Starting phenix.real_space_refine on Fri Mar 6 11:36:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.map" model { file = "/net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r40_14250/03_2026/7r40_14250.cif" } resolution = 2.9 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= 0.001 sd= 0.027 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 132 5.16 5 C 19449 2.51 5 N 5052 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30615 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "C" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} 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: 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: "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: 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: "Q" 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: "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: "A" 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: "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: 6.81, per 1000 atoms: 0.22 Number of scatterers: 30615 At special positions: 0 Unit cell: (152.52, 158.72, 230.64, 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 132 16.00 O 5982 8.00 N 5052 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " 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 Q 1 " - " NAG Q 2 " " 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-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.846A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.527A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.608A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 8.036A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.020A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.538A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.711A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.846A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 98 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 109 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.021A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.537A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.311A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.732A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.205A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.649A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 98 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 109 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.539A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.397A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS E 98 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE E 109 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 92 " --> pdb=" O VAL E 116 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2505 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: 7.44 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9759 1.35 - 1.47: 8051 1.47 - 1.60: 13339 1.60 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 31317 Sorted by residual: bond pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 ... (remaining 31312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 41907 2.54 - 5.08: 572 5.08 - 7.62: 88 7.62 - 10.16: 21 10.16 - 12.71: 3 Bond angle restraints: 42591 Sorted by residual: angle pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.31 12.69 1.40e+00 5.10e-01 8.22e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.33 12.67 1.40e+00 5.10e-01 8.19e+01 angle pdb=" C LYS A 529 " pdb=" CA LYS A 529 " pdb=" CB LYS A 529 " ideal model delta sigma weight residual 115.89 109.77 6.12 1.32e+00 5.74e-01 2.15e+01 angle pdb=" C LYS C 529 " pdb=" CA LYS C 529 " pdb=" CB LYS C 529 " ideal model delta sigma weight residual 115.89 109.80 6.09 1.32e+00 5.74e-01 2.13e+01 ... (remaining 42586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17418 17.63 - 35.26: 1421 35.26 - 52.89: 313 52.89 - 70.52: 52 70.52 - 88.15: 53 Dihedral angle restraints: 19257 sinusoidal: 8148 harmonic: 11109 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.11 -61.89 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.14 -61.86 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.15 -61.85 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4299 0.083 - 0.167: 596 0.167 - 0.250: 19 0.250 - 0.333: 0 0.333 - 0.416: 6 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 4917 not shown) Planarity restraints: 5487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO A 899 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO C 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " 0.066 5.00e-02 4.00e+02 ... (remaining 5484 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9813 2.84 - 3.35: 24845 3.35 - 3.87: 49774 3.87 - 4.38: 54111 4.38 - 4.90: 93784 Nonbonded interactions: 232327 Sorted by model distance: nonbonded pdb=" O THR B1116 " pdb=" OG1 THR B1120 " model vdw 2.324 3.040 nonbonded pdb=" O THR C1116 " pdb=" OG1 THR C1120 " model vdw 2.325 3.040 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.326 3.040 ... (remaining 232322 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.270 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 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 0.058 31419 Z= 0.191 Angle : 0.747 13.268 42840 Z= 0.373 Chirality : 0.052 0.416 4920 Planarity : 0.007 0.130 5448 Dihedral : 13.999 88.155 11991 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.66 (0.12), residues: 3780 helix: -3.72 (0.09), residues: 603 sheet: -0.50 (0.18), residues: 831 loop : -1.75 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 577 TYR 0.010 0.001 TYR C 351 PHE 0.016 0.001 PHE G 49 TRP 0.006 0.001 TRP D 47 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00377 (31317) covalent geometry : angle 0.73238 (42591) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.00020 ( 96) hydrogen bonds : bond 0.28524 ( 871) hydrogen bonds : angle 10.33944 ( 2505) Misc. bond : bond 0.00105 ( 3) link_BETA1-4 : bond 0.00740 ( 12) link_BETA1-4 : angle 1.28309 ( 36) link_NAG-ASN : bond 0.00566 ( 39) link_NAG-ASN : angle 2.74865 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6741 (m) cc_final: 0.6457 (t) REVERT: A 58 PHE cc_start: 0.7383 (m-10) cc_final: 0.7020 (m-80) REVERT: A 129 LYS cc_start: 0.6947 (mppt) cc_final: 0.6628 (mppt) REVERT: A 310 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7785 (ttpp) REVERT: A 319 ARG cc_start: 0.7123 (ptp90) cc_final: 0.6697 (ptt180) REVERT: A 374 PHE cc_start: 0.6948 (m-80) cc_final: 0.6657 (m-10) REVERT: A 511 VAL cc_start: 0.8113 (t) cc_final: 0.7891 (p) REVERT: A 572 THR cc_start: 0.8105 (t) cc_final: 0.7669 (p) REVERT: A 606 ASN cc_start: 0.8119 (m-40) cc_final: 0.7883 (m-40) REVERT: A 612 TYR cc_start: 0.8288 (m-80) cc_final: 0.7890 (m-80) REVERT: A 671 CYS cc_start: 0.5055 (m) cc_final: 0.4817 (m) REVERT: A 673 SER cc_start: 0.8365 (t) cc_final: 0.8029 (p) REVERT: A 725 GLU cc_start: 0.7325 (tt0) cc_final: 0.7069 (tt0) REVERT: A 736 VAL cc_start: 0.7929 (t) cc_final: 0.7715 (m) REVERT: A 790 LYS cc_start: 0.7401 (mmpt) cc_final: 0.7087 (mmpt) REVERT: A 933 LYS cc_start: 0.7924 (mttt) cc_final: 0.7710 (mttt) REVERT: A 936 ASP cc_start: 0.7675 (m-30) cc_final: 0.7327 (m-30) REVERT: A 947 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7615 (mtpp) REVERT: A 964 LYS cc_start: 0.7858 (mttt) cc_final: 0.7642 (mttt) REVERT: A 975 SER cc_start: 0.8576 (p) cc_final: 0.8229 (t) REVERT: A 1045 LYS cc_start: 0.7927 (mttt) cc_final: 0.7533 (mttt) REVERT: A 1082 CYS cc_start: 0.5882 (t) cc_final: 0.5446 (t) REVERT: A 1086 LYS cc_start: 0.6615 (mtmm) cc_final: 0.6110 (mtmm) REVERT: A 1092 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 1101 HIS cc_start: 0.7474 (m-70) cc_final: 0.7185 (m170) REVERT: A 1138 TYR cc_start: 0.7675 (t80) cc_final: 0.7343 (t80) REVERT: L 71 PHE cc_start: 0.5786 (t80) cc_final: 0.5218 (t80) REVERT: B 53 ASP cc_start: 0.5842 (t0) cc_final: 0.5596 (t0) REVERT: B 54 LEU cc_start: 0.7550 (mm) cc_final: 0.7343 (mm) REVERT: B 153 MET cc_start: 0.4381 (mpp) cc_final: 0.4165 (mpp) REVERT: B 192 PHE cc_start: 0.7684 (m-80) cc_final: 0.7336 (m-80) REVERT: B 269 TYR cc_start: 0.6950 (m-80) cc_final: 0.6349 (m-80) REVERT: B 319 ARG cc_start: 0.7154 (ptp90) cc_final: 0.6840 (ptt180) REVERT: B 340 GLU cc_start: 0.6812 (mp0) cc_final: 0.6420 (mp0) REVERT: B 374 PHE cc_start: 0.6793 (m-80) cc_final: 0.6207 (m-80) REVERT: B 427 ASP cc_start: 0.7460 (p0) cc_final: 0.7219 (p0) REVERT: B 511 VAL cc_start: 0.8281 (t) cc_final: 0.7950 (p) REVERT: B 541 PHE cc_start: 0.6432 (p90) cc_final: 0.6086 (p90) REVERT: B 586 ASP cc_start: 0.7245 (m-30) cc_final: 0.6991 (m-30) REVERT: B 612 TYR cc_start: 0.8224 (m-80) cc_final: 0.7990 (m-80) REVERT: B 655 HIS cc_start: 0.7519 (t70) cc_final: 0.7298 (t-170) REVERT: B 675 GLN cc_start: 0.7175 (mt0) cc_final: 0.6971 (mt0) REVERT: B 725 GLU cc_start: 0.7045 (tt0) cc_final: 0.6786 (tt0) REVERT: B 731 MET cc_start: 0.8013 (mtm) cc_final: 0.7718 (mtm) REVERT: B 764 ASN cc_start: 0.7217 (m-40) cc_final: 0.7016 (m-40) REVERT: B 772 VAL cc_start: 0.8514 (p) cc_final: 0.8196 (t) REVERT: B 790 LYS cc_start: 0.7328 (mmpt) cc_final: 0.6851 (mmmt) REVERT: B 933 LYS cc_start: 0.7898 (mttt) cc_final: 0.7306 (mmtm) REVERT: B 947 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7507 (mtpp) REVERT: B 950 ASP cc_start: 0.7513 (m-30) cc_final: 0.7108 (m-30) REVERT: B 1050 MET cc_start: 0.8046 (ptm) cc_final: 0.7769 (ptm) REVERT: B 1082 CYS cc_start: 0.5844 (t) cc_final: 0.5395 (t) REVERT: B 1138 TYR cc_start: 0.7570 (t80) cc_final: 0.7163 (t80) REVERT: F 35 TRP cc_start: 0.4773 (m-10) cc_final: 0.4558 (m-10) REVERT: F 71 PHE cc_start: 0.5833 (t80) cc_final: 0.5451 (t80) REVERT: C 29 THR cc_start: 0.7105 (m) cc_final: 0.6759 (t) REVERT: C 45 SER cc_start: 0.7750 (t) cc_final: 0.7384 (p) REVERT: C 47 VAL cc_start: 0.8166 (m) cc_final: 0.7951 (m) REVERT: C 53 ASP cc_start: 0.6313 (t0) cc_final: 0.6031 (t70) REVERT: C 54 LEU cc_start: 0.7405 (mm) cc_final: 0.7091 (mm) REVERT: C 138 ASP cc_start: 0.6414 (t0) cc_final: 0.6155 (t0) REVERT: C 192 PHE cc_start: 0.7483 (m-80) cc_final: 0.7215 (m-80) REVERT: C 237 ARG cc_start: 0.6765 (mtp85) cc_final: 0.6230 (mpp80) REVERT: C 340 GLU cc_start: 0.6712 (mp0) cc_final: 0.6468 (mp0) REVERT: C 374 PHE cc_start: 0.6729 (m-80) cc_final: 0.6323 (m-80) REVERT: C 427 ASP cc_start: 0.7512 (p0) cc_final: 0.7244 (p0) REVERT: C 453 TYR cc_start: 0.6947 (p90) cc_final: 0.5538 (p90) REVERT: C 511 VAL cc_start: 0.8263 (t) cc_final: 0.7969 (p) REVERT: C 532 ASN cc_start: 0.8300 (t0) cc_final: 0.8088 (t0) REVERT: C 541 PHE cc_start: 0.6507 (p90) cc_final: 0.5978 (p90) REVERT: C 553 THR cc_start: 0.8147 (p) cc_final: 0.7928 (p) REVERT: C 572 THR cc_start: 0.8110 (m) cc_final: 0.7857 (p) REVERT: C 612 TYR cc_start: 0.8135 (m-80) cc_final: 0.7789 (m-80) REVERT: C 725 GLU cc_start: 0.7187 (tt0) cc_final: 0.6903 (tt0) REVERT: C 772 VAL cc_start: 0.8443 (p) cc_final: 0.8235 (t) REVERT: C 773 GLU cc_start: 0.7237 (pt0) cc_final: 0.7033 (tt0) REVERT: C 790 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7024 (mmpt) REVERT: C 868 GLU cc_start: 0.7122 (mp0) cc_final: 0.6829 (mp0) REVERT: C 933 LYS cc_start: 0.7927 (mttt) cc_final: 0.7419 (mptt) REVERT: C 936 ASP cc_start: 0.7347 (m-30) cc_final: 0.7138 (m-30) REVERT: C 947 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7665 (mtpp) REVERT: C 950 ASP cc_start: 0.7478 (m-30) cc_final: 0.7165 (m-30) REVERT: C 954 GLN cc_start: 0.7959 (mt0) cc_final: 0.7629 (mt0) REVERT: C 964 LYS cc_start: 0.7848 (mttt) cc_final: 0.7553 (mttt) REVERT: C 975 SER cc_start: 0.8623 (p) cc_final: 0.8323 (t) REVERT: C 1091 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7369 (mmt90) REVERT: C 1101 HIS cc_start: 0.7635 (m-70) cc_final: 0.7426 (m-70) REVERT: G 71 PHE cc_start: 0.5991 (t80) cc_final: 0.5569 (t80) REVERT: G 92 PHE cc_start: 0.6863 (m-80) cc_final: 0.6616 (m-80) REVERT: E 68 PHE cc_start: 0.7039 (m-10) cc_final: 0.6694 (m-10) outliers start: 0 outliers final: 4 residues processed: 776 average time/residue: 0.6058 time to fit residues: 558.7633 Evaluate side-chains 659 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 655 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 540 ASN A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1010 GLN L 27 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 448 ASN B 540 ASN B 607 GLN B 613 GLN B 804 GLN B 935 GLN B 957 GLN B 960 ASN B 992 GLN B1101 HIS C 49 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN C 960 ASN C 992 GLN C1010 GLN E 112 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.205470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.184226 restraints weight = 59536.510| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.87 r_work: 0.4128 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31419 Z= 0.189 Angle : 0.721 21.691 42840 Z= 0.354 Chirality : 0.049 0.427 4920 Planarity : 0.005 0.062 5448 Dihedral : 7.128 87.846 5209 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.32 % Allowed : 11.62 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.74 (0.13), residues: 3780 helix: -0.63 (0.19), residues: 615 sheet: -0.52 (0.17), residues: 876 loop : -1.61 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 38 TYR 0.020 0.002 TYR D 60 PHE 0.023 0.002 PHE A 490 TRP 0.016 0.002 TRP L 35 HIS 0.006 0.001 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00437 (31317) covalent geometry : angle 0.69275 (42591) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.30652 ( 96) hydrogen bonds : bond 0.04764 ( 871) hydrogen bonds : angle 6.45354 ( 2505) Misc. bond : bond 0.00142 ( 3) link_BETA1-4 : bond 0.00458 ( 12) link_BETA1-4 : angle 1.11346 ( 36) link_NAG-ASN : bond 0.00559 ( 39) link_NAG-ASN : angle 3.72602 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 711 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7792 (m-10) cc_final: 0.7417 (m-10) REVERT: A 153 MET cc_start: 0.3871 (mpp) cc_final: 0.3560 (mpp) REVERT: A 208 THR cc_start: 0.8254 (t) cc_final: 0.8012 (p) REVERT: A 319 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7238 (ptt180) REVERT: A 429 PHE cc_start: 0.5602 (t80) cc_final: 0.5368 (t80) REVERT: A 572 THR cc_start: 0.8366 (t) cc_final: 0.8096 (p) REVERT: A 651 ILE cc_start: 0.8761 (mm) cc_final: 0.8514 (mp) REVERT: A 673 SER cc_start: 0.8492 (t) cc_final: 0.8129 (p) REVERT: A 719 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8130 (p) REVERT: A 725 GLU cc_start: 0.7850 (tt0) cc_final: 0.7500 (tt0) REVERT: A 736 VAL cc_start: 0.8149 (t) cc_final: 0.7818 (m) REVERT: A 776 LYS cc_start: 0.8013 (tmmt) cc_final: 0.7748 (ttpp) REVERT: A 790 LYS cc_start: 0.7540 (mmpt) cc_final: 0.7287 (mmpt) REVERT: A 811 LYS cc_start: 0.6940 (mmpt) cc_final: 0.6516 (mtpt) REVERT: A 933 LYS cc_start: 0.7961 (mttt) cc_final: 0.7583 (mtmm) REVERT: A 936 ASP cc_start: 0.7534 (m-30) cc_final: 0.7256 (m-30) REVERT: A 975 SER cc_start: 0.8672 (p) cc_final: 0.8343 (t) REVERT: A 1038 LYS cc_start: 0.7842 (tppt) cc_final: 0.7584 (mmmt) REVERT: A 1045 LYS cc_start: 0.8368 (mttt) cc_final: 0.7896 (mttt) REVERT: A 1086 LYS cc_start: 0.6958 (mtmm) cc_final: 0.6349 (mtmm) REVERT: A 1101 HIS cc_start: 0.8107 (m-70) cc_final: 0.7895 (m-70) REVERT: A 1141 LEU cc_start: 0.7645 (tm) cc_final: 0.7402 (tt) REVERT: L 81 GLU cc_start: 0.7885 (mp0) cc_final: 0.7567 (mp0) REVERT: H 34 MET cc_start: 0.6398 (ppp) cc_final: 0.5935 (ppp) REVERT: B 49 HIS cc_start: 0.8101 (t-90) cc_final: 0.7800 (t70) REVERT: B 53 ASP cc_start: 0.6622 (t0) cc_final: 0.6331 (t0) REVERT: B 54 LEU cc_start: 0.7968 (mm) cc_final: 0.7731 (mm) REVERT: B 61 ASN cc_start: 0.6700 (p0) cc_final: 0.6452 (p0) REVERT: B 153 MET cc_start: 0.4926 (mpp) cc_final: 0.4641 (mpp) REVERT: B 192 PHE cc_start: 0.8356 (m-80) cc_final: 0.8130 (m-80) REVERT: B 286 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7664 (t) REVERT: B 319 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7457 (ptt180) REVERT: B 340 GLU cc_start: 0.7324 (mp0) cc_final: 0.6862 (mp0) REVERT: B 427 ASP cc_start: 0.7906 (p0) cc_final: 0.7681 (p0) REVERT: B 497 PHE cc_start: 0.4416 (m-10) cc_final: 0.3680 (m-10) REVERT: B 511 VAL cc_start: 0.8616 (t) cc_final: 0.8411 (p) REVERT: B 586 ASP cc_start: 0.7590 (m-30) cc_final: 0.7207 (m-30) REVERT: B 675 GLN cc_start: 0.7706 (mt0) cc_final: 0.7456 (mt0) REVERT: B 725 GLU cc_start: 0.7780 (tt0) cc_final: 0.7468 (tt0) REVERT: B 761 THR cc_start: 0.6972 (m) cc_final: 0.6711 (t) REVERT: B 764 ASN cc_start: 0.7490 (m-40) cc_final: 0.7286 (m-40) REVERT: B 772 VAL cc_start: 0.8566 (p) cc_final: 0.8337 (t) REVERT: B 776 LYS cc_start: 0.8061 (tmmt) cc_final: 0.7856 (ttpp) REVERT: B 780 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: B 859 THR cc_start: 0.8148 (t) cc_final: 0.7912 (p) REVERT: B 931 ILE cc_start: 0.7848 (mm) cc_final: 0.7584 (tp) REVERT: B 933 LYS cc_start: 0.8061 (mttt) cc_final: 0.7351 (mmtm) REVERT: B 947 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7507 (mtpp) REVERT: B 950 ASP cc_start: 0.7731 (m-30) cc_final: 0.7277 (m-30) REVERT: B 1010 GLN cc_start: 0.7687 (mp10) cc_final: 0.7479 (mp10) REVERT: B 1038 LYS cc_start: 0.7920 (tppt) cc_final: 0.7673 (tppt) REVERT: B 1055 SER cc_start: 0.8043 (t) cc_final: 0.7722 (m) REVERT: B 1082 CYS cc_start: 0.7213 (t) cc_final: 0.6738 (t) REVERT: B 1138 TYR cc_start: 0.7883 (t80) cc_final: 0.7292 (t80) REVERT: F 71 PHE cc_start: 0.6755 (t80) cc_final: 0.6151 (t80) REVERT: D 39 GLN cc_start: 0.7217 (tp40) cc_final: 0.6594 (pp30) REVERT: D 114 THR cc_start: 0.4244 (p) cc_final: 0.3884 (m) REVERT: C 45 SER cc_start: 0.8166 (t) cc_final: 0.7907 (p) REVERT: C 53 ASP cc_start: 0.6931 (t0) cc_final: 0.6685 (t70) REVERT: C 81 ASN cc_start: 0.7420 (p0) cc_final: 0.7092 (m110) REVERT: C 84 LEU cc_start: 0.7173 (mt) cc_final: 0.6946 (mp) REVERT: C 121 ASN cc_start: 0.6181 (t0) cc_final: 0.5979 (t0) REVERT: C 192 PHE cc_start: 0.8297 (m-80) cc_final: 0.8070 (m-80) REVERT: C 208 THR cc_start: 0.8346 (t) cc_final: 0.8105 (p) REVERT: C 224 GLU cc_start: 0.6800 (mp0) cc_final: 0.6578 (mp0) REVERT: C 314 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7842 (tp40) REVERT: C 340 GLU cc_start: 0.6951 (mp0) cc_final: 0.6584 (mp0) REVERT: C 392 PHE cc_start: 0.7290 (m-10) cc_final: 0.7054 (m-80) REVERT: C 436 TRP cc_start: 0.6286 (p90) cc_final: 0.5940 (p90) REVERT: C 497 PHE cc_start: 0.4536 (m-10) cc_final: 0.3786 (m-10) REVERT: C 511 VAL cc_start: 0.8711 (t) cc_final: 0.8467 (p) REVERT: C 541 PHE cc_start: 0.6516 (p90) cc_final: 0.6047 (p90) REVERT: C 572 THR cc_start: 0.8328 (m) cc_final: 0.7993 (p) REVERT: C 725 GLU cc_start: 0.7866 (tt0) cc_final: 0.7553 (tt0) REVERT: C 754 LEU cc_start: 0.8478 (mt) cc_final: 0.8189 (mt) REVERT: C 765 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.7202 (ttp80) REVERT: C 790 LYS cc_start: 0.7613 (mmpt) cc_final: 0.7366 (mmpt) REVERT: C 858 LEU cc_start: 0.8283 (mm) cc_final: 0.8020 (mp) REVERT: C 933 LYS cc_start: 0.8119 (mttt) cc_final: 0.7436 (mptt) REVERT: C 947 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7601 (mtpp) REVERT: C 964 LYS cc_start: 0.8326 (mttt) cc_final: 0.8048 (mttt) REVERT: C 995 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7778 (mtp85) REVERT: C 1019 ARG cc_start: 0.7809 (ttp-170) cc_final: 0.7437 (ttp80) REVERT: C 1038 LYS cc_start: 0.7595 (tppt) cc_final: 0.7218 (mmmm) REVERT: C 1045 LYS cc_start: 0.8108 (mttt) cc_final: 0.7800 (tttt) REVERT: C 1072 GLU cc_start: 0.7623 (pm20) cc_final: 0.7299 (pm20) REVERT: C 1101 HIS cc_start: 0.8291 (m-70) cc_final: 0.7868 (m-70) REVERT: C 1114 ILE cc_start: 0.7903 (mm) cc_final: 0.7672 (mt) REVERT: G 71 PHE cc_start: 0.6747 (t80) cc_final: 0.6052 (t80) REVERT: G 92 PHE cc_start: 0.7501 (m-80) cc_final: 0.7239 (m-80) REVERT: E 31 SER cc_start: 0.7901 (p) cc_final: 0.7487 (p) REVERT: E 32 TYR cc_start: 0.7736 (m-80) cc_final: 0.7147 (m-80) outliers start: 77 outliers final: 37 residues processed: 741 average time/residue: 0.5889 time to fit residues: 519.6897 Evaluate side-chains 706 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 665 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A1002 GLN A1101 HIS L 27 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 764 ASN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 ASN ** 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 = 0.4468 r_free = 0.4468 target = 0.198123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.176984 restraints weight = 59063.499| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 3.84 r_work: 0.4031 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 31419 Z= 0.260 Angle : 0.737 15.491 42840 Z= 0.372 Chirality : 0.051 0.611 4920 Planarity : 0.006 0.073 5448 Dihedral : 7.343 116.160 5201 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.58 % Allowed : 14.42 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.66 (0.13), residues: 3780 helix: 0.10 (0.20), residues: 681 sheet: -0.52 (0.17), residues: 870 loop : -1.79 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 995 TYR 0.033 0.002 TYR B 204 PHE 0.033 0.002 PHE B 329 TRP 0.022 0.002 TRP L 35 HIS 0.008 0.002 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00599 (31317) covalent geometry : angle 0.71773 (42591) SS BOND : bond 0.00423 ( 48) SS BOND : angle 1.66658 ( 96) hydrogen bonds : bond 0.04980 ( 871) hydrogen bonds : angle 6.14409 ( 2505) Misc. bond : bond 0.00132 ( 3) link_BETA1-4 : bond 0.00332 ( 12) link_BETA1-4 : angle 1.08403 ( 36) link_NAG-ASN : bond 0.00769 ( 39) link_NAG-ASN : angle 2.93948 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 701 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4138 (mpp) cc_final: 0.3701 (mpp) REVERT: A 282 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7018 (m110) REVERT: A 319 ARG cc_start: 0.7828 (ptp90) cc_final: 0.7372 (ptt180) REVERT: A 421 TYR cc_start: 0.6571 (m-80) cc_final: 0.6341 (m-10) REVERT: A 429 PHE cc_start: 0.6137 (t80) cc_final: 0.5805 (t80) REVERT: A 536 ASN cc_start: 0.8116 (m-40) cc_final: 0.7865 (m-40) REVERT: A 541 PHE cc_start: 0.6957 (p90) cc_final: 0.6594 (p90) REVERT: A 572 THR cc_start: 0.8408 (t) cc_final: 0.7792 (p) REVERT: A 588 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8319 (p) REVERT: A 651 ILE cc_start: 0.8762 (mm) cc_final: 0.8509 (mp) REVERT: A 673 SER cc_start: 0.8349 (t) cc_final: 0.7971 (p) REVERT: A 736 VAL cc_start: 0.8192 (t) cc_final: 0.7884 (m) REVERT: A 763 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6916 (mp) REVERT: A 790 LYS cc_start: 0.7453 (mmpt) cc_final: 0.7176 (mmpt) REVERT: A 811 LYS cc_start: 0.7077 (mmpt) cc_final: 0.6545 (mtpp) REVERT: A 933 LYS cc_start: 0.7948 (mttt) cc_final: 0.7570 (mtmm) REVERT: A 936 ASP cc_start: 0.7535 (m-30) cc_final: 0.7319 (m-30) REVERT: A 1029 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (ttm) REVERT: A 1038 LYS cc_start: 0.8139 (tppt) cc_final: 0.7874 (mmpt) REVERT: A 1045 LYS cc_start: 0.8355 (mttt) cc_final: 0.8007 (mttt) REVERT: A 1072 GLU cc_start: 0.8051 (pm20) cc_final: 0.7511 (pm20) REVERT: A 1107 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7577 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7843 (tm) cc_final: 0.7639 (tt) REVERT: L 37 GLN cc_start: 0.6481 (pm20) cc_final: 0.5627 (pm20) REVERT: L 81 GLU cc_start: 0.7700 (mp0) cc_final: 0.7460 (mp0) REVERT: H 39 GLN cc_start: 0.7221 (tp40) cc_final: 0.6304 (tp40) REVERT: H 95 TYR cc_start: 0.5862 (m-80) cc_final: 0.5389 (m-80) REVERT: B 49 HIS cc_start: 0.8212 (t-90) cc_final: 0.7776 (t70) REVERT: B 153 MET cc_start: 0.5190 (mpp) cc_final: 0.4882 (mpp) REVERT: B 319 ARG cc_start: 0.8062 (ptp90) cc_final: 0.7711 (ptt180) REVERT: B 340 GLU cc_start: 0.7394 (mp0) cc_final: 0.7006 (mp0) REVERT: B 374 PHE cc_start: 0.7646 (m-80) cc_final: 0.7432 (m-80) REVERT: B 427 ASP cc_start: 0.8093 (p0) cc_final: 0.7884 (p0) REVERT: B 448 ASN cc_start: 0.5132 (p0) cc_final: 0.4731 (p0) REVERT: B 511 VAL cc_start: 0.8771 (t) cc_final: 0.8533 (p) REVERT: B 541 PHE cc_start: 0.6905 (p90) cc_final: 0.6518 (p90) REVERT: B 586 ASP cc_start: 0.7640 (m-30) cc_final: 0.7205 (m-30) REVERT: B 675 GLN cc_start: 0.7757 (mt0) cc_final: 0.7524 (mt0) REVERT: B 725 GLU cc_start: 0.7858 (tt0) cc_final: 0.7517 (tt0) REVERT: B 764 ASN cc_start: 0.7395 (m-40) cc_final: 0.7166 (m-40) REVERT: B 772 VAL cc_start: 0.8551 (p) cc_final: 0.8319 (t) REVERT: B 776 LYS cc_start: 0.8085 (tmmt) cc_final: 0.7770 (ttpp) REVERT: B 780 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: B 821 LEU cc_start: 0.7720 (pt) cc_final: 0.7500 (pp) REVERT: B 859 THR cc_start: 0.8185 (t) cc_final: 0.7918 (p) REVERT: B 933 LYS cc_start: 0.8035 (mttt) cc_final: 0.7292 (mmtm) REVERT: B 947 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7560 (mtpp) REVERT: B 950 ASP cc_start: 0.7525 (m-30) cc_final: 0.7079 (m-30) REVERT: B 964 LYS cc_start: 0.8199 (mttt) cc_final: 0.7945 (mttt) REVERT: B 1038 LYS cc_start: 0.7971 (tppt) cc_final: 0.7624 (tppt) REVERT: B 1118 ASP cc_start: 0.7917 (m-30) cc_final: 0.7680 (m-30) REVERT: F 71 PHE cc_start: 0.6749 (t80) cc_final: 0.6363 (t80) REVERT: D 36 TRP cc_start: 0.5746 (m-10) cc_final: 0.5215 (m-10) REVERT: D 83 MET cc_start: 0.5216 (tmt) cc_final: 0.4888 (tmt) REVERT: C 45 SER cc_start: 0.8198 (t) cc_final: 0.7967 (p) REVERT: C 53 ASP cc_start: 0.6984 (t0) cc_final: 0.6756 (t0) REVERT: C 83 VAL cc_start: 0.7239 (OUTLIER) cc_final: 0.5865 (p) REVERT: C 208 THR cc_start: 0.8295 (t) cc_final: 0.8087 (p) REVERT: C 237 ARG cc_start: 0.7410 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: C 314 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7957 (tp40) REVERT: C 340 GLU cc_start: 0.7395 (mp0) cc_final: 0.7051 (mp0) REVERT: C 374 PHE cc_start: 0.7429 (m-80) cc_final: 0.7090 (m-80) REVERT: C 425 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7962 (mm) REVERT: C 429 PHE cc_start: 0.6698 (t80) cc_final: 0.6163 (t80) REVERT: C 436 TRP cc_start: 0.6324 (p90) cc_final: 0.6105 (p90) REVERT: C 453 TYR cc_start: 0.7276 (p90) cc_final: 0.7014 (p90) REVERT: C 495 TYR cc_start: 0.6393 (m-80) cc_final: 0.5695 (m-80) REVERT: C 541 PHE cc_start: 0.6996 (p90) cc_final: 0.6635 (p90) REVERT: C 725 GLU cc_start: 0.7879 (tt0) cc_final: 0.7672 (tt0) REVERT: C 750 SER cc_start: 0.7928 (t) cc_final: 0.7642 (p) REVERT: C 763 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7180 (mt) REVERT: C 773 GLU cc_start: 0.7586 (tt0) cc_final: 0.7378 (tt0) REVERT: C 776 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7958 (ttmm) REVERT: C 815 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7193 (mtm-85) REVERT: C 858 LEU cc_start: 0.8355 (mm) cc_final: 0.8066 (mp) REVERT: C 931 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7090 (mp) REVERT: C 933 LYS cc_start: 0.8147 (mttt) cc_final: 0.7465 (mptt) REVERT: C 947 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7686 (mtpp) REVERT: C 964 LYS cc_start: 0.8453 (mttt) cc_final: 0.8144 (mttt) REVERT: C 1019 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7395 (ttp80) REVERT: C 1030 SER cc_start: 0.8113 (m) cc_final: 0.7820 (p) REVERT: C 1038 LYS cc_start: 0.7894 (tppt) cc_final: 0.7517 (mmpt) REVERT: C 1045 LYS cc_start: 0.8055 (mttt) cc_final: 0.7784 (mttt) REVERT: C 1055 SER cc_start: 0.8485 (t) cc_final: 0.8185 (m) REVERT: C 1072 GLU cc_start: 0.7721 (pm20) cc_final: 0.7392 (pm20) REVERT: C 1101 HIS cc_start: 0.8357 (m-70) cc_final: 0.7912 (m-70) REVERT: G 71 PHE cc_start: 0.6835 (t80) cc_final: 0.6218 (t80) REVERT: G 92 PHE cc_start: 0.7693 (m-80) cc_final: 0.7413 (m-80) REVERT: E 31 SER cc_start: 0.7918 (p) cc_final: 0.7602 (p) REVERT: E 32 TYR cc_start: 0.7784 (m-80) cc_final: 0.7295 (m-80) REVERT: E 34 MET cc_start: 0.7002 (ppp) cc_final: 0.6721 (pmm) outliers start: 119 outliers final: 54 residues processed: 746 average time/residue: 0.5703 time to fit residues: 509.7384 Evaluate side-chains 739 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 672 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 235 optimal weight: 0.0980 chunk 181 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 186 optimal weight: 0.0970 chunk 356 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 955 ASN A1010 GLN A1101 HIS L 27 GLN L 93 ASN B 61 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1101 HIS F 93 ASN C 755 GLN C 764 ASN C 787 GLN C 992 GLN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN E 112 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.202513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.181123 restraints weight = 59015.218| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 3.75 r_work: 0.4073 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31419 Z= 0.133 Angle : 0.653 12.094 42840 Z= 0.320 Chirality : 0.046 0.355 4920 Planarity : 0.005 0.085 5448 Dihedral : 6.629 112.527 5201 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.49 % Allowed : 16.89 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.13), residues: 3780 helix: 0.86 (0.21), residues: 657 sheet: -0.63 (0.17), residues: 906 loop : -1.64 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 45 TYR 0.028 0.001 TYR B 453 PHE 0.026 0.002 PHE B 490 TRP 0.014 0.001 TRP L 35 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00309 (31317) covalent geometry : angle 0.64055 (42591) SS BOND : bond 0.00395 ( 48) SS BOND : angle 1.27400 ( 96) hydrogen bonds : bond 0.03739 ( 871) hydrogen bonds : angle 5.76166 ( 2505) Misc. bond : bond 0.00049 ( 3) link_BETA1-4 : bond 0.00400 ( 12) link_BETA1-4 : angle 1.24180 ( 36) link_NAG-ASN : bond 0.00471 ( 39) link_NAG-ASN : angle 2.26793 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 678 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7364 (tp-100) REVERT: A 153 MET cc_start: 0.4080 (mpp) cc_final: 0.3693 (mpp) REVERT: A 200 TYR cc_start: 0.5574 (m-10) cc_final: 0.5360 (m-10) REVERT: A 282 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6879 (m110) REVERT: A 319 ARG cc_start: 0.7831 (ptp90) cc_final: 0.7332 (ptt180) REVERT: A 429 PHE cc_start: 0.6112 (t80) cc_final: 0.5794 (t80) REVERT: A 490 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 532 ASN cc_start: 0.8554 (t0) cc_final: 0.8350 (t0) REVERT: A 541 PHE cc_start: 0.6914 (p90) cc_final: 0.6602 (p90) REVERT: A 551 VAL cc_start: 0.7834 (OUTLIER) cc_final: 0.7608 (t) REVERT: A 572 THR cc_start: 0.8281 (t) cc_final: 0.7966 (p) REVERT: A 588 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 651 ILE cc_start: 0.8742 (mm) cc_final: 0.8467 (mp) REVERT: A 673 SER cc_start: 0.8237 (t) cc_final: 0.7864 (p) REVERT: A 725 GLU cc_start: 0.7674 (tt0) cc_final: 0.7347 (tt0) REVERT: A 736 VAL cc_start: 0.8156 (t) cc_final: 0.7840 (m) REVERT: A 790 LYS cc_start: 0.7421 (mmpt) cc_final: 0.7178 (mmpt) REVERT: A 795 LYS cc_start: 0.8405 (mptm) cc_final: 0.8173 (mptp) REVERT: A 811 LYS cc_start: 0.7081 (mmpt) cc_final: 0.6581 (mtpt) REVERT: A 933 LYS cc_start: 0.7946 (mttt) cc_final: 0.7562 (mtmm) REVERT: A 936 ASP cc_start: 0.7553 (m-30) cc_final: 0.7346 (m-30) REVERT: A 1038 LYS cc_start: 0.8122 (tppt) cc_final: 0.7842 (mmpt) REVERT: A 1045 LYS cc_start: 0.8329 (mttt) cc_final: 0.7983 (mttt) REVERT: A 1072 GLU cc_start: 0.8018 (pm20) cc_final: 0.7496 (pm20) REVERT: H 34 MET cc_start: 0.6656 (ppp) cc_final: 0.6069 (ppp) REVERT: B 49 HIS cc_start: 0.8203 (t-90) cc_final: 0.7777 (t70) REVERT: B 153 MET cc_start: 0.5169 (mpp) cc_final: 0.4859 (mpp) REVERT: B 206 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7154 (ttmt) REVERT: B 319 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7676 (ptt180) REVERT: B 340 GLU cc_start: 0.7276 (mp0) cc_final: 0.6857 (mp0) REVERT: B 374 PHE cc_start: 0.7593 (m-80) cc_final: 0.7284 (m-80) REVERT: B 421 TYR cc_start: 0.6966 (m-80) cc_final: 0.6686 (m-10) REVERT: B 511 VAL cc_start: 0.8746 (t) cc_final: 0.8511 (p) REVERT: B 541 PHE cc_start: 0.6858 (p90) cc_final: 0.6518 (p90) REVERT: B 586 ASP cc_start: 0.7552 (m-30) cc_final: 0.7054 (m-30) REVERT: B 675 GLN cc_start: 0.7766 (mt0) cc_final: 0.7509 (mt0) REVERT: B 725 GLU cc_start: 0.7810 (tt0) cc_final: 0.7452 (tt0) REVERT: B 764 ASN cc_start: 0.7420 (m-40) cc_final: 0.7150 (m-40) REVERT: B 772 VAL cc_start: 0.8544 (p) cc_final: 0.8292 (t) REVERT: B 780 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: B 859 THR cc_start: 0.8160 (t) cc_final: 0.7891 (p) REVERT: B 933 LYS cc_start: 0.8036 (mttt) cc_final: 0.7295 (mmtm) REVERT: B 947 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7554 (mtpp) REVERT: B 950 ASP cc_start: 0.7547 (m-30) cc_final: 0.7059 (m-30) REVERT: B 964 LYS cc_start: 0.8162 (mttt) cc_final: 0.7920 (mttt) REVERT: B 1038 LYS cc_start: 0.7964 (tppt) cc_final: 0.7594 (tppt) REVERT: B 1118 ASP cc_start: 0.7883 (m-30) cc_final: 0.7681 (m-30) REVERT: F 71 PHE cc_start: 0.6895 (t80) cc_final: 0.6400 (t80) REVERT: D 34 MET cc_start: 0.6678 (ppp) cc_final: 0.6346 (ppp) REVERT: C 53 ASP cc_start: 0.6927 (t0) cc_final: 0.6676 (t0) REVERT: C 83 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.6195 (t) REVERT: C 84 LEU cc_start: 0.7178 (mt) cc_final: 0.6915 (mp) REVERT: C 200 TYR cc_start: 0.5265 (m-10) cc_final: 0.5035 (m-10) REVERT: C 237 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6680 (ttm-80) REVERT: C 267 VAL cc_start: 0.8159 (t) cc_final: 0.7811 (p) REVERT: C 314 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7949 (tp40) REVERT: C 319 ARG cc_start: 0.8160 (ptp90) cc_final: 0.7771 (ptt180) REVERT: C 340 GLU cc_start: 0.7273 (mp0) cc_final: 0.6847 (mp0) REVERT: C 374 PHE cc_start: 0.7426 (m-80) cc_final: 0.7022 (m-80) REVERT: C 392 PHE cc_start: 0.7146 (m-80) cc_final: 0.6945 (m-80) REVERT: C 425 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7897 (mm) REVERT: C 429 PHE cc_start: 0.6663 (t80) cc_final: 0.6238 (t80) REVERT: C 436 TRP cc_start: 0.6241 (p90) cc_final: 0.6000 (p90) REVERT: C 541 PHE cc_start: 0.6980 (p90) cc_final: 0.6628 (p90) REVERT: C 705 VAL cc_start: 0.6836 (OUTLIER) cc_final: 0.6586 (p) REVERT: C 725 GLU cc_start: 0.7880 (tt0) cc_final: 0.7664 (tt0) REVERT: C 750 SER cc_start: 0.7845 (t) cc_final: 0.7541 (p) REVERT: C 776 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7845 (ttmm) REVERT: C 790 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7271 (mmpt) REVERT: C 858 LEU cc_start: 0.8304 (mm) cc_final: 0.8069 (mp) REVERT: C 883 THR cc_start: 0.8251 (m) cc_final: 0.7864 (p) REVERT: C 933 LYS cc_start: 0.8107 (mttt) cc_final: 0.7416 (mptt) REVERT: C 947 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7710 (mtpp) REVERT: C 964 LYS cc_start: 0.8430 (mttt) cc_final: 0.8094 (mttt) REVERT: C 974 SER cc_start: 0.8662 (m) cc_final: 0.8289 (p) REVERT: C 1030 SER cc_start: 0.7998 (m) cc_final: 0.7688 (p) REVERT: C 1038 LYS cc_start: 0.7860 (tppt) cc_final: 0.7368 (mmmm) REVERT: C 1045 LYS cc_start: 0.8069 (mttt) cc_final: 0.7786 (mttt) REVERT: C 1055 SER cc_start: 0.8417 (t) cc_final: 0.8066 (m) REVERT: C 1072 GLU cc_start: 0.7681 (pm20) cc_final: 0.7385 (pm20) REVERT: C 1101 HIS cc_start: 0.8369 (m-70) cc_final: 0.7904 (m-70) REVERT: G 71 PHE cc_start: 0.6775 (t80) cc_final: 0.6251 (t80) REVERT: G 92 PHE cc_start: 0.7651 (m-80) cc_final: 0.7320 (m-80) REVERT: E 31 SER cc_start: 0.7834 (p) cc_final: 0.7603 (p) REVERT: E 32 TYR cc_start: 0.7796 (m-80) cc_final: 0.7303 (m-80) outliers start: 116 outliers final: 62 residues processed: 728 average time/residue: 0.5895 time to fit residues: 511.8965 Evaluate side-chains 721 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 648 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 218 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 375 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 957 GLN B1101 HIS C 764 ASN C 787 GLN C1010 GLN ** G 37 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 = 0.4479 r_free = 0.4479 target = 0.200026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.178297 restraints weight = 58241.128| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 3.74 r_work: 0.4045 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31419 Z= 0.193 Angle : 0.679 13.206 42840 Z= 0.335 Chirality : 0.047 0.347 4920 Planarity : 0.005 0.055 5448 Dihedral : 6.469 111.583 5201 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.94 % Allowed : 18.34 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.41 (0.13), residues: 3780 helix: 0.88 (0.21), residues: 672 sheet: -0.58 (0.17), residues: 888 loop : -1.74 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.030 0.002 TYR B 453 PHE 0.023 0.002 PHE C 329 TRP 0.016 0.002 TRP H 47 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00451 (31317) covalent geometry : angle 0.66534 (42591) SS BOND : bond 0.00384 ( 48) SS BOND : angle 1.46484 ( 96) hydrogen bonds : bond 0.03980 ( 871) hydrogen bonds : angle 5.67630 ( 2505) Misc. bond : bond 0.00041 ( 3) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 1.01681 ( 36) link_NAG-ASN : bond 0.00564 ( 39) link_NAG-ASN : angle 2.37525 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 671 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7419 (tp-100) REVERT: A 153 MET cc_start: 0.4422 (mpp) cc_final: 0.3952 (mpp) REVERT: A 206 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7298 (ttmm) REVERT: A 274 THR cc_start: 0.8668 (t) cc_final: 0.8271 (t) REVERT: A 282 ASN cc_start: 0.7285 (OUTLIER) cc_final: 0.6763 (m110) REVERT: A 319 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7326 (ptt180) REVERT: A 429 PHE cc_start: 0.6350 (t80) cc_final: 0.6023 (t80) REVERT: A 541 PHE cc_start: 0.6997 (p90) cc_final: 0.6340 (p90) REVERT: A 551 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7649 (t) REVERT: A 588 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 651 ILE cc_start: 0.8765 (mm) cc_final: 0.8484 (mp) REVERT: A 673 SER cc_start: 0.8268 (t) cc_final: 0.7903 (p) REVERT: A 725 GLU cc_start: 0.7721 (tt0) cc_final: 0.7438 (tt0) REVERT: A 736 VAL cc_start: 0.8158 (t) cc_final: 0.7870 (m) REVERT: A 790 LYS cc_start: 0.7432 (mmpt) cc_final: 0.7163 (mmpt) REVERT: A 795 LYS cc_start: 0.8433 (mptm) cc_final: 0.8152 (mptp) REVERT: A 811 LYS cc_start: 0.7109 (mmpt) cc_final: 0.6579 (mtpt) REVERT: A 933 LYS cc_start: 0.7956 (mttt) cc_final: 0.7602 (mtmm) REVERT: A 1019 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7604 (ttm110) REVERT: A 1038 LYS cc_start: 0.8171 (tppt) cc_final: 0.7899 (mmpt) REVERT: A 1045 LYS cc_start: 0.8307 (mttt) cc_final: 0.7961 (mttt) REVERT: A 1072 GLU cc_start: 0.8039 (pm20) cc_final: 0.7605 (pm20) REVERT: A 1141 LEU cc_start: 0.7852 (tt) cc_final: 0.7651 (tt) REVERT: H 34 MET cc_start: 0.6632 (ppp) cc_final: 0.5748 (ppp) REVERT: B 49 HIS cc_start: 0.8218 (t-90) cc_final: 0.7760 (t70) REVERT: B 53 ASP cc_start: 0.6881 (t0) cc_final: 0.6433 (t0) REVERT: B 153 MET cc_start: 0.5295 (mpp) cc_final: 0.4950 (mpp) REVERT: B 206 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7191 (ttmt) REVERT: B 319 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7775 (ptt180) REVERT: B 340 GLU cc_start: 0.7454 (mp0) cc_final: 0.6976 (mp0) REVERT: B 374 PHE cc_start: 0.7631 (m-80) cc_final: 0.7411 (m-80) REVERT: B 421 TYR cc_start: 0.7006 (m-80) cc_final: 0.6654 (m-10) REVERT: B 454 ARG cc_start: 0.8560 (mmt90) cc_final: 0.8103 (mmt90) REVERT: B 508 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: B 511 VAL cc_start: 0.8778 (t) cc_final: 0.8537 (p) REVERT: B 541 PHE cc_start: 0.6901 (p90) cc_final: 0.6516 (p90) REVERT: B 586 ASP cc_start: 0.7571 (m-30) cc_final: 0.7081 (m-30) REVERT: B 675 GLN cc_start: 0.7750 (mt0) cc_final: 0.7517 (mt0) REVERT: B 725 GLU cc_start: 0.7845 (tt0) cc_final: 0.7493 (tt0) REVERT: B 748 GLU cc_start: 0.7979 (pp20) cc_final: 0.7677 (pp20) REVERT: B 764 ASN cc_start: 0.7492 (m-40) cc_final: 0.7210 (m-40) REVERT: B 772 VAL cc_start: 0.8548 (p) cc_final: 0.8301 (t) REVERT: B 859 THR cc_start: 0.8161 (t) cc_final: 0.7874 (p) REVERT: B 933 LYS cc_start: 0.8055 (mttt) cc_final: 0.7326 (mmtm) REVERT: B 947 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7551 (mtpp) REVERT: B 949 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7434 (tp40) REVERT: B 950 ASP cc_start: 0.7527 (m-30) cc_final: 0.7055 (m-30) REVERT: B 1038 LYS cc_start: 0.7948 (tppt) cc_final: 0.7581 (tppt) REVERT: B 1118 ASP cc_start: 0.7887 (m-30) cc_final: 0.7686 (m-30) REVERT: F 71 PHE cc_start: 0.6872 (t80) cc_final: 0.6434 (t80) REVERT: D 20 LEU cc_start: 0.4360 (OUTLIER) cc_final: 0.2532 (tm) REVERT: D 83 MET cc_start: 0.3811 (tmt) cc_final: 0.3362 (tmt) REVERT: C 53 ASP cc_start: 0.6969 (t0) cc_final: 0.6701 (t0) REVERT: C 83 VAL cc_start: 0.7389 (OUTLIER) cc_final: 0.6234 (t) REVERT: C 84 LEU cc_start: 0.7253 (mt) cc_final: 0.6953 (mp) REVERT: C 206 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7149 (ttmm) REVERT: C 237 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6714 (ttm-80) REVERT: C 314 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: C 319 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7706 (ptt180) REVERT: C 340 GLU cc_start: 0.7311 (mp0) cc_final: 0.6894 (mp0) REVERT: C 374 PHE cc_start: 0.7467 (m-80) cc_final: 0.7076 (m-80) REVERT: C 436 TRP cc_start: 0.6209 (p90) cc_final: 0.5954 (p90) REVERT: C 541 PHE cc_start: 0.6996 (p90) cc_final: 0.6709 (p90) REVERT: C 705 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6788 (p) REVERT: C 725 GLU cc_start: 0.7870 (tt0) cc_final: 0.7633 (tt0) REVERT: C 750 SER cc_start: 0.7922 (t) cc_final: 0.7638 (p) REVERT: C 776 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7897 (ttmm) REVERT: C 790 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7271 (mmpt) REVERT: C 858 LEU cc_start: 0.8343 (mm) cc_final: 0.8098 (mp) REVERT: C 883 THR cc_start: 0.8174 (m) cc_final: 0.7856 (p) REVERT: C 931 ILE cc_start: 0.7535 (mm) cc_final: 0.7045 (mp) REVERT: C 933 LYS cc_start: 0.8112 (mttt) cc_final: 0.7430 (mptt) REVERT: C 947 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7719 (mtpp) REVERT: C 964 LYS cc_start: 0.8434 (mttt) cc_final: 0.8114 (mttt) REVERT: C 1019 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7467 (ttp80) REVERT: C 1030 SER cc_start: 0.7983 (m) cc_final: 0.7713 (p) REVERT: C 1038 LYS cc_start: 0.7906 (tppt) cc_final: 0.7469 (mmpt) REVERT: C 1045 LYS cc_start: 0.7993 (mttt) cc_final: 0.7770 (mttt) REVERT: C 1055 SER cc_start: 0.8418 (t) cc_final: 0.8077 (m) REVERT: C 1072 GLU cc_start: 0.7752 (pm20) cc_final: 0.7475 (pm20) REVERT: C 1101 HIS cc_start: 0.8369 (m-70) cc_final: 0.7874 (m-70) REVERT: C 1141 LEU cc_start: 0.8001 (tp) cc_final: 0.7708 (tm) REVERT: G 71 PHE cc_start: 0.6795 (t80) cc_final: 0.6280 (t80) REVERT: G 92 PHE cc_start: 0.7358 (m-80) cc_final: 0.6892 (m-80) REVERT: E 31 SER cc_start: 0.8051 (p) cc_final: 0.7798 (p) REVERT: E 32 TYR cc_start: 0.7791 (m-80) cc_final: 0.7315 (m-80) outliers start: 131 outliers final: 76 residues processed: 730 average time/residue: 0.5727 time to fit residues: 500.7632 Evaluate side-chains 745 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 656 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 323 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 606 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN L 93 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 540 ASN B 564 GLN B 957 GLN B1101 HIS F 93 ASN C 764 ASN C 787 GLN C1010 GLN G 93 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.200828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.179074 restraints weight = 58527.040| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 3.67 r_work: 0.4061 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31419 Z= 0.147 Angle : 0.672 15.637 42840 Z= 0.329 Chirality : 0.047 0.349 4920 Planarity : 0.005 0.086 5448 Dihedral : 6.333 110.472 5199 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.07 % Allowed : 19.03 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3780 helix: 1.00 (0.21), residues: 675 sheet: -0.62 (0.17), residues: 885 loop : -1.68 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 346 TYR 0.026 0.001 TYR B 453 PHE 0.027 0.002 PHE B 490 TRP 0.018 0.002 TRP E 47 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00344 (31317) covalent geometry : angle 0.65938 (42591) SS BOND : bond 0.00630 ( 48) SS BOND : angle 1.68331 ( 96) hydrogen bonds : bond 0.03613 ( 871) hydrogen bonds : angle 5.56148 ( 2505) Misc. bond : bond 0.00858 ( 3) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 0.94239 ( 36) link_NAG-ASN : bond 0.00517 ( 39) link_NAG-ASN : angle 2.11612 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 662 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7392 (tp-100) REVERT: A 140 PHE cc_start: 0.7216 (p90) cc_final: 0.6433 (p90) REVERT: A 153 MET cc_start: 0.4343 (mpp) cc_final: 0.3883 (mpp) REVERT: A 177 MET cc_start: 0.0128 (mtt) cc_final: -0.0744 (mtt) REVERT: A 200 TYR cc_start: 0.5252 (m-10) cc_final: 0.5018 (m-10) REVERT: A 206 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7233 (ttmm) REVERT: A 274 THR cc_start: 0.8714 (t) cc_final: 0.8279 (t) REVERT: A 319 ARG cc_start: 0.7869 (ptp90) cc_final: 0.7354 (ptt180) REVERT: A 429 PHE cc_start: 0.6392 (t80) cc_final: 0.6088 (t80) REVERT: A 541 PHE cc_start: 0.7015 (p90) cc_final: 0.6330 (p90) REVERT: A 588 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8379 (p) REVERT: A 651 ILE cc_start: 0.8763 (mm) cc_final: 0.8478 (mp) REVERT: A 673 SER cc_start: 0.8219 (t) cc_final: 0.7863 (p) REVERT: A 725 GLU cc_start: 0.7715 (tt0) cc_final: 0.7427 (tt0) REVERT: A 736 VAL cc_start: 0.8171 (t) cc_final: 0.7895 (m) REVERT: A 790 LYS cc_start: 0.7445 (mmpt) cc_final: 0.7154 (mmpt) REVERT: A 795 LYS cc_start: 0.8437 (mptm) cc_final: 0.8163 (mptp) REVERT: A 811 LYS cc_start: 0.7177 (mmpt) cc_final: 0.6664 (mtpt) REVERT: A 933 LYS cc_start: 0.7965 (mttt) cc_final: 0.7603 (mtmm) REVERT: A 1019 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7582 (ttm110) REVERT: A 1038 LYS cc_start: 0.8159 (tppt) cc_final: 0.7897 (mmpt) REVERT: A 1045 LYS cc_start: 0.8352 (mttt) cc_final: 0.8018 (mttt) REVERT: A 1072 GLU cc_start: 0.8003 (pm20) cc_final: 0.7589 (pm20) REVERT: A 1141 LEU cc_start: 0.7822 (tt) cc_final: 0.7603 (tt) REVERT: B 49 HIS cc_start: 0.8211 (t-90) cc_final: 0.7761 (t70) REVERT: B 53 ASP cc_start: 0.6871 (t0) cc_final: 0.6424 (t0) REVERT: B 153 MET cc_start: 0.5461 (mpp) cc_final: 0.5068 (mpp) REVERT: B 206 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7253 (ttmm) REVERT: B 319 ARG cc_start: 0.8102 (ptp90) cc_final: 0.7735 (ptt180) REVERT: B 340 GLU cc_start: 0.7476 (mp0) cc_final: 0.7059 (mp0) REVERT: B 374 PHE cc_start: 0.7540 (m-80) cc_final: 0.6995 (m-80) REVERT: B 421 TYR cc_start: 0.6717 (m-80) cc_final: 0.6488 (m-10) REVERT: B 436 TRP cc_start: 0.6668 (p90) cc_final: 0.6421 (p90) REVERT: B 454 ARG cc_start: 0.8519 (mmt90) cc_final: 0.7997 (mmt90) REVERT: B 490 PHE cc_start: 0.8123 (t80) cc_final: 0.7725 (t80) REVERT: B 508 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6911 (m-10) REVERT: B 511 VAL cc_start: 0.8778 (t) cc_final: 0.8520 (p) REVERT: B 534 VAL cc_start: 0.8231 (t) cc_final: 0.8016 (p) REVERT: B 541 PHE cc_start: 0.6906 (p90) cc_final: 0.6500 (p90) REVERT: B 586 ASP cc_start: 0.7582 (m-30) cc_final: 0.7073 (m-30) REVERT: B 675 GLN cc_start: 0.7754 (mt0) cc_final: 0.7511 (mt0) REVERT: B 725 GLU cc_start: 0.7821 (tt0) cc_final: 0.7553 (tt0) REVERT: B 748 GLU cc_start: 0.7994 (pp20) cc_final: 0.7780 (pp20) REVERT: B 764 ASN cc_start: 0.7552 (m-40) cc_final: 0.7245 (m-40) REVERT: B 772 VAL cc_start: 0.8569 (p) cc_final: 0.8313 (t) REVERT: B 859 THR cc_start: 0.8136 (t) cc_final: 0.7873 (p) REVERT: B 933 LYS cc_start: 0.8079 (mttt) cc_final: 0.7348 (mmtm) REVERT: B 935 GLN cc_start: 0.8013 (mt0) cc_final: 0.7637 (mt0) REVERT: B 947 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7576 (mtpp) REVERT: B 950 ASP cc_start: 0.7617 (m-30) cc_final: 0.7046 (m-30) REVERT: B 964 LYS cc_start: 0.8291 (mttt) cc_final: 0.7833 (mptt) REVERT: F 36 TYR cc_start: 0.5735 (m-10) cc_final: 0.5345 (m-10) REVERT: F 71 PHE cc_start: 0.6841 (t80) cc_final: 0.6392 (t80) REVERT: D 20 LEU cc_start: 0.4307 (OUTLIER) cc_final: 0.2502 (tm) REVERT: D 34 MET cc_start: 0.6788 (ppp) cc_final: 0.5857 (ppp) REVERT: D 46 GLU cc_start: 0.6896 (pm20) cc_final: 0.6624 (mp0) REVERT: C 53 ASP cc_start: 0.6902 (t0) cc_final: 0.6633 (t0) REVERT: C 83 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.6134 (p) REVERT: C 84 LEU cc_start: 0.7204 (mt) cc_final: 0.6894 (mp) REVERT: C 129 LYS cc_start: 0.7619 (mmtm) cc_final: 0.7411 (mmtm) REVERT: C 200 TYR cc_start: 0.5468 (m-10) cc_final: 0.5215 (m-10) REVERT: C 206 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7147 (ttmm) REVERT: C 237 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6633 (ttm-80) REVERT: C 314 GLN cc_start: 0.8167 (tt0) cc_final: 0.7898 (tp40) REVERT: C 319 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7825 (ptt180) REVERT: C 326 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.6208 (tt) REVERT: C 329 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6628 (t80) REVERT: C 340 GLU cc_start: 0.7327 (mp0) cc_final: 0.6895 (mp0) REVERT: C 374 PHE cc_start: 0.7519 (m-80) cc_final: 0.7124 (m-80) REVERT: C 436 TRP cc_start: 0.6125 (p90) cc_final: 0.5921 (p90) REVERT: C 453 TYR cc_start: 0.7455 (p90) cc_final: 0.7138 (p90) REVERT: C 541 PHE cc_start: 0.7021 (p90) cc_final: 0.6689 (p90) REVERT: C 574 ASP cc_start: 0.7542 (t70) cc_final: 0.7044 (t70) REVERT: C 651 ILE cc_start: 0.8742 (mm) cc_final: 0.8466 (mt) REVERT: C 705 VAL cc_start: 0.7025 (OUTLIER) cc_final: 0.6769 (p) REVERT: C 725 GLU cc_start: 0.7867 (tt0) cc_final: 0.7643 (tt0) REVERT: C 750 SER cc_start: 0.7890 (t) cc_final: 0.7581 (p) REVERT: C 776 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7832 (ttmm) REVERT: C 858 LEU cc_start: 0.8323 (mm) cc_final: 0.8080 (mp) REVERT: C 868 GLU cc_start: 0.7262 (mp0) cc_final: 0.7062 (mp0) REVERT: C 883 THR cc_start: 0.8128 (m) cc_final: 0.7814 (p) REVERT: C 933 LYS cc_start: 0.8125 (mttt) cc_final: 0.7435 (mptt) REVERT: C 947 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7703 (mtpp) REVERT: C 964 LYS cc_start: 0.8382 (mttt) cc_final: 0.8111 (mttt) REVERT: C 974 SER cc_start: 0.8696 (m) cc_final: 0.8296 (p) REVERT: C 994 ASP cc_start: 0.7565 (t70) cc_final: 0.7302 (m-30) REVERT: C 1019 ARG cc_start: 0.7687 (ttp-170) cc_final: 0.7404 (ttp80) REVERT: C 1030 SER cc_start: 0.7942 (m) cc_final: 0.7669 (p) REVERT: C 1038 LYS cc_start: 0.7880 (tppt) cc_final: 0.7426 (mmpt) REVERT: C 1045 LYS cc_start: 0.7997 (mttt) cc_final: 0.7762 (mttt) REVERT: C 1055 SER cc_start: 0.8402 (t) cc_final: 0.8062 (m) REVERT: C 1072 GLU cc_start: 0.7584 (pm20) cc_final: 0.7253 (pm20) REVERT: C 1101 HIS cc_start: 0.8356 (m-70) cc_final: 0.7903 (m-70) REVERT: C 1141 LEU cc_start: 0.7926 (tp) cc_final: 0.7629 (tm) REVERT: G 71 PHE cc_start: 0.6748 (t80) cc_final: 0.6274 (t80) REVERT: G 92 PHE cc_start: 0.7452 (m-80) cc_final: 0.6840 (m-80) REVERT: E 31 SER cc_start: 0.8015 (p) cc_final: 0.7780 (p) REVERT: E 32 TYR cc_start: 0.7780 (m-80) cc_final: 0.7307 (m-80) REVERT: E 102 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7970 (m-10) outliers start: 135 outliers final: 83 residues processed: 728 average time/residue: 0.5780 time to fit residues: 503.7553 Evaluate side-chains 739 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 643 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 258 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 277 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B 957 GLN B1101 HIS C 540 ASN C 764 ASN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.201152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.179533 restraints weight = 58329.523| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.66 r_work: 0.4063 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31419 Z= 0.145 Angle : 0.667 16.820 42840 Z= 0.325 Chirality : 0.046 0.348 4920 Planarity : 0.005 0.055 5448 Dihedral : 6.282 110.022 5199 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.61 % Allowed : 19.81 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3780 helix: 1.07 (0.21), residues: 675 sheet: -0.60 (0.17), residues: 885 loop : -1.71 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 346 TYR 0.031 0.002 TYR B 453 PHE 0.027 0.002 PHE C 490 TRP 0.014 0.002 TRP E 110 HIS 0.005 0.001 HIS G 30 Details of bonding type rmsd covalent geometry : bond 0.00341 (31317) covalent geometry : angle 0.65534 (42591) SS BOND : bond 0.00495 ( 48) SS BOND : angle 1.51690 ( 96) hydrogen bonds : bond 0.03514 ( 871) hydrogen bonds : angle 5.47517 ( 2505) Misc. bond : bond 0.00389 ( 3) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 0.91426 ( 36) link_NAG-ASN : bond 0.00506 ( 39) link_NAG-ASN : angle 2.07203 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 662 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7371 (tp-100) REVERT: A 140 PHE cc_start: 0.7283 (p90) cc_final: 0.6584 (p90) REVERT: A 153 MET cc_start: 0.4386 (mpp) cc_final: 0.3940 (mpp) REVERT: A 177 MET cc_start: 0.0100 (mtt) cc_final: -0.0786 (mtt) REVERT: A 206 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (ttmm) REVERT: A 274 THR cc_start: 0.8714 (t) cc_final: 0.8283 (t) REVERT: A 319 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7363 (ptt180) REVERT: A 429 PHE cc_start: 0.6371 (t80) cc_final: 0.6075 (t80) REVERT: A 454 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7830 (mmt90) REVERT: A 541 PHE cc_start: 0.7021 (p90) cc_final: 0.6337 (p90) REVERT: A 588 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8347 (p) REVERT: A 651 ILE cc_start: 0.8763 (mm) cc_final: 0.8480 (mp) REVERT: A 673 SER cc_start: 0.8255 (t) cc_final: 0.7889 (p) REVERT: A 725 GLU cc_start: 0.7709 (tt0) cc_final: 0.7455 (tt0) REVERT: A 736 VAL cc_start: 0.8199 (t) cc_final: 0.7923 (m) REVERT: A 795 LYS cc_start: 0.8454 (mptm) cc_final: 0.8182 (mptp) REVERT: A 811 LYS cc_start: 0.7174 (mmpt) cc_final: 0.6676 (mtpt) REVERT: A 933 LYS cc_start: 0.7950 (mttt) cc_final: 0.7593 (mtmm) REVERT: A 1019 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7621 (ttm110) REVERT: A 1045 LYS cc_start: 0.8390 (mttt) cc_final: 0.8068 (mttt) REVERT: A 1072 GLU cc_start: 0.8025 (pm20) cc_final: 0.7618 (pm20) REVERT: A 1141 LEU cc_start: 0.7837 (tt) cc_final: 0.7619 (tt) REVERT: H 34 MET cc_start: 0.6308 (ppp) cc_final: 0.5966 (ppp) REVERT: B 49 HIS cc_start: 0.8209 (t-90) cc_final: 0.7768 (t70) REVERT: B 153 MET cc_start: 0.5455 (mpp) cc_final: 0.5042 (mpp) REVERT: B 206 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7244 (ttmm) REVERT: B 319 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7764 (ptt180) REVERT: B 340 GLU cc_start: 0.7518 (mp0) cc_final: 0.7103 (mp0) REVERT: B 346 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7381 (ttp80) REVERT: B 374 PHE cc_start: 0.7443 (m-80) cc_final: 0.6946 (m-80) REVERT: B 421 TYR cc_start: 0.6705 (m-80) cc_final: 0.6425 (m-10) REVERT: B 436 TRP cc_start: 0.6665 (p90) cc_final: 0.6397 (p90) REVERT: B 454 ARG cc_start: 0.8501 (mmt90) cc_final: 0.7973 (mmt90) REVERT: B 490 PHE cc_start: 0.8099 (t80) cc_final: 0.7660 (t80) REVERT: B 508 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6943 (m-10) REVERT: B 511 VAL cc_start: 0.8774 (t) cc_final: 0.8506 (p) REVERT: B 534 VAL cc_start: 0.8231 (t) cc_final: 0.8011 (p) REVERT: B 541 PHE cc_start: 0.6862 (p90) cc_final: 0.6434 (p90) REVERT: B 586 ASP cc_start: 0.7597 (m-30) cc_final: 0.7117 (m-30) REVERT: B 606 ASN cc_start: 0.8456 (m-40) cc_final: 0.8246 (m-40) REVERT: B 675 GLN cc_start: 0.7738 (mt0) cc_final: 0.7495 (mt0) REVERT: B 725 GLU cc_start: 0.7829 (tt0) cc_final: 0.7572 (tt0) REVERT: B 748 GLU cc_start: 0.8014 (pp20) cc_final: 0.7793 (pp20) REVERT: B 764 ASN cc_start: 0.7570 (m-40) cc_final: 0.7241 (m-40) REVERT: B 772 VAL cc_start: 0.8569 (p) cc_final: 0.8316 (t) REVERT: B 859 THR cc_start: 0.8148 (t) cc_final: 0.7862 (p) REVERT: B 933 LYS cc_start: 0.8078 (mttt) cc_final: 0.7342 (mmtm) REVERT: B 935 GLN cc_start: 0.8034 (mt0) cc_final: 0.7751 (mt0) REVERT: B 947 LYS cc_start: 0.7877 (mtpt) cc_final: 0.7554 (mtpp) REVERT: B 950 ASP cc_start: 0.7625 (m-30) cc_final: 0.7036 (m-30) REVERT: B 964 LYS cc_start: 0.8291 (mttt) cc_final: 0.7818 (mptt) REVERT: B 1050 MET cc_start: 0.8257 (ptm) cc_final: 0.8053 (ptt) REVERT: F 71 PHE cc_start: 0.6857 (t80) cc_final: 0.6413 (t80) REVERT: D 20 LEU cc_start: 0.4320 (OUTLIER) cc_final: 0.2523 (tm) REVERT: D 34 MET cc_start: 0.6743 (ppp) cc_final: 0.5818 (ppp) REVERT: C 53 ASP cc_start: 0.6893 (t0) cc_final: 0.6647 (t0) REVERT: C 83 VAL cc_start: 0.7434 (OUTLIER) cc_final: 0.6178 (p) REVERT: C 84 LEU cc_start: 0.7211 (mt) cc_final: 0.6912 (mp) REVERT: C 129 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7381 (mmtm) REVERT: C 200 TYR cc_start: 0.5478 (m-10) cc_final: 0.5229 (m-10) REVERT: C 206 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7201 (ttmm) REVERT: C 237 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6704 (ttm-80) REVERT: C 314 GLN cc_start: 0.8172 (tt0) cc_final: 0.7887 (tp40) REVERT: C 319 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7799 (ptt180) REVERT: C 326 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6094 (tt) REVERT: C 329 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6583 (t80) REVERT: C 340 GLU cc_start: 0.7315 (mp0) cc_final: 0.6925 (mp0) REVERT: C 374 PHE cc_start: 0.7525 (m-80) cc_final: 0.7141 (m-80) REVERT: C 453 TYR cc_start: 0.7497 (p90) cc_final: 0.7180 (p90) REVERT: C 455 LEU cc_start: 0.8928 (tm) cc_final: 0.8650 (mm) REVERT: C 541 PHE cc_start: 0.7023 (p90) cc_final: 0.6711 (p90) REVERT: C 574 ASP cc_start: 0.7537 (t70) cc_final: 0.7044 (t70) REVERT: C 651 ILE cc_start: 0.8737 (mm) cc_final: 0.8468 (mt) REVERT: C 705 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6783 (p) REVERT: C 725 GLU cc_start: 0.7871 (tt0) cc_final: 0.7661 (tt0) REVERT: C 750 SER cc_start: 0.7852 (t) cc_final: 0.7564 (p) REVERT: C 776 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: C 790 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7250 (mmpt) REVERT: C 815 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: C 858 LEU cc_start: 0.8327 (mm) cc_final: 0.8091 (mp) REVERT: C 883 THR cc_start: 0.8163 (m) cc_final: 0.7812 (p) REVERT: C 933 LYS cc_start: 0.8109 (mttt) cc_final: 0.7434 (mptt) REVERT: C 947 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7706 (mtpp) REVERT: C 964 LYS cc_start: 0.8400 (mttt) cc_final: 0.8140 (mttt) REVERT: C 974 SER cc_start: 0.8707 (m) cc_final: 0.8310 (p) REVERT: C 994 ASP cc_start: 0.7597 (t70) cc_final: 0.7339 (m-30) REVERT: C 1030 SER cc_start: 0.7937 (m) cc_final: 0.7690 (p) REVERT: C 1038 LYS cc_start: 0.7894 (tppt) cc_final: 0.7373 (mmmm) REVERT: C 1045 LYS cc_start: 0.8019 (mttt) cc_final: 0.7784 (mttt) REVERT: C 1055 SER cc_start: 0.8391 (t) cc_final: 0.8047 (m) REVERT: C 1072 GLU cc_start: 0.7592 (pm20) cc_final: 0.7279 (pm20) REVERT: C 1073 LYS cc_start: 0.7333 (pttp) cc_final: 0.7048 (ptmm) REVERT: C 1101 HIS cc_start: 0.8353 (m-70) cc_final: 0.7872 (m-70) REVERT: C 1123 SER cc_start: 0.8512 (t) cc_final: 0.8214 (m) REVERT: C 1141 LEU cc_start: 0.7870 (tp) cc_final: 0.7584 (tm) REVERT: G 71 PHE cc_start: 0.6713 (t80) cc_final: 0.6261 (t80) REVERT: G 92 PHE cc_start: 0.7290 (m-80) cc_final: 0.6710 (m-80) REVERT: E 31 SER cc_start: 0.8000 (p) cc_final: 0.7768 (p) REVERT: E 32 TYR cc_start: 0.7755 (m-80) cc_final: 0.7292 (m-80) REVERT: E 68 PHE cc_start: 0.7916 (m-10) cc_final: 0.7486 (m-10) outliers start: 120 outliers final: 84 residues processed: 716 average time/residue: 0.5784 time to fit residues: 495.9879 Evaluate side-chains 747 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 650 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 76 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 129 optimal weight: 0.0570 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 367 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 228 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B1101 HIS C 755 GLN C 764 ASN C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.200241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.178625 restraints weight = 58347.475| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.66 r_work: 0.4050 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31419 Z= 0.160 Angle : 0.682 19.064 42840 Z= 0.333 Chirality : 0.047 0.344 4920 Planarity : 0.005 0.055 5448 Dihedral : 6.252 109.373 5199 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.91 % Allowed : 19.99 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.33 (0.13), residues: 3780 helix: 1.15 (0.21), residues: 669 sheet: -0.60 (0.17), residues: 885 loop : -1.72 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 346 TYR 0.031 0.002 TYR B 453 PHE 0.023 0.002 PHE B 168 TRP 0.015 0.002 TRP C 886 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (31317) covalent geometry : angle 0.67113 (42591) SS BOND : bond 0.00457 ( 48) SS BOND : angle 1.52246 ( 96) hydrogen bonds : bond 0.03577 ( 871) hydrogen bonds : angle 5.45227 ( 2505) Misc. bond : bond 0.00396 ( 3) link_BETA1-4 : bond 0.00369 ( 12) link_BETA1-4 : angle 0.92855 ( 36) link_NAG-ASN : bond 0.00582 ( 39) link_NAG-ASN : angle 2.06131 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 661 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7406 (tp-100) REVERT: A 140 PHE cc_start: 0.7279 (p90) cc_final: 0.6550 (p90) REVERT: A 153 MET cc_start: 0.4323 (mpp) cc_final: 0.3870 (mpp) REVERT: A 168 PHE cc_start: 0.5154 (t80) cc_final: 0.4697 (t80) REVERT: A 177 MET cc_start: 0.0304 (mtt) cc_final: -0.0589 (mtt) REVERT: A 206 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7304 (ttmm) REVERT: A 274 THR cc_start: 0.8717 (t) cc_final: 0.8295 (t) REVERT: A 319 ARG cc_start: 0.7861 (ptp90) cc_final: 0.7387 (ptt180) REVERT: A 429 PHE cc_start: 0.6476 (t80) cc_final: 0.6198 (t80) REVERT: A 454 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7902 (mmt90) REVERT: A 541 PHE cc_start: 0.7075 (p90) cc_final: 0.6422 (p90) REVERT: A 651 ILE cc_start: 0.8757 (mm) cc_final: 0.8470 (mp) REVERT: A 673 SER cc_start: 0.8271 (t) cc_final: 0.7895 (p) REVERT: A 725 GLU cc_start: 0.7817 (tt0) cc_final: 0.7569 (tt0) REVERT: A 736 VAL cc_start: 0.8201 (t) cc_final: 0.7914 (m) REVERT: A 748 GLU cc_start: 0.7647 (pp20) cc_final: 0.7426 (pm20) REVERT: A 795 LYS cc_start: 0.8457 (mptm) cc_final: 0.8194 (mptp) REVERT: A 811 LYS cc_start: 0.7184 (mmpt) cc_final: 0.6709 (mtpt) REVERT: A 933 LYS cc_start: 0.7954 (mttt) cc_final: 0.7594 (mtmm) REVERT: A 947 LYS cc_start: 0.7603 (mtpt) cc_final: 0.7300 (mtmt) REVERT: A 1019 ARG cc_start: 0.7931 (ttp-170) cc_final: 0.7597 (ttm110) REVERT: A 1045 LYS cc_start: 0.8304 (mttt) cc_final: 0.7975 (mttt) REVERT: A 1072 GLU cc_start: 0.8008 (pm20) cc_final: 0.7488 (pm20) REVERT: A 1111 GLU cc_start: 0.7622 (tt0) cc_final: 0.7314 (tt0) REVERT: A 1141 LEU cc_start: 0.7864 (tt) cc_final: 0.7650 (tt) REVERT: H 33 VAL cc_start: 0.8113 (t) cc_final: 0.7804 (p) REVERT: H 34 MET cc_start: 0.6333 (ppp) cc_final: 0.6006 (ppp) REVERT: H 102 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7449 (t80) REVERT: B 49 HIS cc_start: 0.8220 (t-90) cc_final: 0.7758 (t70) REVERT: B 153 MET cc_start: 0.5511 (mpp) cc_final: 0.5099 (mpp) REVERT: B 206 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7277 (ttmm) REVERT: B 319 ARG cc_start: 0.8145 (ptp90) cc_final: 0.7795 (ptt180) REVERT: B 340 GLU cc_start: 0.7584 (mp0) cc_final: 0.7160 (mp0) REVERT: B 374 PHE cc_start: 0.7497 (m-80) cc_final: 0.6994 (m-80) REVERT: B 421 TYR cc_start: 0.6599 (m-80) cc_final: 0.6249 (m-10) REVERT: B 436 TRP cc_start: 0.6745 (p90) cc_final: 0.6419 (p90) REVERT: B 454 ARG cc_start: 0.8486 (mmt90) cc_final: 0.8062 (mmt90) REVERT: B 508 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6870 (m-10) REVERT: B 511 VAL cc_start: 0.8806 (t) cc_final: 0.8541 (p) REVERT: B 534 VAL cc_start: 0.8224 (t) cc_final: 0.8004 (p) REVERT: B 541 PHE cc_start: 0.6849 (p90) cc_final: 0.6416 (p90) REVERT: B 586 ASP cc_start: 0.7567 (m-30) cc_final: 0.7075 (m-30) REVERT: B 606 ASN cc_start: 0.8446 (m-40) cc_final: 0.8245 (m-40) REVERT: B 675 GLN cc_start: 0.7714 (mt0) cc_final: 0.7468 (mt0) REVERT: B 725 GLU cc_start: 0.7838 (tt0) cc_final: 0.7494 (tt0) REVERT: B 748 GLU cc_start: 0.8031 (pp20) cc_final: 0.7808 (pp20) REVERT: B 764 ASN cc_start: 0.7587 (m-40) cc_final: 0.7241 (m-40) REVERT: B 772 VAL cc_start: 0.8577 (p) cc_final: 0.8334 (t) REVERT: B 859 THR cc_start: 0.8136 (t) cc_final: 0.7856 (p) REVERT: B 933 LYS cc_start: 0.8100 (mttt) cc_final: 0.7361 (mmtm) REVERT: B 935 GLN cc_start: 0.8049 (mt0) cc_final: 0.7787 (mt0) REVERT: B 947 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7571 (mtpp) REVERT: B 950 ASP cc_start: 0.7622 (m-30) cc_final: 0.7039 (m-30) REVERT: B 1014 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7808 (mtm-85) REVERT: F 71 PHE cc_start: 0.6903 (t80) cc_final: 0.6442 (t80) REVERT: D 34 MET cc_start: 0.6404 (ppp) cc_final: 0.5808 (ppp) REVERT: D 62 ASP cc_start: 0.8621 (p0) cc_final: 0.8379 (p0) REVERT: C 53 ASP cc_start: 0.6893 (t0) cc_final: 0.6612 (t0) REVERT: C 83 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.6247 (p) REVERT: C 129 LYS cc_start: 0.7617 (mmtm) cc_final: 0.7397 (mmtm) REVERT: C 200 TYR cc_start: 0.5615 (m-10) cc_final: 0.5358 (m-10) REVERT: C 206 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7214 (ttmm) REVERT: C 224 GLU cc_start: 0.6774 (mp0) cc_final: 0.6566 (mp0) REVERT: C 237 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6683 (ttm-80) REVERT: C 314 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7906 (tp40) REVERT: C 319 ARG cc_start: 0.8130 (ptp90) cc_final: 0.7826 (ptt180) REVERT: C 326 ILE cc_start: 0.6282 (OUTLIER) cc_final: 0.6070 (tt) REVERT: C 340 GLU cc_start: 0.7348 (mp0) cc_final: 0.6902 (mp0) REVERT: C 541 PHE cc_start: 0.7049 (p90) cc_final: 0.6743 (p90) REVERT: C 574 ASP cc_start: 0.7512 (t70) cc_final: 0.7009 (t70) REVERT: C 651 ILE cc_start: 0.8753 (mm) cc_final: 0.8481 (mt) REVERT: C 705 VAL cc_start: 0.7069 (OUTLIER) cc_final: 0.6805 (p) REVERT: C 725 GLU cc_start: 0.7872 (tt0) cc_final: 0.7665 (tt0) REVERT: C 750 SER cc_start: 0.7860 (t) cc_final: 0.7545 (p) REVERT: C 776 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7852 (ttmm) REVERT: C 790 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7241 (mmpt) REVERT: C 815 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7324 (mtm-85) REVERT: C 858 LEU cc_start: 0.8381 (mm) cc_final: 0.8141 (mp) REVERT: C 883 THR cc_start: 0.8198 (m) cc_final: 0.7795 (p) REVERT: C 933 LYS cc_start: 0.8137 (mttt) cc_final: 0.7466 (mptt) REVERT: C 947 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7715 (mtpp) REVERT: C 964 LYS cc_start: 0.8381 (mttt) cc_final: 0.8121 (mttt) REVERT: C 974 SER cc_start: 0.8735 (m) cc_final: 0.8330 (p) REVERT: C 994 ASP cc_start: 0.7582 (t70) cc_final: 0.7331 (m-30) REVERT: C 1030 SER cc_start: 0.7918 (m) cc_final: 0.7666 (p) REVERT: C 1038 LYS cc_start: 0.7919 (tppt) cc_final: 0.7384 (mmmm) REVERT: C 1045 LYS cc_start: 0.7996 (mttt) cc_final: 0.7764 (mttt) REVERT: C 1055 SER cc_start: 0.8412 (t) cc_final: 0.8061 (m) REVERT: C 1072 GLU cc_start: 0.7586 (pm20) cc_final: 0.7280 (pm20) REVERT: C 1101 HIS cc_start: 0.8365 (m-70) cc_final: 0.7905 (m-70) REVERT: C 1123 SER cc_start: 0.8510 (t) cc_final: 0.8206 (m) REVERT: C 1141 LEU cc_start: 0.7883 (tp) cc_final: 0.7598 (tm) REVERT: G 71 PHE cc_start: 0.6870 (t80) cc_final: 0.6466 (t80) REVERT: G 92 PHE cc_start: 0.7395 (m-80) cc_final: 0.6990 (m-80) REVERT: E 31 SER cc_start: 0.7987 (p) cc_final: 0.7765 (p) REVERT: E 32 TYR cc_start: 0.7727 (m-80) cc_final: 0.7258 (m-80) REVERT: E 68 PHE cc_start: 0.7934 (m-10) cc_final: 0.7387 (m-10) outliers start: 130 outliers final: 92 residues processed: 722 average time/residue: 0.5785 time to fit residues: 498.2225 Evaluate side-chains 755 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 651 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 247 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 chunk 318 optimal weight: 0.5980 chunk 186 optimal weight: 0.0980 chunk 160 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B 957 GLN B1101 HIS C 755 GLN C 764 ASN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.201080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.179450 restraints weight = 58367.019| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.67 r_work: 0.4067 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31419 Z= 0.138 Angle : 0.681 20.356 42840 Z= 0.330 Chirality : 0.047 0.344 4920 Planarity : 0.005 0.074 5448 Dihedral : 6.169 109.066 5199 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.37 % Allowed : 20.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.26 (0.13), residues: 3780 helix: 1.25 (0.21), residues: 669 sheet: -0.51 (0.17), residues: 897 loop : -1.71 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 346 TYR 0.064 0.001 TYR E 60 PHE 0.027 0.002 PHE C 490 TRP 0.022 0.002 TRP E 47 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (31317) covalent geometry : angle 0.67056 (42591) SS BOND : bond 0.00472 ( 48) SS BOND : angle 1.38618 ( 96) hydrogen bonds : bond 0.03394 ( 871) hydrogen bonds : angle 5.36765 ( 2505) Misc. bond : bond 0.00458 ( 3) link_BETA1-4 : bond 0.00367 ( 12) link_BETA1-4 : angle 0.92509 ( 36) link_NAG-ASN : bond 0.00564 ( 39) link_NAG-ASN : angle 2.02055 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 652 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7324 (tp-100) REVERT: A 140 PHE cc_start: 0.7345 (p90) cc_final: 0.6636 (p90) REVERT: A 153 MET cc_start: 0.4379 (mpp) cc_final: 0.3954 (mpp) REVERT: A 177 MET cc_start: 0.0196 (mtt) cc_final: -0.0711 (mtt) REVERT: A 200 TYR cc_start: 0.5245 (m-10) cc_final: 0.5029 (m-10) REVERT: A 206 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7300 (ttmm) REVERT: A 274 THR cc_start: 0.8717 (t) cc_final: 0.8286 (t) REVERT: A 282 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6566 (m110) REVERT: A 319 ARG cc_start: 0.7790 (ptp90) cc_final: 0.7317 (ptt180) REVERT: A 429 PHE cc_start: 0.6415 (t80) cc_final: 0.6128 (t80) REVERT: A 454 ARG cc_start: 0.8206 (mmt90) cc_final: 0.7824 (mmt90) REVERT: A 500 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (p) REVERT: A 541 PHE cc_start: 0.7080 (p90) cc_final: 0.6359 (p90) REVERT: A 673 SER cc_start: 0.8264 (t) cc_final: 0.7877 (p) REVERT: A 736 VAL cc_start: 0.8197 (t) cc_final: 0.7933 (m) REVERT: A 790 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7445 (mtmt) REVERT: A 795 LYS cc_start: 0.8459 (mptm) cc_final: 0.8202 (mptp) REVERT: A 811 LYS cc_start: 0.7177 (mmpt) cc_final: 0.6692 (mtpt) REVERT: A 864 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 933 LYS cc_start: 0.7927 (mttt) cc_final: 0.7569 (mtmm) REVERT: A 947 LYS cc_start: 0.7596 (mtpt) cc_final: 0.7287 (mtmt) REVERT: A 1019 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7629 (ttm110) REVERT: A 1045 LYS cc_start: 0.8342 (mttt) cc_final: 0.8034 (mttt) REVERT: A 1072 GLU cc_start: 0.7950 (pm20) cc_final: 0.7546 (pm20) REVERT: A 1111 GLU cc_start: 0.7599 (tt0) cc_final: 0.7294 (tt0) REVERT: A 1141 LEU cc_start: 0.7880 (tt) cc_final: 0.7668 (tt) REVERT: H 33 VAL cc_start: 0.8102 (t) cc_final: 0.7833 (p) REVERT: H 34 MET cc_start: 0.6171 (ppp) cc_final: 0.5914 (ppp) REVERT: H 102 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 49 HIS cc_start: 0.8213 (t-90) cc_final: 0.7768 (t70) REVERT: B 153 MET cc_start: 0.5469 (mpp) cc_final: 0.5076 (mpp) REVERT: B 206 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7262 (ttmm) REVERT: B 319 ARG cc_start: 0.8135 (ptp90) cc_final: 0.7797 (ptt180) REVERT: B 340 GLU cc_start: 0.7574 (mp0) cc_final: 0.7139 (mp0) REVERT: B 374 PHE cc_start: 0.7460 (m-80) cc_final: 0.6875 (m-80) REVERT: B 436 TRP cc_start: 0.6715 (p90) cc_final: 0.6405 (p90) REVERT: B 454 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8219 (mmt90) REVERT: B 490 PHE cc_start: 0.7999 (t80) cc_final: 0.7447 (t80) REVERT: B 511 VAL cc_start: 0.8793 (t) cc_final: 0.8521 (p) REVERT: B 541 PHE cc_start: 0.6850 (p90) cc_final: 0.6425 (p90) REVERT: B 586 ASP cc_start: 0.7596 (m-30) cc_final: 0.7096 (m-30) REVERT: B 606 ASN cc_start: 0.8455 (m-40) cc_final: 0.8243 (m-40) REVERT: B 675 GLN cc_start: 0.7756 (mt0) cc_final: 0.7530 (mt0) REVERT: B 725 GLU cc_start: 0.7831 (tt0) cc_final: 0.7495 (tt0) REVERT: B 748 GLU cc_start: 0.8047 (pp20) cc_final: 0.7845 (pp20) REVERT: B 764 ASN cc_start: 0.7594 (m-40) cc_final: 0.7254 (m-40) REVERT: B 772 VAL cc_start: 0.8581 (p) cc_final: 0.8334 (t) REVERT: B 859 THR cc_start: 0.8139 (t) cc_final: 0.7866 (p) REVERT: B 933 LYS cc_start: 0.8077 (mttt) cc_final: 0.7305 (mmtm) REVERT: B 935 GLN cc_start: 0.8056 (mt0) cc_final: 0.7792 (mt0) REVERT: B 947 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7535 (mtpp) REVERT: B 950 ASP cc_start: 0.7633 (m-30) cc_final: 0.7049 (m-30) REVERT: B 1014 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: B 1050 MET cc_start: 0.8262 (ptm) cc_final: 0.8055 (ptt) REVERT: F 71 PHE cc_start: 0.6930 (t80) cc_final: 0.6480 (t80) REVERT: D 34 MET cc_start: 0.6219 (ppp) cc_final: 0.5747 (ppp) REVERT: D 57 ASN cc_start: 0.7406 (t0) cc_final: 0.7175 (t0) REVERT: D 62 ASP cc_start: 0.8631 (p0) cc_final: 0.8411 (p0) REVERT: C 53 ASP cc_start: 0.6890 (t0) cc_final: 0.6608 (t0) REVERT: C 83 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.6286 (p) REVERT: C 84 LEU cc_start: 0.7197 (mt) cc_final: 0.6966 (mp) REVERT: C 129 LYS cc_start: 0.7571 (mmtm) cc_final: 0.7357 (mmtm) REVERT: C 200 TYR cc_start: 0.5521 (m-10) cc_final: 0.5288 (m-10) REVERT: C 206 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7194 (ttmm) REVERT: C 224 GLU cc_start: 0.6810 (mp0) cc_final: 0.6607 (mp0) REVERT: C 237 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6777 (ttm-80) REVERT: C 267 VAL cc_start: 0.8127 (t) cc_final: 0.7775 (p) REVERT: C 314 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7905 (tp40) REVERT: C 319 ARG cc_start: 0.8086 (ptp90) cc_final: 0.7774 (ptt180) REVERT: C 340 GLU cc_start: 0.7364 (mp0) cc_final: 0.6898 (mp0) REVERT: C 541 PHE cc_start: 0.7041 (p90) cc_final: 0.6751 (p90) REVERT: C 574 ASP cc_start: 0.7440 (t70) cc_final: 0.7130 (t70) REVERT: C 651 ILE cc_start: 0.8750 (mm) cc_final: 0.8475 (mt) REVERT: C 705 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6750 (p) REVERT: C 725 GLU cc_start: 0.7867 (tt0) cc_final: 0.7657 (tt0) REVERT: C 750 SER cc_start: 0.7798 (t) cc_final: 0.7509 (p) REVERT: C 776 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7716 (tmmm) REVERT: C 790 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7214 (mmpt) REVERT: C 815 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7230 (mtm-85) REVERT: C 858 LEU cc_start: 0.8367 (mm) cc_final: 0.8054 (mp) REVERT: C 859 THR cc_start: 0.8139 (t) cc_final: 0.7757 (p) REVERT: C 883 THR cc_start: 0.8167 (m) cc_final: 0.7769 (p) REVERT: C 933 LYS cc_start: 0.8081 (mttt) cc_final: 0.7405 (mptt) REVERT: C 947 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7725 (mtpp) REVERT: C 964 LYS cc_start: 0.8400 (mttt) cc_final: 0.8140 (mttt) REVERT: C 974 SER cc_start: 0.8772 (m) cc_final: 0.8402 (p) REVERT: C 994 ASP cc_start: 0.7561 (t70) cc_final: 0.7315 (m-30) REVERT: C 1030 SER cc_start: 0.7916 (m) cc_final: 0.7670 (p) REVERT: C 1038 LYS cc_start: 0.7933 (tppt) cc_final: 0.7396 (mmmm) REVERT: C 1045 LYS cc_start: 0.8022 (mttt) cc_final: 0.7795 (mttt) REVERT: C 1055 SER cc_start: 0.8379 (t) cc_final: 0.8017 (m) REVERT: C 1072 GLU cc_start: 0.7614 (pm20) cc_final: 0.7307 (pm20) REVERT: C 1101 HIS cc_start: 0.8354 (m-70) cc_final: 0.7853 (m-70) REVERT: C 1123 SER cc_start: 0.8522 (t) cc_final: 0.8224 (m) REVERT: C 1141 LEU cc_start: 0.7864 (tp) cc_final: 0.7585 (tm) REVERT: G 71 PHE cc_start: 0.6782 (t80) cc_final: 0.6377 (t80) REVERT: G 92 PHE cc_start: 0.7360 (m-80) cc_final: 0.6906 (m-80) REVERT: E 31 SER cc_start: 0.7938 (p) cc_final: 0.7725 (p) REVERT: E 32 TYR cc_start: 0.7694 (m-80) cc_final: 0.7244 (m-80) outliers start: 112 outliers final: 91 residues processed: 707 average time/residue: 0.5772 time to fit residues: 487.9642 Evaluate side-chains 739 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 635 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 16 optimal weight: 6.9990 chunk 132 optimal weight: 0.2980 chunk 202 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B 957 GLN B1101 HIS C 764 ASN C 787 GLN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.198253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.176616 restraints weight = 57654.551| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.69 r_work: 0.4024 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31419 Z= 0.211 Angle : 0.723 16.314 42840 Z= 0.355 Chirality : 0.049 0.335 4920 Planarity : 0.005 0.068 5448 Dihedral : 6.302 108.364 5199 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.34 % Allowed : 21.32 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3780 helix: 1.11 (0.21), residues: 657 sheet: -0.69 (0.17), residues: 906 loop : -1.73 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 273 TYR 0.042 0.002 TYR E 60 PHE 0.026 0.002 PHE B 92 TRP 0.022 0.002 TRP L 35 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00496 (31317) covalent geometry : angle 0.71109 (42591) SS BOND : bond 0.00472 ( 48) SS BOND : angle 1.65532 ( 96) hydrogen bonds : bond 0.03878 ( 871) hydrogen bonds : angle 5.48805 ( 2505) Misc. bond : bond 0.00440 ( 3) link_BETA1-4 : bond 0.00370 ( 12) link_BETA1-4 : angle 0.96823 ( 36) link_NAG-ASN : bond 0.00684 ( 39) link_NAG-ASN : angle 2.13708 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 653 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7411 (tp-100) REVERT: A 140 PHE cc_start: 0.7383 (p90) cc_final: 0.6658 (p90) REVERT: A 153 MET cc_start: 0.4151 (mpp) cc_final: 0.3767 (mpp) REVERT: A 177 MET cc_start: 0.0489 (mtt) cc_final: -0.0415 (mtt) REVERT: A 206 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7348 (ttmm) REVERT: A 319 ARG cc_start: 0.7811 (ptp90) cc_final: 0.7411 (ptt180) REVERT: A 500 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7950 (p) REVERT: A 541 PHE cc_start: 0.7113 (p90) cc_final: 0.6466 (p90) REVERT: A 673 SER cc_start: 0.8321 (t) cc_final: 0.7935 (p) REVERT: A 736 VAL cc_start: 0.8253 (t) cc_final: 0.7975 (m) REVERT: A 790 LYS cc_start: 0.7813 (mtmm) cc_final: 0.7365 (mtpt) REVERT: A 795 LYS cc_start: 0.8486 (mptm) cc_final: 0.8218 (mptp) REVERT: A 811 LYS cc_start: 0.7196 (mmpt) cc_final: 0.6699 (mtpt) REVERT: A 933 LYS cc_start: 0.7935 (mttt) cc_final: 0.7570 (mtmm) REVERT: A 1019 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7735 (ttm110) REVERT: A 1045 LYS cc_start: 0.8293 (mttt) cc_final: 0.7965 (mttt) REVERT: A 1072 GLU cc_start: 0.8085 (pm20) cc_final: 0.7691 (pm20) REVERT: A 1111 GLU cc_start: 0.7619 (tt0) cc_final: 0.7325 (tt0) REVERT: A 1141 LEU cc_start: 0.7870 (tt) cc_final: 0.7655 (tt) REVERT: H 34 MET cc_start: 0.6389 (ppp) cc_final: 0.6155 (ppp) REVERT: H 102 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7555 (t80) REVERT: B 49 HIS cc_start: 0.8222 (t-90) cc_final: 0.7760 (t70) REVERT: B 153 MET cc_start: 0.5609 (mpp) cc_final: 0.5179 (mpp) REVERT: B 319 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7757 (ptt180) REVERT: B 340 GLU cc_start: 0.7680 (mp0) cc_final: 0.7436 (mp0) REVERT: B 374 PHE cc_start: 0.7615 (m-80) cc_final: 0.7389 (m-80) REVERT: B 454 ARG cc_start: 0.8513 (mmt90) cc_final: 0.8176 (mmt90) REVERT: B 490 PHE cc_start: 0.8083 (t80) cc_final: 0.7554 (t80) REVERT: B 493 GLN cc_start: 0.7879 (tp40) cc_final: 0.7649 (tm-30) REVERT: B 511 VAL cc_start: 0.8806 (t) cc_final: 0.8557 (p) REVERT: B 541 PHE cc_start: 0.6902 (p90) cc_final: 0.6426 (p90) REVERT: B 586 ASP cc_start: 0.7584 (m-30) cc_final: 0.7094 (m-30) REVERT: B 606 ASN cc_start: 0.8468 (m-40) cc_final: 0.8254 (m-40) REVERT: B 675 GLN cc_start: 0.7737 (mt0) cc_final: 0.7528 (mt0) REVERT: B 725 GLU cc_start: 0.7869 (tt0) cc_final: 0.7519 (tt0) REVERT: B 764 ASN cc_start: 0.7608 (m-40) cc_final: 0.7351 (m110) REVERT: B 772 VAL cc_start: 0.8588 (p) cc_final: 0.8349 (t) REVERT: B 859 THR cc_start: 0.8156 (t) cc_final: 0.7871 (p) REVERT: B 933 LYS cc_start: 0.8088 (mttt) cc_final: 0.7353 (mmtm) REVERT: B 935 GLN cc_start: 0.8047 (mt0) cc_final: 0.7796 (mt0) REVERT: B 947 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7549 (mtpp) REVERT: B 950 ASP cc_start: 0.7642 (m-30) cc_final: 0.7070 (m-30) REVERT: B 994 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7404 (t0) REVERT: B 1014 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: F 71 PHE cc_start: 0.6973 (t80) cc_final: 0.6553 (t80) REVERT: D 34 MET cc_start: 0.6384 (ppp) cc_final: 0.5932 (ppp) REVERT: D 39 GLN cc_start: 0.7563 (tp40) cc_final: 0.6966 (pp30) REVERT: C 53 ASP cc_start: 0.6920 (t0) cc_final: 0.6672 (t0) REVERT: C 83 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.6381 (p) REVERT: C 84 LEU cc_start: 0.7268 (mt) cc_final: 0.7031 (mp) REVERT: C 200 TYR cc_start: 0.5668 (m-10) cc_final: 0.5411 (m-10) REVERT: C 206 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7298 (ttmm) REVERT: C 224 GLU cc_start: 0.6889 (mp0) cc_final: 0.6664 (mp0) REVERT: C 237 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6785 (ttm-80) REVERT: C 314 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: C 319 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7829 (ptt180) REVERT: C 340 GLU cc_start: 0.7549 (mp0) cc_final: 0.7056 (mp0) REVERT: C 437 ASN cc_start: 0.7669 (t0) cc_final: 0.7449 (t0) REVERT: C 541 PHE cc_start: 0.7125 (p90) cc_final: 0.6823 (p90) REVERT: C 574 ASP cc_start: 0.7536 (t70) cc_final: 0.7182 (t70) REVERT: C 651 ILE cc_start: 0.8755 (mm) cc_final: 0.8512 (mt) REVERT: C 705 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6894 (p) REVERT: C 725 GLU cc_start: 0.7908 (tt0) cc_final: 0.7690 (tt0) REVERT: C 750 SER cc_start: 0.7858 (t) cc_final: 0.7591 (p) REVERT: C 776 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (ttmm) REVERT: C 790 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7224 (mmpt) REVERT: C 815 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7319 (mtm-85) REVERT: C 858 LEU cc_start: 0.8394 (mm) cc_final: 0.8109 (mp) REVERT: C 883 THR cc_start: 0.8242 (m) cc_final: 0.7801 (p) REVERT: C 918 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7221 (mp0) REVERT: C 931 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7023 (mp) REVERT: C 933 LYS cc_start: 0.8117 (mttt) cc_final: 0.7441 (mptt) REVERT: C 947 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7730 (mtpp) REVERT: C 964 LYS cc_start: 0.8397 (mttt) cc_final: 0.8157 (mttt) REVERT: C 994 ASP cc_start: 0.7612 (t70) cc_final: 0.7363 (m-30) REVERT: C 1030 SER cc_start: 0.7966 (m) cc_final: 0.7710 (p) REVERT: C 1038 LYS cc_start: 0.7982 (tppt) cc_final: 0.7460 (mmmm) REVERT: C 1045 LYS cc_start: 0.8008 (mttt) cc_final: 0.7794 (mttt) REVERT: C 1055 SER cc_start: 0.8422 (t) cc_final: 0.8078 (m) REVERT: C 1072 GLU cc_start: 0.7636 (pm20) cc_final: 0.7339 (pm20) REVERT: C 1101 HIS cc_start: 0.8414 (m-70) cc_final: 0.7948 (m-70) REVERT: C 1141 LEU cc_start: 0.7919 (tp) cc_final: 0.7623 (tm) REVERT: G 71 PHE cc_start: 0.6897 (t80) cc_final: 0.6433 (t80) REVERT: G 92 PHE cc_start: 0.7462 (m-80) cc_final: 0.6927 (m-80) REVERT: E 31 SER cc_start: 0.8030 (p) cc_final: 0.7746 (p) REVERT: E 32 TYR cc_start: 0.7733 (m-80) cc_final: 0.7328 (m-80) outliers start: 111 outliers final: 82 residues processed: 707 average time/residue: 0.5760 time to fit residues: 487.1704 Evaluate side-chains 743 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 649 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 TRP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 0.5980 chunk 301 optimal weight: 0.5980 chunk 351 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 291 optimal weight: 0.5980 chunk 346 optimal weight: 0.6980 chunk 292 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 764 ASN A 804 GLN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN B 540 ASN B 564 GLN B 957 GLN B1101 HIS C 764 ASN C 919 ASN C1010 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.200235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.178647 restraints weight = 58276.493| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.66 r_work: 0.4055 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31419 Z= 0.141 Angle : 0.689 15.184 42840 Z= 0.335 Chirality : 0.047 0.340 4920 Planarity : 0.004 0.055 5448 Dihedral : 6.178 107.873 5199 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.07 % Allowed : 21.95 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.13), residues: 3780 helix: 1.35 (0.21), residues: 651 sheet: -0.55 (0.17), residues: 897 loop : -1.69 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 61 TYR 0.040 0.002 TYR E 60 PHE 0.028 0.002 PHE B 168 TRP 0.021 0.002 TRP H 47 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00334 (31317) covalent geometry : angle 0.67851 (42591) SS BOND : bond 0.00446 ( 48) SS BOND : angle 1.44509 ( 96) hydrogen bonds : bond 0.03426 ( 871) hydrogen bonds : angle 5.37542 ( 2505) Misc. bond : bond 0.00430 ( 3) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 0.95853 ( 36) link_NAG-ASN : bond 0.00582 ( 39) link_NAG-ASN : angle 2.02241 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12792.64 seconds wall clock time: 217 minutes 48.62 seconds (13068.62 seconds total)