352 Z= 0.120 Angle : 0.598 14.455 40057 Z= 0.295 Chirality : 0.044 0.422 4692 Planarity : 0.004 0.050 5032 Dihedral : 4.679 43.951 3783 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.04 % Allowed : 14.58 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3488 helix: 0.29 (0.20), residues: 707 sheet: -0.33 (0.19), residues: 735 loop : -1.65 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 99 TYR 0.016 0.001 TYR B1152 PHE 0.027 0.001 PHE B 756 TRP 0.010 0.001 TRP B 255 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (29243) covalent geometry : angle 0.57953 / 0.29 (39780) SS BOND : bond 0.00271 / 0.18 ( 41) SS BOND : angle 0.90908 / 0.60 ( 82) hydrogen bonds : bond 0.04877 / 3.18 ( 907) hydrogen bonds : angle 5.87211 / 4.02 ( 2418) Misc. bond : bond 0.00005 / 0.00 ( 3) link_BETA1-4 : bond 0.00520 / 0.33 ( 24) link_BETA1-4 : angle 1.33981 / 0.96 ( 72) link_NAG-ASN : bond 0.00394 / 0.32 ( 41) link_NAG-ASN : angle 2.50833 / 1.82 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8481 (mm) REVERT: A 133 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: A 318 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: A 633 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6249 (t80) REVERT: A 742 ASP cc_start: 0.6792 (p0) cc_final: 0.6277 (t0) REVERT: B 84 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 314 ASN cc_start: 0.7362 (t0) cc_final: 0.7075 (t0) REVERT: B 448 TYR cc_start: 0.6626 (m-10) cc_final: 0.5576 (m-80) REVERT: B 737 MET cc_start: 0.9266 (tpt) cc_final: 0.8920 (tpp) REVERT: B 783 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8469 (mmmt) REVERT: B 999 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8300 (tm-30) REVERT: C 165 TYR cc_start: 0.8307 (t80) cc_final: 0.8061 (t80) REVERT: C 516 HIS cc_start: 0.8253 (m90) cc_final: 0.7736 (m90) REVERT: C 633 TYR cc_start: 0.8210 (t80) cc_final: 0.7740 (t80) REVERT: C 737 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8472 (ttm) REVERT: C 952 ASN cc_start: 0.8680 (m-40) cc_final: 0.8214 (m110) REVERT: C 954 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8479 (tm-30) REVERT: C 1047 MET cc_start: 0.8285 (ptp) cc_final: 0.7932 (mtm) REVERT: H 87 MET cc_start: 0.5297 (pmm) cc_final: 0.4889 (pmm) REVERT: H 106 PHE cc_start: 0.7705 (m-80) cc_final: 0.7212 (m-80) REVERT: L 52 TYR cc_start: 0.8093 (p90) cc_final: 0.7799 (p90) outliers start: 63 outliers final: 41 residues processed: 176 average time/residue: 0.1488 time to fit residues: 45.9335 Evaluate side-chains 167 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 978 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 346 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.071152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047214 restraints weight = 144264.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048820 restraints weight = 69487.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049826 restraints weight = 44969.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.050428 restraints weight = 34591.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050816 restraints weight = 29628.473| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29352 Z= 0.178 Angle : 0.633 14.024 40057 Z= 0.312 Chirality : 0.045 0.445 4692 Planarity : 0.004 0.068 5032 Dihedral : 4.754 43.073 3783 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.04 % Allowed : 15.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3488 helix: 0.25 (0.20), residues: 717 sheet: -0.37 (0.19), residues: 737 loop : -1.69 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 99 TYR 0.017 0.001 TYR B1064 PHE 0.037 0.001 PHE L 103 TRP 0.011 0.001 TRP H 109 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (29243) covalent geometry : angle 0.61411 / 0.31 (39780) SS BOND : bond 0.00304 / 0.20 ( 41) SS BOND : angle 1.13138 / 0.76 ( 82) hydrogen bonds : bond 0.05080 / 3.30 ( 907) hydrogen bonds : angle 5.92990 / 4.07 ( 2418) Misc. bond : bond 0.00005 / 0.00 ( 3) link_BETA1-4 : bond 0.00463 / 0.30 ( 24) link_BETA1-4 : angle 1.34672 / 0.96 ( 72) link_NAG-ASN : bond 0.00389 / 0.30 ( 41) link_NAG-ASN : angle 2.54595 / 1.80 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 133 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: A 318 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 633 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 84 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7210 (t80) REVERT: B 86 ASP cc_start: 0.4849 (OUTLIER) cc_final: 0.4185 (t0) REVERT: B 195 TYR cc_start: 0.8446 (m-80) cc_final: 0.8131 (t80) REVERT: B 314 ASN cc_start: 0.7514 (t0) cc_final: 0.7144 (t0) REVERT: B 448 TYR cc_start: 0.6701 (m-10) cc_final: 0.5652 (m-80) REVERT: B 633 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.5926 (t80) REVERT: B 999 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 126 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8272 (mm) REVERT: C 165 TYR cc_start: 0.8284 (t80) cc_final: 0.8056 (t80) REVERT: C 516 HIS cc_start: 0.8254 (m90) cc_final: 0.7765 (m90) REVERT: C 633 TYR cc_start: 0.8324 (t80) cc_final: 0.7829 (t80) REVERT: C 737 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8513 (ttm) REVERT: C 863 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9072 (p) REVERT: C 954 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8474 (tm-30) REVERT: H 87 MET cc_start: 0.5440 (pmm) cc_final: 0.5223 (pmm) REVERT: L 52 TYR cc_start: 0.8088 (p90) cc_final: 0.7811 (p90) outliers start: 63 outliers final: 43 residues processed: 170 average time/residue: 0.1535 time to fit residues: 44.2759 Evaluate side-chains 168 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 115 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 30 optimal weight: 0.0010 chunk 37 optimal weight: 10.0000 chunk 318 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 242 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 overall best weight: 0.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1098 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 ASN C 622 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.072879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.048911 restraints weight = 144712.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050600 restraints weight = 68626.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051648 restraints weight = 43933.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.052300 restraints weight = 33584.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052698 restraints weight = 28623.552| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29352 Z= 0.103 Angle : 0.592 13.219 40057 Z= 0.289 Chirality : 0.044 0.392 4692 Planarity : 0.004 0.054 5032 Dihedral : 4.439 41.782 3783 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.43 % Allowed : 16.26 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.14), residues: 3488 helix: 0.49 (0.20), residues: 708 sheet: -0.16 (0.20), residues: 727 loop : -1.61 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 99 TYR 0.015 0.001 TYR C1064 PHE 0.028 0.001 PHE B 756 TRP 0.008 0.001 TRP A 147 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (29243) covalent geometry : angle 0.57517 / 0.28 (39780) SS BOND : bond 0.00359 / 0.22 ( 41) SS BOND : angle 0.98162 / 0.66 ( 82) hydrogen bonds : bond 0.04217 / 2.77 ( 907) hydrogen bonds : angle 5.53711 / 3.78 ( 2418) Misc. bond : bond 0.00025 / 0.01 ( 3) link_BETA1-4 : bond 0.00572 / 0.36 ( 24) link_BETA1-4 : angle 1.34610 / 0.96 ( 72) link_NAG-ASN : bond 0.00422 / 0.33 ( 41) link_NAG-ASN : angle 2.33740 / 1.66 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 126 ILE cc_start: 0.8355 (tp) cc_final: 0.8056 (tp) REVERT: A 133 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: A 318 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: A 633 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6228 (t80) REVERT: A 742 ASP cc_start: 0.6669 (p0) cc_final: 0.6146 (t0) REVERT: B 84 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7131 (t80) REVERT: B 86 ASP cc_start: 0.5192 (OUTLIER) cc_final: 0.4543 (t0) REVERT: B 195 TYR cc_start: 0.8323 (m-80) cc_final: 0.8086 (t80) REVERT: B 314 ASN cc_start: 0.7339 (t0) cc_final: 0.7057 (t0) REVERT: B 448 TYR cc_start: 0.6604 (m-10) cc_final: 0.5593 (m-80) REVERT: B 777 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7701 (mt-10) REVERT: B 999 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 516 HIS cc_start: 0.8202 (m90) cc_final: 0.7723 (m90) REVERT: C 633 TYR cc_start: 0.8175 (t80) cc_final: 0.7659 (t80) REVERT: C 737 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8420 (ttm) REVERT: C 954 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 999 GLN cc_start: 0.8948 (tt0) cc_final: 0.8178 (tm-30) REVERT: H 87 MET cc_start: 0.5509 (pmm) cc_final: 0.5286 (pmm) REVERT: L 52 TYR cc_start: 0.8152 (p90) cc_final: 0.7867 (p90) outliers start: 44 outliers final: 31 residues processed: 172 average time/residue: 0.1515 time to fit residues: 44.7877 Evaluate side-chains 156 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 46 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 310 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.080433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.058779 restraints weight = 167185.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.060391 restraints weight = 79697.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.061307 restraints weight = 51534.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.061970 restraints weight = 39975.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.062250 restraints weight = 34652.072| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29352 Z= 0.213 Angle : 0.667 15.183 40057 Z= 0.328 Chirality : 0.046 0.453 4692 Planarity : 0.004 0.050 5032 Dihedral : 4.733 43.053 3783 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.85 % Favored : 93.12 % Rotamer: Outliers : 1.81 % Allowed : 16.39 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3488 helix: 0.34 (0.20), residues: 725 sheet: -0.36 (0.19), residues: 743 loop : -1.69 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 99 TYR 0.027 0.001 TYR C 498 PHE 0.045 0.002 PHE C 756 TRP 0.036 0.002 TRP C 102 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (29243) covalent geometry : angle 0.64991 / 0.32 (39780) SS BOND : bond 0.00371 / 0.20 ( 41) SS BOND : angle 1.31604 / 0.83 ( 82) hydrogen bonds : bond 0.05137 / 3.33 ( 907) hydrogen bonds : angle 5.82830 / 4.00 ( 2418) Misc. bond : bond 0.00023 / 0.01 ( 3) link_BETA1-4 : bond 0.00438 / 0.29 ( 24) link_BETA1-4 : angle 1.36699 / 0.98 ( 72) link_NAG-ASN : bond 0.00425 / 0.31 ( 41) link_NAG-ASN : angle 2.45186 / 1.69 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 115 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 126 ILE cc_start: 0.8336 (tp) cc_final: 0.8059 (tp) REVERT: A 133 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: A 318 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: A 633 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.6367 (t80) REVERT: B 84 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 86 ASP cc_start: 0.4687 (OUTLIER) cc_final: 0.4001 (t0) REVERT: B 195 TYR cc_start: 0.8372 (m-80) cc_final: 0.8113 (t80) REVERT: B 314 ASN cc_start: 0.7550 (t0) cc_final: 0.7163 (t0) REVERT: B 448 TYR cc_start: 0.7037 (m-10) cc_final: 0.6035 (m-80) REVERT: B 999 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8337 (tm-30) REVERT: C 516 HIS cc_start: 0.8116 (m90) cc_final: 0.7684 (m90) REVERT: C 633 TYR cc_start: 0.8244 (t80) cc_final: 0.7816 (t80) REVERT: C 737 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: C 954 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 999 GLN cc_start: 0.8833 (tt0) cc_final: 0.8269 (tm-30) REVERT: L 52 TYR cc_start: 0.8089 (p90) cc_final: 0.7797 (p90) outliers start: 56 outliers final: 41 residues processed: 162 average time/residue: 0.1388 time to fit residues: 39.2322 Evaluate side-chains 161 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 78 optimal weight: 0.9980 chunk 329 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN C 457 ASN H 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.073046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049141 restraints weight = 151952.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050801 restraints weight = 72519.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051803 restraints weight = 46864.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.052464 restraints weight = 36327.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052868 restraints weight = 31193.725| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29352 Z= 0.118 Angle : 0.614 12.542 40057 Z= 0.299 Chirality : 0.044 0.424 4692 Planarity : 0.004 0.050 5032 Dihedral : 4.564 41.254 3783 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 1.49 % Allowed : 16.68 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3488 helix: 0.47 (0.20), residues: 722 sheet: -0.22 (0.19), residues: 739 loop : -1.66 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.015 0.001 TYR C 165 PHE 0.043 0.001 PHE C 756 TRP 0.012 0.001 TRP C 102 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (29243) covalent geometry : angle 0.59753 / 0.30 (39780) SS BOND : bond 0.00278 / 0.18 ( 41) SS BOND : angle 1.11444 / 0.72 ( 82) hydrogen bonds : bond 0.04578 / 2.99 ( 907) hydrogen bonds : angle 5.64026 / 3.86 ( 2418) Misc. bond : bond 0.00010 / 0.01 ( 3) link_BETA1-4 : bond 0.00496 / 0.32 ( 24) link_BETA1-4 : angle 1.36976 / 0.97 ( 72) link_NAG-ASN : bond 0.00370 / 0.30 ( 41) link_NAG-ASN : angle 2.32025 / 1.61 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 126 ILE cc_start: 0.8399 (tp) cc_final: 0.8125 (tp) REVERT: A 133 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 318 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: A 633 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 84 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7132 (t80) REVERT: B 86 ASP cc_start: 0.5119 (OUTLIER) cc_final: 0.4449 (t0) REVERT: B 314 ASN cc_start: 0.7460 (t0) cc_final: 0.7086 (t0) REVERT: B 448 TYR cc_start: 0.6875 (m-10) cc_final: 0.5800 (m-80) REVERT: B 777 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 999 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 516 HIS cc_start: 0.8210 (m90) cc_final: 0.7735 (m90) REVERT: C 633 TYR cc_start: 0.8221 (t80) cc_final: 0.7714 (t80) REVERT: C 737 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8432 (ttm) REVERT: C 954 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8393 (tm-30) REVERT: H 106 PHE cc_start: 0.7660 (m-80) cc_final: 0.7181 (m-80) REVERT: L 52 TYR cc_start: 0.8150 (p90) cc_final: 0.7879 (p90) outliers start: 46 outliers final: 37 residues processed: 156 average time/residue: 0.1422 time to fit residues: 38.6640 Evaluate side-chains 160 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 129 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.072996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049091 restraints weight = 152973.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050741 restraints weight = 72587.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051782 restraints weight = 46952.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052409 restraints weight = 36253.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.052801 restraints weight = 31203.831| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 29352 Z= 0.154 Angle : 0.723 59.198 40057 Z= 0.393 Chirality : 0.045 0.425 4692 Planarity : 0.004 0.050 5032 Dihedral : 4.562 41.250 3783 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 1.72 % Allowed : 16.46 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3488 helix: 0.47 (0.20), residues: 722 sheet: -0.23 (0.19), residues: 729 loop : -1.65 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 99 TYR 0.023 0.001 TYR B 195 PHE 0.037 0.001 PHE C 756 TRP 0.009 0.001 TRP C 102 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (29243) covalent geometry : angle 0.70906 / 0.39 (39780) SS BOND : bond 0.00359 / 0.23 ( 41) SS BOND : angle 1.17602 / 0.73 ( 82) hydrogen bonds : bond 0.04655 / 3.05 ( 907) hydrogen bonds : angle 5.63789 / 3.86 ( 2418) Misc. bond : bond 0.00007 / 0.00 ( 3) link_BETA1-4 : bond 0.00463 / 0.31 ( 24) link_BETA1-4 : angle 1.38093 / 0.98 ( 72) link_NAG-ASN : bond 0.00368 / 0.30 ( 41) link_NAG-ASN : angle 2.32019 / 1.61 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.09 seconds wall clock time: 95 minutes 22.97 seconds (5722.97 seconds total)