Starting phenix.real_space_refine on Fri Feb 6 23:07:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7we8_32442/02_2026/7we8_32442.cif Found real_map, /net/cci-nas-00/data/ceres_data/7we8_32442/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/7we8_32442/02_2026/7we8_32442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7we8_32442/02_2026/7we8_32442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7we8_32442/02_2026/7we8_32442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7we8_32442/02_2026/7we8_32442.map" } 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-2.0-5952/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 24 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 dihedrals: 27 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.53, per 1000 atoms: 0.23 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: 2.64 Conformation dependent library (CDL) restraints added in 1.3 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: 1.17 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: 6.26 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 - 24.79: 17341 24.79 - 49.58: 826 49.58 - 74.37: 83 74.37 - 99.16: 46 99.16 - 123.95: 24 Dihedral angle restraints: 18320 sinusoidal: 8047 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 18317 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.400 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 14.729 123.949 11585 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 covalent geometry : bond 0.00387 (29243) covalent geometry : angle 0.66288 (39780) SS BOND : bond 0.00302 ( 41) SS BOND : angle 1.01161 ( 82) hydrogen bonds : bond 0.27070 ( 907) hydrogen bonds : angle 8.70942 ( 2418) Misc. bond : bond 0.00036 ( 3) link_BETA1-4 : bond 0.00496 ( 24) link_BETA1-4 : angle 1.62655 ( 72) link_NAG-ASN : bond 0.00599 ( 41) link_NAG-ASN : angle 3.13552 ( 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 : 1.074 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: 0.1740 time to fit residues: 51.4682 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 : 1.059 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.072159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048066 restraints weight = 143063.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049683 restraints weight = 68914.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050692 restraints weight = 44561.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051275 restraints weight = 34239.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051692 restraints weight = 29406.624| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1395 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= 0.217 Angle : 0.701 18.424 40057 Z= 0.352 Chirality : 0.047 0.525 4692 Planarity : 0.004 0.056 5032 Dihedral : 9.779 110.381 5224 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.81 % Allowed : 7.22 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3488 helix: -0.03 (0.20), residues: 697 sheet: -0.48 (0.19), residues: 746 loop : -1.72 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1104 TYR 0.020 0.002 TYR A 393 PHE 0.020 0.002 PHE B 426 TRP 0.024 0.001 TRP H 109 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00485 (29243) covalent geometry : angle 0.67658 (39780) SS BOND : bond 0.00316 ( 41) SS BOND : angle 1.16464 ( 82) hydrogen bonds : bond 0.07149 ( 907) hydrogen bonds : angle 6.80939 ( 2418) Misc. bond : bond 0.00022 ( 3) link_BETA1-4 : bond 0.00449 ( 24) link_BETA1-4 : angle 1.94361 ( 72) link_NAG-ASN : bond 0.00423 ( 41) link_NAG-ASN : angle 2.98997 ( 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 164 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8622 (p90) cc_final: 0.8419 (p90) REVERT: A 633 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.5989 (t80) REVERT: A 742 ASP cc_start: 0.7032 (p0) cc_final: 0.6373 (t0) REVERT: B 84 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 314 ASN cc_start: 0.7360 (t0) cc_final: 0.7131 (t0) REVERT: B 448 TYR cc_start: 0.6749 (m-10) cc_final: 0.5761 (m-80) REVERT: B 737 MET cc_start: 0.9282 (tpt) cc_final: 0.8843 (tpp) REVERT: C 119 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7736 (m-40) REVERT: C 424 ASP cc_start: 0.8829 (m-30) cc_final: 0.8600 (m-30) REVERT: C 516 HIS cc_start: 0.8212 (m90) cc_final: 0.7868 (m-70) REVERT: C 633 TYR cc_start: 0.8303 (t80) cc_final: 0.7855 (t80) REVERT: H 84 MET cc_start: 0.8240 (tpt) cc_final: 0.7981 (tpt) outliers start: 25 outliers final: 14 residues processed: 153 average time/residue: 0.1625 time to fit residues: 41.9674 Evaluate side-chains 131 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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: 7.9990 chunk 161 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 294 optimal weight: 0.0170 chunk 226 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 240 optimal weight: 9.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 898 GLN ** 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 622 HIS B 759 GLN C 119 ASN C 962 GLN C1007 GLN ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.071482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047342 restraints weight = 144823.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048970 restraints weight = 69620.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049988 restraints weight = 44955.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050606 restraints weight = 34499.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050976 restraints weight = 29502.188| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29352 Z= 0.205 Angle : 0.670 16.791 40057 Z= 0.333 Chirality : 0.047 0.524 4692 Planarity : 0.004 0.051 5032 Dihedral : 8.103 105.323 5224 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.39 % Allowed : 11.05 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3488 helix: -0.01 (0.20), residues: 700 sheet: -0.50 (0.19), residues: 725 loop : -1.72 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 100 TYR 0.018 0.001 TYR A 393 PHE 0.021 0.002 PHE B 133 TRP 0.019 0.001 TRP H 109 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00460 (29243) covalent geometry : angle 0.64619 (39780) SS BOND : bond 0.00286 ( 41) SS BOND : angle 1.04330 ( 82) hydrogen bonds : bond 0.06011 ( 907) hydrogen bonds : angle 6.39112 ( 2418) Misc. bond : bond 0.00014 ( 3) link_BETA1-4 : bond 0.00508 ( 24) link_BETA1-4 : angle 1.76984 ( 72) link_NAG-ASN : bond 0.00448 ( 41) link_NAG-ASN : angle 2.89659 ( 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 170 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8722 (p90) cc_final: 0.8478 (p90) REVERT: A 318 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: A 633 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6025 (t80) REVERT: A 742 ASP cc_start: 0.7009 (p0) cc_final: 0.6415 (t0) REVERT: B 84 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7387 (t80) REVERT: B 314 ASN cc_start: 0.7511 (t0) cc_final: 0.7233 (t0) REVERT: B 448 TYR cc_start: 0.6794 (m-10) cc_final: 0.5725 (m-80) REVERT: B 737 MET cc_start: 0.9305 (tpt) cc_final: 0.8923 (tpp) REVERT: B 999 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 119 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7567 (m-40) REVERT: C 165 TYR cc_start: 0.8473 (t80) cc_final: 0.8201 (t80) REVERT: C 516 HIS cc_start: 0.8274 (m90) cc_final: 0.7799 (m90) REVERT: C 633 TYR cc_start: 0.8414 (t80) cc_final: 0.7828 (t80) REVERT: C 737 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8519 (ttp) REVERT: H 87 MET cc_start: 0.5133 (pmm) cc_final: 0.4722 (pmm) outliers start: 43 outliers final: 26 residues processed: 159 average time/residue: 0.1656 time to fit residues: 44.2625 Evaluate side-chains 148 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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 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 11 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: 0.9980 chunk 215 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 277 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 759 GLN B1103 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.072438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048406 restraints weight = 142113.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050058 restraints weight = 67989.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051092 restraints weight = 43792.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051692 restraints weight = 33517.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052121 restraints weight = 28695.713| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29352 Z= 0.121 Angle : 0.606 16.378 40057 Z= 0.298 Chirality : 0.045 0.491 4692 Planarity : 0.004 0.061 5032 Dihedral : 7.064 102.421 5222 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.68 % Allowed : 12.34 % Favored : 85.97 % 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: -1.43 (0.14), residues: 3488 helix: 0.13 (0.20), residues: 706 sheet: -0.33 (0.19), residues: 737 loop : -1.64 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 99 TYR 0.015 0.001 TYR B1064 PHE 0.023 0.001 PHE L 103 TRP 0.013 0.001 TRP H 109 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00260 (29243) covalent geometry : angle 0.58220 (39780) SS BOND : bond 0.00258 ( 41) SS BOND : angle 0.87094 ( 82) hydrogen bonds : bond 0.05046 ( 907) hydrogen bonds : angle 6.02795 ( 2418) Misc. bond : bond 0.00017 ( 3) link_BETA1-4 : bond 0.00488 ( 24) link_BETA1-4 : angle 1.75624 ( 72) link_NAG-ASN : bond 0.00405 ( 41) link_NAG-ASN : angle 2.75921 ( 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 183 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 148 MET cc_start: 0.7314 (mmm) cc_final: 0.7100 (mmm) REVERT: A 235 PHE cc_start: 0.8709 (p90) cc_final: 0.8466 (p90) REVERT: A 633 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.6152 (t80) REVERT: A 742 ASP cc_start: 0.6863 (p0) cc_final: 0.6325 (t0) REVERT: B 84 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 314 ASN cc_start: 0.7329 (t0) cc_final: 0.7054 (t0) REVERT: B 448 TYR cc_start: 0.6729 (m-10) cc_final: 0.5921 (m-80) REVERT: B 737 MET cc_start: 0.9277 (tpt) cc_final: 0.8897 (tpp) REVERT: B 777 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7873 (mt-10) REVERT: B 783 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8255 (mmmt) REVERT: B 999 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 116 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8225 (tp) REVERT: C 165 TYR cc_start: 0.8231 (t80) cc_final: 0.7981 (t80) REVERT: C 516 HIS cc_start: 0.8238 (m90) cc_final: 0.7755 (m90) REVERT: C 633 TYR cc_start: 0.8302 (t80) cc_final: 0.7674 (t80) REVERT: C 952 ASN cc_start: 0.8686 (m-40) cc_final: 0.8211 (m110) REVERT: C 954 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 1047 MET cc_start: 0.8323 (ptp) cc_final: 0.7952 (mtm) REVERT: H 87 MET cc_start: 0.5324 (pmm) cc_final: 0.4957 (pmm) REVERT: H 106 PHE cc_start: 0.7732 (m-80) cc_final: 0.7221 (m-80) REVERT: L 52 TYR cc_start: 0.8067 (p90) cc_final: 0.7786 (p90) outliers start: 52 outliers final: 21 residues processed: 173 average time/residue: 0.1661 time to fit residues: 48.9434 Evaluate side-chains 144 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 163 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 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 86 ASP 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: 10.0000 chunk 175 optimal weight: 9.9990 chunk 247 optimal weight: 0.0980 chunk 266 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 346 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 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 759 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3666 r_free = 0.3666 target = 0.070683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046639 restraints weight = 144598.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048238 restraints weight = 69690.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049228 restraints weight = 45030.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049856 restraints weight = 34594.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050220 restraints weight = 29551.310| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29352 Z= 0.244 Angle : 0.694 15.384 40057 Z= 0.345 Chirality : 0.047 0.525 4692 Planarity : 0.004 0.052 5032 Dihedral : 7.043 99.941 5222 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.14 % Allowed : 13.86 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3488 helix: -0.03 (0.19), residues: 718 sheet: -0.45 (0.19), residues: 724 loop : -1.77 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 99 TYR 0.020 0.002 TYR B1064 PHE 0.025 0.002 PHE C 756 TRP 0.016 0.002 TRP B 255 HIS 0.012 0.002 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00551 (29243) covalent geometry : angle 0.67263 (39780) SS BOND : bond 0.00347 ( 41) SS BOND : angle 1.08263 ( 82) hydrogen bonds : bond 0.05742 ( 907) hydrogen bonds : angle 6.25732 ( 2418) Misc. bond : bond 0.00011 ( 3) link_BETA1-4 : bond 0.00420 ( 24) link_BETA1-4 : angle 1.76112 ( 72) link_NAG-ASN : bond 0.00497 ( 41) link_NAG-ASN : angle 2.84280 ( 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 179 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 117 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8457 (mm) REVERT: A 318 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: A 633 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.6258 (t80) REVERT: A 983 LYS cc_start: 0.7860 (pttt) cc_final: 0.6837 (mmtm) REVERT: B 84 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7269 (t80) REVERT: B 314 ASN cc_start: 0.7516 (t0) cc_final: 0.7118 (t0) REVERT: B 448 TYR cc_start: 0.6662 (m-10) cc_final: 0.5686 (m-80) REVERT: B 783 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8369 (mmmt) REVERT: B 999 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 126 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8404 (mm) REVERT: C 165 TYR cc_start: 0.8342 (t80) cc_final: 0.8115 (t80) REVERT: C 516 HIS cc_start: 0.8259 (m90) cc_final: 0.7970 (m-70) REVERT: C 633 TYR cc_start: 0.8468 (t80) cc_final: 0.7981 (t80) REVERT: C 737 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8580 (ttm) REVERT: C 954 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8561 (tm-30) REVERT: H 87 MET cc_start: 0.5329 (pmm) cc_final: 0.4972 (pmm) REVERT: H 106 PHE cc_start: 0.7799 (m-80) cc_final: 0.7358 (m-80) REVERT: L 52 TYR cc_start: 0.8109 (p90) cc_final: 0.7833 (p90) outliers start: 66 outliers final: 43 residues processed: 170 average time/residue: 0.1582 time to fit residues: 46.4989 Evaluate side-chains 158 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 139 LEU 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 528 THR Chi-restraints excluded: chain B residue 596 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 60 optimal weight: 7.9990 chunk 46 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 300 optimal weight: 0.0270 chunk 198 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 312 optimal weight: 0.1980 chunk 343 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN C 577 GLN C 622 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.073853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.049924 restraints weight = 150563.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051621 restraints weight = 72170.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052659 restraints weight = 46688.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053305 restraints weight = 36134.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053678 restraints weight = 31024.794| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29352 Z= 0.107 Angle : 0.601 15.949 40057 Z= 0.294 Chirality : 0.045 0.475 4692 Planarity : 0.004 0.051 5032 Dihedral : 6.190 96.437 5222 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.52 % Allowed : 15.42 % Favored : 83.06 % 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: -1.37 (0.14), residues: 3488 helix: 0.28 (0.20), residues: 709 sheet: -0.28 (0.19), residues: 733 loop : -1.65 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.017 0.001 TYR B1152 PHE 0.023 0.001 PHE B 133 TRP 0.009 0.001 TRP B 255 HIS 0.005 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00222 (29243) covalent geometry : angle 0.57821 (39780) SS BOND : bond 0.00270 ( 41) SS BOND : angle 0.86528 ( 82) hydrogen bonds : bond 0.04664 ( 907) hydrogen bonds : angle 5.80511 ( 2418) Misc. bond : bond 0.00018 ( 3) link_BETA1-4 : bond 0.00497 ( 24) link_BETA1-4 : angle 1.65328 ( 72) link_NAG-ASN : bond 0.00435 ( 41) link_NAG-ASN : angle 2.69796 ( 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 172 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 235 PHE cc_start: 0.8723 (p90) cc_final: 0.8467 (p90) REVERT: A 318 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: A 633 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6175 (t80) REVERT: A 742 ASP cc_start: 0.6753 (p0) cc_final: 0.6254 (t0) REVERT: B 84 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7103 (t80) REVERT: B 314 ASN cc_start: 0.7301 (t0) cc_final: 0.7036 (t0) REVERT: B 448 TYR cc_start: 0.6913 (m-10) cc_final: 0.5839 (m-80) REVERT: B 783 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8405 (mmmt) REVERT: B 999 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8260 (tm-30) REVERT: C 165 TYR cc_start: 0.8266 (t80) cc_final: 0.8011 (t80) REVERT: C 516 HIS cc_start: 0.8307 (m90) cc_final: 0.7810 (m90) REVERT: C 633 TYR cc_start: 0.8179 (t80) cc_final: 0.7700 (t80) REVERT: C 737 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8455 (ttm) REVERT: C 952 ASN cc_start: 0.8646 (m-40) cc_final: 0.8198 (m110) REVERT: C 954 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8472 (tm-30) REVERT: H 87 MET cc_start: 0.5414 (pmm) cc_final: 0.5093 (pmm) REVERT: L 52 TYR cc_start: 0.8157 (p90) cc_final: 0.7887 (p90) outliers start: 47 outliers final: 28 residues processed: 162 average time/residue: 0.1585 time to fit residues: 43.6685 Evaluate side-chains 149 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE 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 814 PHE Chi-restraints excluded: chain A residue 906 ILE 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 309 ILE Chi-restraints excluded: chain B residue 326 PHE 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 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 639 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 26 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 0.4980 chunk 346 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.081697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.060253 restraints weight = 166332.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.061893 restraints weight = 78772.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062879 restraints weight = 50654.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.063429 restraints weight = 39238.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063831 restraints weight = 34124.772| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29352 Z= 0.142 Angle : 0.607 15.394 40057 Z= 0.298 Chirality : 0.044 0.481 4692 Planarity : 0.004 0.050 5032 Dihedral : 6.086 93.764 5222 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.72 % Allowed : 15.78 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.14), residues: 3488 helix: 0.32 (0.20), residues: 718 sheet: -0.25 (0.19), residues: 749 loop : -1.65 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.015 0.001 TYR B1064 PHE 0.027 0.001 PHE B 756 TRP 0.010 0.001 TRP H 109 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00319 (29243) covalent geometry : angle 0.58483 (39780) SS BOND : bond 0.00268 ( 41) SS BOND : angle 1.07957 ( 82) hydrogen bonds : bond 0.04746 ( 907) hydrogen bonds : angle 5.78487 ( 2418) Misc. bond : bond 0.00014 ( 3) link_BETA1-4 : bond 0.00415 ( 24) link_BETA1-4 : angle 1.59619 ( 72) link_NAG-ASN : bond 0.00389 ( 41) link_NAG-ASN : angle 2.68770 ( 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 175 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: A 633 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 742 ASP cc_start: 0.6713 (p0) cc_final: 0.6295 (t0) REVERT: B 84 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7215 (t80) REVERT: B 314 ASN cc_start: 0.7410 (t0) cc_final: 0.7067 (t0) REVERT: B 448 TYR cc_start: 0.6892 (m-10) cc_final: 0.5827 (m-80) REVERT: B 999 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8268 (tm-30) REVERT: C 516 HIS cc_start: 0.8140 (m90) cc_final: 0.7690 (m90) REVERT: C 633 TYR cc_start: 0.8145 (t80) cc_final: 0.7731 (t80) REVERT: C 737 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8337 (ttm) REVERT: C 954 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 999 GLN cc_start: 0.8855 (tt0) cc_final: 0.8237 (tm-30) REVERT: H 87 MET cc_start: 0.5547 (pmm) cc_final: 0.5273 (pmm) REVERT: H 106 PHE cc_start: 0.7790 (m-80) cc_final: 0.7329 (m-80) REVERT: L 52 TYR cc_start: 0.8082 (p90) cc_final: 0.7803 (p90) outliers start: 53 outliers final: 38 residues processed: 162 average time/residue: 0.1548 time to fit residues: 43.4770 Evaluate side-chains 158 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 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 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 429 CYS Chi-restraints excluded: chain C residue 16 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 318 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 200 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A1051 GLN B 178 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.083061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.061891 restraints weight = 167356.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.063555 restraints weight = 78283.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.064559 restraints weight = 49782.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.065184 restraints weight = 38330.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.065520 restraints weight = 33008.334| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29352 Z= 0.102 Angle : 0.585 15.167 40057 Z= 0.285 Chirality : 0.044 0.457 4692 Planarity : 0.003 0.051 5032 Dihedral : 5.660 89.569 5222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.46 % Allowed : 16.46 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3488 helix: 0.44 (0.20), residues: 721 sheet: -0.09 (0.19), residues: 741 loop : -1.60 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.016 0.001 TYR C 165 PHE 0.029 0.001 PHE B 756 TRP 0.009 0.001 TRP H 109 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00217 (29243) covalent geometry : angle 0.56355 (39780) SS BOND : bond 0.00339 ( 41) SS BOND : angle 0.97987 ( 82) hydrogen bonds : bond 0.04186 ( 907) hydrogen bonds : angle 5.55592 ( 2418) Misc. bond : bond 0.00015 ( 3) link_BETA1-4 : bond 0.00482 ( 24) link_BETA1-4 : angle 1.55226 ( 72) link_NAG-ASN : bond 0.00419 ( 41) link_NAG-ASN : angle 2.58895 ( 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 176 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 633 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.6230 (t80) REVERT: A 742 ASP cc_start: 0.6605 (p0) cc_final: 0.6174 (t0) REVERT: B 84 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7169 (t80) REVERT: B 195 TYR cc_start: 0.8427 (m-80) cc_final: 0.8018 (t80) REVERT: B 314 ASN cc_start: 0.7307 (t0) cc_final: 0.7019 (t0) REVERT: B 448 TYR cc_start: 0.6897 (m-10) cc_final: 0.5875 (m-80) REVERT: B 777 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 999 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 516 HIS cc_start: 0.8146 (m90) cc_final: 0.7725 (m90) REVERT: C 633 TYR cc_start: 0.8100 (t80) cc_final: 0.7662 (t80) REVERT: C 737 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8275 (ttm) REVERT: C 999 GLN cc_start: 0.8819 (tt0) cc_final: 0.8174 (tm-30) REVERT: H 87 MET cc_start: 0.5587 (pmm) cc_final: 0.5340 (pmm) REVERT: L 52 TYR cc_start: 0.8154 (p90) cc_final: 0.7877 (p90) outliers start: 45 outliers final: 35 residues processed: 167 average time/residue: 0.1576 time to fit residues: 45.5380 Evaluate side-chains 154 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 103 ILE 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 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 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 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 C residue 16 VAL 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 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 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: 0.9980 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 301 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.081510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.060047 restraints weight = 167018.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.061675 restraints weight = 78944.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.062666 restraints weight = 50898.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.063207 restraints weight = 39468.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.063632 restraints weight = 34301.491| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29352 Z= 0.158 Angle : 0.624 14.669 40057 Z= 0.307 Chirality : 0.044 0.480 4692 Planarity : 0.004 0.049 5032 Dihedral : 5.822 87.277 5222 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.72 % Allowed : 16.39 % Favored : 81.89 % 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: -1.25 (0.14), residues: 3488 helix: 0.44 (0.20), residues: 721 sheet: -0.21 (0.19), residues: 761 loop : -1.62 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 762 TYR 0.015 0.001 TYR B1064 PHE 0.035 0.001 PHE C 756 TRP 0.011 0.001 TRP H 109 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00357 (29243) covalent geometry : angle 0.60327 (39780) SS BOND : bond 0.00331 ( 41) SS BOND : angle 1.12225 ( 82) hydrogen bonds : bond 0.04631 ( 907) hydrogen bonds : angle 5.65018 ( 2418) Misc. bond : bond 0.00009 ( 3) link_BETA1-4 : bond 0.00401 ( 24) link_BETA1-4 : angle 1.53310 ( 72) link_NAG-ASN : bond 0.00386 ( 41) link_NAG-ASN : angle 2.64070 ( 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 170 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 318 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 633 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6337 (t80) REVERT: A 742 ASP cc_start: 0.6663 (p0) cc_final: 0.6214 (t0) REVERT: B 84 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7196 (t80) REVERT: B 195 TYR cc_start: 0.8464 (m-80) cc_final: 0.8103 (t80) REVERT: B 314 ASN cc_start: 0.7468 (t0) cc_final: 0.7149 (t0) REVERT: B 448 TYR cc_start: 0.6940 (m-10) cc_final: 0.5875 (m-80) REVERT: B 633 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6122 (t80) REVERT: B 777 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 999 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 516 HIS cc_start: 0.8123 (m90) cc_final: 0.7670 (m90) REVERT: C 633 TYR cc_start: 0.8191 (t80) cc_final: 0.7773 (t80) REVERT: C 737 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8205 (ttp) REVERT: H 87 MET cc_start: 0.5674 (pmm) cc_final: 0.5362 (pmm) REVERT: H 106 PHE cc_start: 0.7769 (m-80) cc_final: 0.7292 (m-80) REVERT: L 35 TYR cc_start: 0.6763 (m-80) cc_final: 0.6544 (m-80) REVERT: L 52 TYR cc_start: 0.8127 (p90) cc_final: 0.7856 (p90) outliers start: 53 outliers final: 41 residues processed: 160 average time/residue: 0.1537 time to fit residues: 42.7009 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 : 0.710 ------------------------------------------------------------------------------- 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 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 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 705 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 956 LEU 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 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 633 TYR 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 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 874 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain H residue 12 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 78 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 302 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 overall best weight: 3.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 178 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** C1139 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 = 0.3943 r_free = 0.3943 target = 0.080442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.058852 restraints weight = 166641.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.060462 restraints weight = 79154.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.061432 restraints weight = 51212.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.062047 restraints weight = 39842.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 74)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.062419 restraints weight = 34399.844| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29352 Z= 0.193 Angle : 0.665 14.062 40057 Z= 0.327 Chirality : 0.045 0.511 4692 Planarity : 0.004 0.050 5032 Dihedral : 6.206 84.824 5222 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.65 % Favored : 93.32 % Rotamer: Outliers : 1.68 % Allowed : 16.59 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.14), residues: 3488 helix: 0.35 (0.20), residues: 721 sheet: -0.28 (0.20), residues: 716 loop : -1.72 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.017 0.001 TYR B1064 PHE 0.032 0.002 PHE B1145 TRP 0.012 0.001 TRP H 109 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00437 (29243) covalent geometry : angle 0.64455 (39780) SS BOND : bond 0.00377 ( 41) SS BOND : angle 1.29507 ( 82) hydrogen bonds : bond 0.05099 ( 907) hydrogen bonds : angle 5.88178 ( 2418) Misc. bond : bond 0.00015 ( 3) link_BETA1-4 : bond 0.00424 ( 24) link_BETA1-4 : angle 1.52202 ( 72) link_NAG-ASN : bond 0.00418 ( 41) link_NAG-ASN : angle 2.70586 ( 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 164 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8653 (mp) REVERT: A 633 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.6388 (t80) REVERT: B 84 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7275 (t80) REVERT: B 195 TYR cc_start: 0.8407 (m-80) cc_final: 0.8060 (t80) REVERT: B 314 ASN cc_start: 0.7551 (t0) cc_final: 0.7190 (t0) REVERT: B 448 TYR cc_start: 0.6903 (m-10) cc_final: 0.5886 (m-80) REVERT: B 633 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6026 (t80) REVERT: B 999 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 516 HIS cc_start: 0.8130 (m90) cc_final: 0.7687 (m90) REVERT: C 633 TYR cc_start: 0.8206 (t80) cc_final: 0.7778 (t80) REVERT: C 737 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8357 (ttm) REVERT: H 87 MET cc_start: 0.5708 (pmm) cc_final: 0.5426 (pmm) REVERT: L 52 TYR cc_start: 0.8063 (p90) cc_final: 0.7777 (p90) outliers start: 52 outliers final: 42 residues processed: 156 average time/residue: 0.1630 time to fit residues: 44.0925 Evaluate side-chains 156 residues out of total 3087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 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 630 TRP 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 791 ILE Chi-restraints excluded: chain A residue 814 PHE Chi-restraints excluded: chain A residue 956 LEU 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 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 633 TYR 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 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 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 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: 1.9990 chunk 12 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 329 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 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 622 HIS ** C1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.072915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049002 restraints weight = 153005.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050673 restraints weight = 73177.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051711 restraints weight = 47379.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.052349 restraints weight = 36577.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052760 restraints weight = 31424.539| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29352 Z= 0.119 Angle : 0.613 14.122 40057 Z= 0.300 Chirality : 0.044 0.479 4692 Planarity : 0.004 0.050 5032 Dihedral : 5.853 81.340 5222 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 1.62 % Allowed : 16.78 % Favored : 81.60 % 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: -1.24 (0.14), residues: 3488 helix: 0.47 (0.20), residues: 726 sheet: -0.18 (0.19), residues: 744 loop : -1.62 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 99 TYR 0.018 0.001 TYR C 366 PHE 0.044 0.001 PHE C 756 TRP 0.010 0.001 TRP H 109 HIS 0.003 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00265 (29243) covalent geometry : angle 0.59208 (39780) SS BOND : bond 0.00314 ( 41) SS BOND : angle 1.18321 ( 82) hydrogen bonds : bond 0.04476 ( 907) hydrogen bonds : angle 5.60475 ( 2418) Misc. bond : bond 0.00015 ( 3) link_BETA1-4 : bond 0.00450 ( 24) link_BETA1-4 : angle 1.52405 ( 72) link_NAG-ASN : bond 0.00382 ( 41) link_NAG-ASN : angle 2.58929 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6064.37 seconds wall clock time: 105 minutes 10.04 seconds (6310.04 seconds total)