Starting phenix.real_space_refine on Thu Jun 26 13:41:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r40_14250/06_2025/7r40_14250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r40_14250/06_2025/7r40_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_14250/06_2025/7r40_14250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r40_14250/06_2025/7r40_14250.map" model { file = "/net/cci-nas-00/data/ceres_data/7r40_14250/06_2025/7r40_14250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r40_14250/06_2025/7r40_14250.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.86, per 1000 atoms: 0.62 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: 8.48 Conformation dependent library (CDL) restraints added in 3.9 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: 4.61 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: 13.73 Time building geometry restraints manager: 8.65 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: 0.20 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: 7.630 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: 0.040 Extract box with map and model: 1.270 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 71.100 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP D 47 HIS 0.003 0.000 HIS B1048 PHE 0.016 0.001 PHE G 49 TYR 0.010 0.001 TYR C 351 ARG 0.005 0.000 ARG B 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 39) link_NAG-ASN : angle 2.74865 ( 117) link_BETA1-4 : bond 0.00740 ( 12) link_BETA1-4 : angle 1.28309 ( 36) hydrogen bonds : bond 0.28524 ( 871) hydrogen bonds : angle 10.33944 ( 2505) SS BOND : bond 0.00387 ( 48) SS BOND : angle 1.00020 ( 96) covalent geometry : bond 0.00377 (31317) covalent geometry : angle 0.73238 (42591) Misc. bond : bond 0.00105 ( 3) *********************** 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 : 3.091 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: 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: 0.7019 (m-80) REVERT: A 129 LYS cc_start: 0.6947 (mppt) cc_final: 0.6629 (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: 0.6659 (m-10) REVERT: A 455 LEU cc_start: 0.8268 (mm) cc_final: 0.7864 (mm) REVERT: A 511 VAL cc_start: 0.8113 (t) cc_final: 0.7894 (p) REVERT: A 572 THR cc_start: 0.8105 (t) cc_final: 0.7668 (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: 0.7643 (mttt) REVERT: A 975 SER cc_start: 0.8576 (p) cc_final: 0.8228 (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: 0.7475 (m-70) cc_final: 0.7185 (m170) REVERT: A 1138 TYR cc_start: 0.7675 (t80) cc_final: 0.7439 (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: 0.5597 (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: 0.4166 (mpp) REVERT: B 192 PHE cc_start: 0.7684 (m-80) cc_final: 0.7335 (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: 0.6841 (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: 0.6208 (m-80) REVERT: B 427 ASP cc_start: 0.7460 (p0) cc_final: 0.7215 (p0) REVERT: B 511 VAL cc_start: 0.8281 (t) cc_final: 0.7949 (p) REVERT: B 541 PHE cc_start: 0.6432 (p90) cc_final: 0.6087 (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: 0.7299 (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: 0.7218 (m-40) cc_final: 0.7015 (m-40) REVERT: B 772 VAL cc_start: 0.8514 (p) cc_final: 0.8195 (t) REVERT: B 790 LYS cc_start: 0.7328 (mmpt) cc_final: 0.6852 (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: 0.7508 (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: 0.5394 (t) REVERT: B 1138 TYR cc_start: 0.7570 (t80) cc_final: 0.7204 (t80) REVERT: F 35 TRP cc_start: 0.4773 (m-10) cc_final: 0.4556 (m-10) REVERT: F 71 PHE cc_start: 0.5833 (t80) cc_final: 0.5452 (t80) REVERT: C 29 THR cc_start: 0.7104 (m) cc_final: 0.6759 (t) REVERT: C 45 SER cc_start: 0.7750 (t) cc_final: 0.7383 (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: 0.7214 (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: 0.6322 (m-80) REVERT: C 427 ASP cc_start: 0.7512 (p0) cc_final: 0.7240 (p0) REVERT: C 453 TYR cc_start: 0.6947 (p90) cc_final: 0.5541 (p90) REVERT: C 511 VAL cc_start: 0.8263 (t) cc_final: 0.7968 (p) REVERT: C 532 ASN cc_start: 0.8300 (t0) cc_final: 0.8090 (t0) REVERT: C 541 PHE cc_start: 0.6507 (p90) cc_final: 0.5979 (p90) REVERT: C 553 THR cc_start: 0.8147 (p) cc_final: 0.7929 (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: 0.6904 (tt0) REVERT: C 772 VAL cc_start: 0.8442 (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: 0.7023 (mmpt) REVERT: C 868 GLU cc_start: 0.7122 (mp0) cc_final: 0.6830 (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: 0.7664 (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: 0.7554 (mttt) REVERT: C 975 SER cc_start: 0.8623 (p) cc_final: 0.8324 (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: 0.5570 (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: 1.7330 time to fit residues: 1599.9789 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 : 3.337 ------------------------------------------------------------------------------- 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 321 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 345 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 804 GLN 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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 607 GLN B 613 GLN B 804 GLN B 919 ASN 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 804 GLN C 960 ASN C 992 GLN C1010 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.205004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183225 restraints weight = 59481.296| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 3.80 r_work: 0.4120 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31419 Z= 0.207 Angle : 0.722 20.687 42840 Z= 0.356 Chirality : 0.049 0.510 4920 Planarity : 0.005 0.064 5448 Dihedral : 7.210 96.021 5209 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.26 % Allowed : 11.86 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 3780 helix: -0.72 (0.19), residues: 615 sheet: -0.44 (0.17), residues: 879 loop : -1.63 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.006 0.001 HIS C 49 PHE 0.023 0.002 PHE C 559 TYR 0.021 0.002 TYR A 453 ARG 0.008 0.001 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00894 ( 39) link_NAG-ASN : angle 3.82404 ( 117) link_BETA1-4 : bond 0.00378 ( 12) link_BETA1-4 : angle 1.19131 ( 36) hydrogen bonds : bond 0.05532 ( 871) hydrogen bonds : angle 6.57068 ( 2505) SS BOND : bond 0.00325 ( 48) SS BOND : angle 1.41749 ( 96) covalent geometry : bond 0.00480 (31317) covalent geometry : angle 0.69203 (42591) Misc. bond : bond 0.00143 ( 3) *********************** 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 793 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 3.486 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: 0.7793 (m-10) cc_final: 0.7420 (m-10) REVERT: A 153 MET cc_start: 0.3756 (mpp) cc_final: 0.3493 (mpp) REVERT: A 208 THR cc_start: 0.8289 (t) cc_final: 0.8036 (p) REVERT: A 319 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7264 (ptt180) REVERT: A 421 TYR cc_start: 0.6790 (m-80) cc_final: 0.6586 (m-80) REVERT: A 429 PHE cc_start: 0.5585 (t80) cc_final: 0.5328 (t80) REVERT: A 572 THR cc_start: 0.8353 (t) cc_final: 0.8045 (p) REVERT: A 612 TYR cc_start: 0.8498 (m-80) cc_final: 0.8132 (m-80) REVERT: A 651 ILE cc_start: 0.8754 (mm) cc_final: 0.8548 (mp) REVERT: A 673 SER cc_start: 0.8514 (t) cc_final: 0.8145 (p) REVERT: A 719 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 736 VAL cc_start: 0.8158 (t) cc_final: 0.7812 (m) REVERT: A 776 LYS cc_start: 0.8018 (tmmt) cc_final: 0.7752 (ttpp) REVERT: A 790 LYS cc_start: 0.7536 (mmpt) cc_final: 0.7283 (mmpt) REVERT: A 811 LYS cc_start: 0.7092 (mmpt) cc_final: 0.6605 (mtpp) REVERT: A 902 MET cc_start: 0.8175 (tpt) cc_final: 0.7974 (mmt) REVERT: A 933 LYS cc_start: 0.7984 (mttt) cc_final: 0.7606 (mtmm) REVERT: A 936 ASP cc_start: 0.7568 (m-30) cc_final: 0.7289 (m-30) REVERT: A 947 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7589 (mtpp) REVERT: A 975 SER cc_start: 0.8673 (p) cc_final: 0.8349 (t) REVERT: A 1038 LYS cc_start: 0.7980 (tppt) cc_final: 0.7725 (mmmt) REVERT: A 1045 LYS cc_start: 0.8367 (mttt) cc_final: 0.7891 (mttt) REVERT: A 1086 LYS cc_start: 0.6969 (mtmm) cc_final: 0.6356 (mtmm) REVERT: A 1101 HIS cc_start: 0.8107 (m-70) cc_final: 0.7886 (m-70) REVERT: A 1141 LEU cc_start: 0.7698 (tm) cc_final: 0.7451 (tt) REVERT: L 81 GLU cc_start: 0.7743 (mp0) cc_final: 0.7410 (mp0) REVERT: H 34 MET cc_start: 0.6321 (ppp) cc_final: 0.5492 (ppp) REVERT: B 49 HIS cc_start: 0.8115 (t-90) cc_final: 0.7851 (t70) REVERT: B 53 ASP cc_start: 0.6627 (t0) cc_final: 0.6335 (t0) REVERT: B 54 LEU cc_start: 0.7968 (mm) cc_final: 0.7726 (mm) REVERT: B 61 ASN cc_start: 0.6739 (p0) cc_final: 0.6485 (p0) REVERT: B 153 MET cc_start: 0.4911 (mpp) cc_final: 0.4622 (mpp) REVERT: B 192 PHE cc_start: 0.8350 (m-80) cc_final: 0.8139 (m-80) REVERT: B 286 THR cc_start: 0.7954 (OUTLIER) cc_final: 0.7666 (t) REVERT: B 319 ARG cc_start: 0.7845 (ptp90) cc_final: 0.7459 (ptt180) REVERT: B 340 GLU cc_start: 0.7330 (mp0) cc_final: 0.6875 (mp0) REVERT: B 421 TYR cc_start: 0.6891 (m-80) cc_final: 0.6519 (m-10) REVERT: B 427 ASP cc_start: 0.7960 (p0) cc_final: 0.7738 (p0) REVERT: B 497 PHE cc_start: 0.4509 (m-10) cc_final: 0.3553 (m-10) REVERT: B 511 VAL cc_start: 0.8638 (t) cc_final: 0.8418 (p) REVERT: B 586 ASP cc_start: 0.7612 (m-30) cc_final: 0.7234 (m-30) REVERT: B 675 GLN cc_start: 0.7702 (mt0) cc_final: 0.7448 (mt0) REVERT: B 725 GLU cc_start: 0.7783 (tt0) cc_final: 0.7474 (tt0) REVERT: B 761 THR cc_start: 0.7138 (m) cc_final: 0.6892 (t) REVERT: B 764 ASN cc_start: 0.7498 (m-40) cc_final: 0.7256 (m-40) REVERT: B 772 VAL cc_start: 0.8563 (p) cc_final: 0.8339 (t) REVERT: B 780 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: B 859 THR cc_start: 0.8141 (t) cc_final: 0.7891 (p) REVERT: B 931 ILE cc_start: 0.7847 (mm) cc_final: 0.7576 (tp) REVERT: B 933 LYS cc_start: 0.8071 (mttt) cc_final: 0.7353 (mmtm) REVERT: B 947 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7520 (mtpp) REVERT: B 950 ASP cc_start: 0.7742 (m-30) cc_final: 0.7309 (m-30) REVERT: B 1038 LYS cc_start: 0.7942 (tppt) cc_final: 0.7696 (tppt) REVERT: B 1055 SER cc_start: 0.8065 (t) cc_final: 0.7748 (m) REVERT: B 1082 CYS cc_start: 0.7167 (t) cc_final: 0.6687 (t) REVERT: B 1138 TYR cc_start: 0.7902 (t80) cc_final: 0.7420 (t80) REVERT: F 71 PHE cc_start: 0.6730 (t80) cc_final: 0.6135 (t80) REVERT: D 39 GLN cc_start: 0.7230 (tp40) cc_final: 0.6571 (pp30) REVERT: C 45 SER cc_start: 0.8159 (t) cc_final: 0.7913 (p) REVERT: C 53 ASP cc_start: 0.6962 (t0) cc_final: 0.6724 (t70) REVERT: C 81 ASN cc_start: 0.7456 (p0) cc_final: 0.7064 (m-40) REVERT: C 84 LEU cc_start: 0.7239 (mt) cc_final: 0.6997 (mp) REVERT: C 121 ASN cc_start: 0.6214 (t0) cc_final: 0.5995 (t0) REVERT: C 138 ASP cc_start: 0.6586 (t0) cc_final: 0.6137 (t0) REVERT: C 192 PHE cc_start: 0.8280 (m-80) cc_final: 0.8036 (m-80) REVERT: C 208 THR cc_start: 0.8340 (t) cc_final: 0.8100 (p) REVERT: C 224 GLU cc_start: 0.6759 (mp0) cc_final: 0.6526 (mp0) REVERT: C 314 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: C 340 GLU cc_start: 0.6957 (mp0) cc_final: 0.6641 (mp0) REVERT: C 392 PHE cc_start: 0.7317 (m-10) cc_final: 0.7088 (m-80) REVERT: C 436 TRP cc_start: 0.6277 (p90) cc_final: 0.5878 (p90) REVERT: C 497 PHE cc_start: 0.4563 (m-10) cc_final: 0.3712 (m-10) REVERT: C 511 VAL cc_start: 0.8725 (t) cc_final: 0.8483 (p) REVERT: C 541 PHE cc_start: 0.6547 (p90) cc_final: 0.6026 (p90) REVERT: C 572 THR cc_start: 0.8270 (m) cc_final: 0.7853 (p) REVERT: C 725 GLU cc_start: 0.7849 (tt0) cc_final: 0.7539 (tt0) REVERT: C 750 SER cc_start: 0.7667 (t) cc_final: 0.7294 (m) REVERT: C 754 LEU cc_start: 0.8509 (mt) cc_final: 0.8236 (mt) REVERT: C 773 GLU cc_start: 0.7697 (pt0) cc_final: 0.7487 (tt0) REVERT: C 858 LEU cc_start: 0.8286 (mm) cc_final: 0.8029 (mp) REVERT: C 933 LYS cc_start: 0.8118 (mttt) cc_final: 0.7440 (mptt) REVERT: C 947 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7604 (mtpp) REVERT: C 964 LYS cc_start: 0.8348 (mttt) cc_final: 0.8072 (mttt) REVERT: C 1019 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7382 (ttp80) REVERT: C 1038 LYS cc_start: 0.7621 (tppt) cc_final: 0.7242 (mmmm) REVERT: C 1045 LYS cc_start: 0.8101 (mttt) cc_final: 0.7791 (tttt) REVERT: C 1072 GLU cc_start: 0.7623 (pm20) cc_final: 0.7307 (pm20) REVERT: C 1101 HIS cc_start: 0.8300 (m-70) cc_final: 0.7871 (m-70) REVERT: C 1114 ILE cc_start: 0.7914 (mm) cc_final: 0.7686 (mt) REVERT: C 1138 TYR cc_start: 0.7916 (t80) cc_final: 0.7668 (t80) REVERT: G 71 PHE cc_start: 0.6760 (t80) cc_final: 0.6165 (t80) REVERT: G 81 GLU cc_start: 0.8079 (mp0) cc_final: 0.7874 (mp0) REVERT: G 92 PHE cc_start: 0.7497 (m-80) cc_final: 0.7238 (m-80) REVERT: E 32 TYR cc_start: 0.7747 (m-80) cc_final: 0.7352 (m-80) REVERT: E 83 MET cc_start: 0.4424 (mmm) cc_final: 0.4175 (ppp) outliers start: 75 outliers final: 40 residues processed: 745 average time/residue: 1.3067 time to fit residues: 1166.4744 Evaluate side-chains 709 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 665 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 303 LEU 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 329 PHE 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 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 45 ARG 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 157 optimal weight: 0.0000 chunk 133 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 chunk 313 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 357 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1002 GLN A1010 GLN L 27 GLN ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN B1101 HIS F 93 ASN C 764 ASN ** C1010 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.204926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.183087 restraints weight = 59626.184| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.79 r_work: 0.4108 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31419 Z= 0.174 Angle : 0.844 59.198 42840 Z= 0.425 Chirality : 0.053 1.477 4920 Planarity : 0.006 0.149 5448 Dihedral : 6.687 56.295 5201 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.77 % Allowed : 15.21 % Favored : 82.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3780 helix: 0.16 (0.21), residues: 615 sheet: -0.50 (0.17), residues: 888 loop : -1.58 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.006 0.001 HIS C 146 PHE 0.025 0.002 PHE B 497 TYR 0.035 0.002 TYR A 453 ARG 0.023 0.001 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00879 ( 39) link_NAG-ASN : angle 4.27304 ( 117) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.07491 ( 36) hydrogen bonds : bond 0.04826 ( 871) hydrogen bonds : angle 6.40103 ( 2505) SS BOND : bond 0.00357 ( 48) SS BOND : angle 1.36880 ( 96) covalent geometry : bond 0.00396 (31317) covalent geometry : angle 0.81282 (42591) Misc. bond : bond 0.00459 ( 3) *********************** 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 754 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 662 time to evaluate : 3.218 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: 0.7809 (tm-30) cc_final: 0.7221 (tp-100) REVERT: A 58 PHE cc_start: 0.7770 (m-10) cc_final: 0.7401 (m-10) REVERT: A 153 MET cc_start: 0.3735 (mpp) cc_final: 0.3366 (mpp) REVERT: A 208 THR cc_start: 0.8242 (t) cc_final: 0.7996 (p) REVERT: A 282 ASN cc_start: 0.6907 (m110) cc_final: 0.6704 (t0) REVERT: A 319 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7279 (ptt180) REVERT: A 429 PHE cc_start: 0.5584 (t80) cc_final: 0.5364 (t80) REVERT: A 572 THR cc_start: 0.8397 (t) cc_final: 0.8116 (p) REVERT: A 651 ILE cc_start: 0.8753 (mm) cc_final: 0.8492 (mp) REVERT: A 673 SER cc_start: 0.8497 (t) cc_final: 0.8118 (p) REVERT: A 719 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 725 GLU cc_start: 0.7954 (tt0) cc_final: 0.7673 (tt0) REVERT: A 736 VAL cc_start: 0.8060 (t) cc_final: 0.7792 (m) REVERT: A 776 LYS cc_start: 0.8033 (tmmt) cc_final: 0.7802 (ttpp) REVERT: A 790 LYS cc_start: 0.7529 (mmpt) cc_final: 0.7257 (mmpt) REVERT: A 811 LYS cc_start: 0.6985 (mmpt) cc_final: 0.6489 (mtpp) REVERT: A 933 LYS cc_start: 0.7991 (mttt) cc_final: 0.7620 (mtmm) REVERT: A 936 ASP cc_start: 0.7578 (m-30) cc_final: 0.7375 (m-30) REVERT: A 975 SER cc_start: 0.8677 (p) cc_final: 0.8347 (t) REVERT: A 1038 LYS cc_start: 0.7967 (tppt) cc_final: 0.7716 (mmmt) REVERT: A 1045 LYS cc_start: 0.8335 (mttt) cc_final: 0.7871 (mttt) REVERT: A 1072 GLU cc_start: 0.7942 (pm20) cc_final: 0.7482 (pm20) REVERT: A 1086 LYS cc_start: 0.6979 (mtmm) cc_final: 0.6318 (mtmm) REVERT: L 37 GLN cc_start: 0.6380 (pm20) cc_final: 0.5798 (pm20) REVERT: L 81 GLU cc_start: 0.7777 (mp0) cc_final: 0.7541 (mp0) REVERT: H 34 MET cc_start: 0.6549 (ppp) cc_final: 0.6056 (ppp) REVERT: H 39 GLN cc_start: 0.7030 (tp40) cc_final: 0.5994 (tp40) REVERT: H 95 TYR cc_start: 0.5564 (m-80) cc_final: 0.5237 (m-80) REVERT: B 49 HIS cc_start: 0.8127 (t-90) cc_final: 0.7816 (t70) REVERT: B 53 ASP cc_start: 0.6704 (t0) cc_final: 0.6325 (t0) REVERT: B 54 LEU cc_start: 0.7971 (mm) cc_final: 0.7740 (mm) REVERT: B 61 ASN cc_start: 0.6720 (p0) cc_final: 0.6469 (p0) REVERT: B 153 MET cc_start: 0.4921 (mpp) cc_final: 0.4645 (mpp) REVERT: B 192 PHE cc_start: 0.8387 (m-80) cc_final: 0.8174 (m-80) REVERT: B 319 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7460 (ptt180) REVERT: B 340 GLU cc_start: 0.7324 (mp0) cc_final: 0.6928 (mp0) REVERT: B 421 TYR cc_start: 0.6880 (m-80) cc_final: 0.6430 (m-10) REVERT: B 427 ASP cc_start: 0.8022 (p0) cc_final: 0.7810 (p0) REVERT: B 508 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6600 (m-10) REVERT: B 511 VAL cc_start: 0.8636 (t) cc_final: 0.8401 (p) REVERT: B 586 ASP cc_start: 0.7579 (m-30) cc_final: 0.7161 (m-30) REVERT: B 675 GLN cc_start: 0.7708 (mt0) cc_final: 0.7461 (mt0) REVERT: B 725 GLU cc_start: 0.7795 (tt0) cc_final: 0.7484 (tt0) REVERT: B 772 VAL cc_start: 0.8560 (p) cc_final: 0.8340 (t) REVERT: B 780 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7623 (pt0) REVERT: B 859 THR cc_start: 0.8128 (t) cc_final: 0.7884 (p) REVERT: B 931 ILE cc_start: 0.7809 (mm) cc_final: 0.7538 (tp) REVERT: B 933 LYS cc_start: 0.8000 (mttt) cc_final: 0.7288 (mmtm) REVERT: B 947 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7544 (mtpp) REVERT: B 950 ASP cc_start: 0.7713 (m-30) cc_final: 0.7257 (m-30) REVERT: B 1006 THR cc_start: 0.8252 (m) cc_final: 0.7931 (p) REVERT: B 1038 LYS cc_start: 0.7948 (tppt) cc_final: 0.7694 (tppt) REVERT: B 1055 SER cc_start: 0.8043 (t) cc_final: 0.7739 (m) REVERT: B 1082 CYS cc_start: 0.7171 (t) cc_final: 0.6687 (t) REVERT: B 1118 ASP cc_start: 0.7756 (m-30) cc_final: 0.7515 (m-30) REVERT: B 1138 TYR cc_start: 0.7902 (t80) cc_final: 0.7354 (t80) REVERT: F 71 PHE cc_start: 0.6631 (t80) cc_final: 0.6062 (t80) REVERT: D 36 TRP cc_start: 0.5333 (m-90) cc_final: 0.4759 (m-10) REVERT: D 39 GLN cc_start: 0.7209 (tp40) cc_final: 0.6597 (pp30) REVERT: C 45 SER cc_start: 0.8144 (t) cc_final: 0.7919 (p) REVERT: C 53 ASP cc_start: 0.6979 (t0) cc_final: 0.6724 (t0) REVERT: C 81 ASN cc_start: 0.7549 (p0) cc_final: 0.7169 (m-40) REVERT: C 83 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.6608 (p) REVERT: C 192 PHE cc_start: 0.8283 (m-80) cc_final: 0.8063 (m-80) REVERT: C 208 THR cc_start: 0.8278 (t) cc_final: 0.8039 (p) REVERT: C 224 GLU cc_start: 0.6814 (mp0) cc_final: 0.6570 (mp0) REVERT: C 237 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7002 (ttt-90) REVERT: C 314 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (tp40) REVERT: C 324 GLU cc_start: 0.6960 (pm20) cc_final: 0.6665 (pm20) REVERT: C 340 GLU cc_start: 0.6930 (mp0) cc_final: 0.6582 (mp0) REVERT: C 436 TRP cc_start: 0.6379 (p90) cc_final: 0.6163 (p90) REVERT: C 455 LEU cc_start: 0.8956 (tm) cc_final: 0.8593 (mm) REVERT: C 511 VAL cc_start: 0.8725 (t) cc_final: 0.8462 (p) REVERT: C 541 PHE cc_start: 0.6579 (p90) cc_final: 0.6072 (p90) REVERT: C 572 THR cc_start: 0.8279 (m) cc_final: 0.7952 (p) REVERT: C 725 GLU cc_start: 0.7839 (tt0) cc_final: 0.7602 (tt0) REVERT: C 790 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7394 (mmmt) REVERT: C 815 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7107 (mtm-85) REVERT: C 918 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: C 933 LYS cc_start: 0.8153 (mttt) cc_final: 0.7454 (mptt) REVERT: C 947 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7623 (mtpp) REVERT: C 964 LYS cc_start: 0.8350 (mttt) cc_final: 0.8058 (mttt) REVERT: C 1038 LYS cc_start: 0.7617 (tppt) cc_final: 0.7233 (mmmm) REVERT: C 1045 LYS cc_start: 0.8088 (mttt) cc_final: 0.7773 (tttt) REVERT: C 1072 GLU cc_start: 0.7614 (pm20) cc_final: 0.7309 (pm20) REVERT: C 1101 HIS cc_start: 0.8312 (m-70) cc_final: 0.7886 (m-70) REVERT: C 1114 ILE cc_start: 0.7925 (mm) cc_final: 0.7703 (mt) REVERT: C 1138 TYR cc_start: 0.7921 (t80) cc_final: 0.7665 (t80) REVERT: G 71 PHE cc_start: 0.6655 (t80) cc_final: 0.6071 (t80) REVERT: G 81 GLU cc_start: 0.8054 (mp0) cc_final: 0.7845 (mp0) REVERT: G 92 PHE cc_start: 0.7523 (m-80) cc_final: 0.7192 (m-80) REVERT: E 32 TYR cc_start: 0.7712 (m-80) cc_final: 0.7311 (m-80) REVERT: E 34 MET cc_start: 0.6879 (ppp) cc_final: 0.6627 (ppp) outliers start: 92 outliers final: 56 residues processed: 697 average time/residue: 1.2362 time to fit residues: 1035.6702 Evaluate side-chains 717 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 653 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE 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 478 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 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR 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 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 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 298 GLU 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 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 918 GLU 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 1010 GLN Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 93 ASN 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 8 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 375 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 283 optimal weight: 0.0010 chunk 300 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 138 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 919 ASN A 957 GLN A1101 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS B1135 ASN C 764 ASN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.205012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.183298 restraints weight = 59940.181| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 3.77 r_work: 0.4116 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31419 Z= 0.166 Angle : 0.808 59.200 42840 Z= 0.412 Chirality : 0.048 0.373 4920 Planarity : 0.006 0.116 5448 Dihedral : 6.767 63.083 5201 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.56 % Allowed : 16.29 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3780 helix: 0.70 (0.21), residues: 594 sheet: -0.48 (0.17), residues: 897 loop : -1.62 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.019 0.001 HIS G 30 PHE 0.025 0.002 PHE A 464 TYR 0.035 0.002 TYR G 32 ARG 0.010 0.001 ARG G 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 39) link_NAG-ASN : angle 3.64757 ( 117) link_BETA1-4 : bond 0.00481 ( 12) link_BETA1-4 : angle 1.01172 ( 36) hydrogen bonds : bond 0.04581 ( 871) hydrogen bonds : angle 6.30737 ( 2505) SS BOND : bond 0.00341 ( 48) SS BOND : angle 1.22251 ( 96) covalent geometry : bond 0.00380 (31317) covalent geometry : angle 0.78517 (42591) Misc. bond : bond 0.00347 ( 3) *********************** 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 738 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 653 time to evaluate : 3.180 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: 0.7561 (tm-30) cc_final: 0.7234 (tp-100) REVERT: A 58 PHE cc_start: 0.7768 (m-10) cc_final: 0.6973 (m-10) REVERT: A 153 MET cc_start: 0.3800 (mpp) cc_final: 0.3405 (mpp) REVERT: A 208 THR cc_start: 0.8246 (t) cc_final: 0.8007 (p) REVERT: A 282 ASN cc_start: 0.7033 (m110) cc_final: 0.6816 (t0) REVERT: A 319 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7279 (ptt180) REVERT: A 429 PHE cc_start: 0.5580 (t80) cc_final: 0.5359 (t80) REVERT: A 453 TYR cc_start: 0.6751 (p90) cc_final: 0.6172 (p90) REVERT: A 454 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7559 (mmt90) REVERT: A 572 THR cc_start: 0.8404 (t) cc_final: 0.8138 (p) REVERT: A 651 ILE cc_start: 0.8756 (mm) cc_final: 0.8486 (mp) REVERT: A 673 SER cc_start: 0.8371 (t) cc_final: 0.7973 (p) REVERT: A 719 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 725 GLU cc_start: 0.7951 (tt0) cc_final: 0.7663 (tt0) REVERT: A 736 VAL cc_start: 0.8062 (t) cc_final: 0.7796 (m) REVERT: A 776 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7795 (ttpp) REVERT: A 790 LYS cc_start: 0.7548 (mmpt) cc_final: 0.7327 (mmpt) REVERT: A 811 LYS cc_start: 0.7005 (mmpt) cc_final: 0.6523 (mtpp) REVERT: A 933 LYS cc_start: 0.7982 (mttt) cc_final: 0.7611 (mtmm) REVERT: A 975 SER cc_start: 0.8675 (p) cc_final: 0.8345 (t) REVERT: A 1038 LYS cc_start: 0.7981 (tppt) cc_final: 0.7723 (mmmt) REVERT: A 1045 LYS cc_start: 0.8334 (mttt) cc_final: 0.7874 (mttt) REVERT: A 1072 GLU cc_start: 0.7945 (pm20) cc_final: 0.7482 (pm20) REVERT: A 1086 LYS cc_start: 0.6974 (mtmm) cc_final: 0.6380 (mtmm) REVERT: L 81 GLU cc_start: 0.7743 (mp0) cc_final: 0.7525 (mp0) REVERT: H 34 MET cc_start: 0.6470 (ppp) cc_final: 0.6252 (ppp) REVERT: H 39 GLN cc_start: 0.7003 (tp40) cc_final: 0.5940 (tp40) REVERT: H 95 TYR cc_start: 0.5396 (m-80) cc_final: 0.5163 (m-80) REVERT: B 49 HIS cc_start: 0.8122 (t-90) cc_final: 0.7833 (t70) REVERT: B 53 ASP cc_start: 0.6664 (t0) cc_final: 0.6306 (t0) REVERT: B 54 LEU cc_start: 0.7954 (mm) cc_final: 0.7734 (mm) REVERT: B 61 ASN cc_start: 0.6723 (p0) cc_final: 0.6479 (p0) REVERT: B 153 MET cc_start: 0.4921 (mpp) cc_final: 0.4637 (mpp) REVERT: B 192 PHE cc_start: 0.8382 (m-80) cc_final: 0.8155 (m-80) REVERT: B 319 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7445 (ptt180) REVERT: B 340 GLU cc_start: 0.7297 (mp0) cc_final: 0.6877 (mp0) REVERT: B 421 TYR cc_start: 0.6805 (m-80) cc_final: 0.6386 (m-10) REVERT: B 427 ASP cc_start: 0.8020 (p0) cc_final: 0.7803 (p0) REVERT: B 508 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.6759 (m-10) REVERT: B 511 VAL cc_start: 0.8626 (t) cc_final: 0.8387 (p) REVERT: B 586 ASP cc_start: 0.7563 (m-30) cc_final: 0.7138 (m-30) REVERT: B 675 GLN cc_start: 0.7716 (mt0) cc_final: 0.7479 (mt0) REVERT: B 725 GLU cc_start: 0.7780 (tt0) cc_final: 0.7479 (tt0) REVERT: B 772 VAL cc_start: 0.8567 (p) cc_final: 0.8342 (t) REVERT: B 780 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: B 859 THR cc_start: 0.8127 (t) cc_final: 0.7869 (p) REVERT: B 931 ILE cc_start: 0.7807 (mm) cc_final: 0.7530 (tp) REVERT: B 933 LYS cc_start: 0.8009 (mttt) cc_final: 0.7302 (mmtm) REVERT: B 947 LYS cc_start: 0.7854 (mtpt) cc_final: 0.7547 (mtpp) REVERT: B 950 ASP cc_start: 0.7712 (m-30) cc_final: 0.7246 (m-30) REVERT: B 1038 LYS cc_start: 0.7939 (tppt) cc_final: 0.7692 (tppt) REVERT: B 1055 SER cc_start: 0.8044 (t) cc_final: 0.7747 (m) REVERT: B 1082 CYS cc_start: 0.7191 (t) cc_final: 0.6719 (t) REVERT: B 1118 ASP cc_start: 0.7756 (m-30) cc_final: 0.7519 (m-30) REVERT: B 1138 TYR cc_start: 0.7897 (t80) cc_final: 0.7348 (t80) REVERT: F 71 PHE cc_start: 0.6543 (t80) cc_final: 0.6061 (t80) REVERT: D 36 TRP cc_start: 0.5262 (m-90) cc_final: 0.4734 (m-10) REVERT: D 39 GLN cc_start: 0.7204 (tp40) cc_final: 0.6628 (pp30) REVERT: C 45 SER cc_start: 0.8136 (t) cc_final: 0.7905 (p) REVERT: C 53 ASP cc_start: 0.6984 (t0) cc_final: 0.6722 (t70) REVERT: C 81 ASN cc_start: 0.7529 (p0) cc_final: 0.7162 (m110) REVERT: C 83 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6578 (p) REVERT: C 129 LYS cc_start: 0.7291 (mppt) cc_final: 0.7053 (mmtm) REVERT: C 192 PHE cc_start: 0.8293 (m-80) cc_final: 0.8053 (m-80) REVERT: C 208 THR cc_start: 0.8313 (t) cc_final: 0.8077 (p) REVERT: C 224 GLU cc_start: 0.6789 (mp0) cc_final: 0.6554 (mp0) REVERT: C 237 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.6996 (ttt-90) REVERT: C 314 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: C 324 GLU cc_start: 0.6948 (pm20) cc_final: 0.6704 (pm20) REVERT: C 340 GLU cc_start: 0.6913 (mp0) cc_final: 0.6633 (mp0) REVERT: C 392 PHE cc_start: 0.7227 (m-10) cc_final: 0.6988 (m-80) REVERT: C 436 TRP cc_start: 0.6367 (p90) cc_final: 0.5939 (p90) REVERT: C 508 TYR cc_start: 0.7698 (m-80) cc_final: 0.6843 (m-80) REVERT: C 511 VAL cc_start: 0.8694 (t) cc_final: 0.8453 (p) REVERT: C 541 PHE cc_start: 0.6577 (p90) cc_final: 0.6140 (p90) REVERT: C 572 THR cc_start: 0.8340 (m) cc_final: 0.7928 (p) REVERT: C 725 GLU cc_start: 0.7845 (tt0) cc_final: 0.7610 (tt0) REVERT: C 750 SER cc_start: 0.7720 (t) cc_final: 0.7295 (p) REVERT: C 765 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7154 (ttp80) REVERT: C 776 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (tmmm) REVERT: C 815 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7113 (mtm-85) REVERT: C 918 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: C 933 LYS cc_start: 0.8144 (mttt) cc_final: 0.7446 (mptt) REVERT: C 947 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7611 (mtpp) REVERT: C 964 LYS cc_start: 0.8336 (mttt) cc_final: 0.8048 (mttt) REVERT: C 1019 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7422 (ttp80) REVERT: C 1038 LYS cc_start: 0.7624 (tppt) cc_final: 0.7244 (mmmm) REVERT: C 1045 LYS cc_start: 0.8080 (mttt) cc_final: 0.7765 (tttt) REVERT: C 1072 GLU cc_start: 0.7579 (pm20) cc_final: 0.7303 (pm20) REVERT: C 1101 HIS cc_start: 0.8309 (m-70) cc_final: 0.7906 (m-70) REVERT: C 1114 ILE cc_start: 0.7936 (mm) cc_final: 0.7720 (mt) REVERT: C 1138 TYR cc_start: 0.7924 (t80) cc_final: 0.7683 (t80) REVERT: G 71 PHE cc_start: 0.6689 (t80) cc_final: 0.6107 (t80) REVERT: G 92 PHE cc_start: 0.7512 (m-80) cc_final: 0.7249 (m-80) REVERT: E 32 TYR cc_start: 0.7657 (m-80) cc_final: 0.7257 (m-80) outliers start: 85 outliers final: 65 residues processed: 685 average time/residue: 1.2071 time to fit residues: 999.6858 Evaluate side-chains 718 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 645 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 329 PHE 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 495 TYR 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 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 875 SER 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 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 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR 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 740 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 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 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 396 TYR 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 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 918 GLU 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 1029 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 183 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 361 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 919 ASN A 957 GLN A1101 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4523 r_free = 0.4523 target = 0.203250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181522 restraints weight = 60128.200| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 3.65 r_work: 0.4113 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.159 31419 Z= 0.238 Angle : 0.832 59.199 42840 Z= 0.425 Chirality : 0.049 0.369 4920 Planarity : 0.006 0.108 5448 Dihedral : 6.832 76.451 5201 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.98 % Allowed : 16.77 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3780 helix: 0.72 (0.21), residues: 594 sheet: -0.51 (0.17), residues: 897 loop : -1.64 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 36 HIS 0.005 0.001 HIS G 30 PHE 0.022 0.002 PHE B 486 TYR 0.034 0.002 TYR A 453 ARG 0.025 0.001 ARG G 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 39) link_NAG-ASN : angle 3.57842 ( 117) link_BETA1-4 : bond 0.00278 ( 12) link_BETA1-4 : angle 1.10844 ( 36) hydrogen bonds : bond 0.04656 ( 871) hydrogen bonds : angle 6.28364 ( 2505) SS BOND : bond 0.00835 ( 48) SS BOND : angle 1.73516 ( 96) covalent geometry : bond 0.00571 (31317) covalent geometry : angle 0.80857 (42591) Misc. bond : bond 0.00047 ( 3) *********************** 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 747 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 648 time to evaluate : 3.006 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 52 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7232 (tp-100) REVERT: A 58 PHE cc_start: 0.7777 (m-10) cc_final: 0.7427 (m-10) REVERT: A 153 MET cc_start: 0.3903 (mpp) cc_final: 0.3504 (mpp) REVERT: A 208 THR cc_start: 0.8252 (t) cc_final: 0.8013 (p) REVERT: A 319 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7302 (ptt180) REVERT: A 429 PHE cc_start: 0.5605 (t80) cc_final: 0.5355 (t80) REVERT: A 453 TYR cc_start: 0.6799 (p90) cc_final: 0.6229 (p90) REVERT: A 454 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7565 (mmt90) REVERT: A 572 THR cc_start: 0.8414 (t) cc_final: 0.8150 (p) REVERT: A 651 ILE cc_start: 0.8751 (mm) cc_final: 0.8480 (mp) REVERT: A 673 SER cc_start: 0.8377 (t) cc_final: 0.7986 (p) REVERT: A 719 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 725 GLU cc_start: 0.7912 (tt0) cc_final: 0.7643 (tt0) REVERT: A 736 VAL cc_start: 0.8058 (t) cc_final: 0.7810 (m) REVERT: A 776 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7776 (ttpp) REVERT: A 811 LYS cc_start: 0.7010 (mmpt) cc_final: 0.6553 (mtpt) REVERT: A 933 LYS cc_start: 0.8018 (mttt) cc_final: 0.7639 (mtmm) REVERT: A 975 SER cc_start: 0.8680 (p) cc_final: 0.8349 (t) REVERT: A 1038 LYS cc_start: 0.7977 (tppt) cc_final: 0.7719 (mmmt) REVERT: A 1045 LYS cc_start: 0.8343 (mttt) cc_final: 0.7890 (mttt) REVERT: A 1072 GLU cc_start: 0.7923 (pm20) cc_final: 0.7462 (pm20) REVERT: A 1086 LYS cc_start: 0.6973 (mtmm) cc_final: 0.6385 (mtmm) REVERT: L 81 GLU cc_start: 0.7756 (mp0) cc_final: 0.7540 (mp0) REVERT: H 39 GLN cc_start: 0.7025 (tp40) cc_final: 0.5963 (tp40) REVERT: H 95 TYR cc_start: 0.5390 (m-80) cc_final: 0.5171 (m-80) REVERT: B 49 HIS cc_start: 0.8108 (t-90) cc_final: 0.7794 (t70) REVERT: B 53 ASP cc_start: 0.6682 (t0) cc_final: 0.6311 (t0) REVERT: B 54 LEU cc_start: 0.7950 (mm) cc_final: 0.7731 (mm) REVERT: B 61 ASN cc_start: 0.6724 (p0) cc_final: 0.6481 (p0) REVERT: B 153 MET cc_start: 0.4901 (mpp) cc_final: 0.4619 (mpp) REVERT: B 192 PHE cc_start: 0.8367 (m-80) cc_final: 0.8144 (m-80) REVERT: B 319 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7465 (ptt180) REVERT: B 340 GLU cc_start: 0.7300 (mp0) cc_final: 0.6928 (mp0) REVERT: B 421 TYR cc_start: 0.6809 (m-80) cc_final: 0.6377 (m-10) REVERT: B 427 ASP cc_start: 0.8032 (p0) cc_final: 0.7823 (p0) REVERT: B 508 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6802 (m-10) REVERT: B 511 VAL cc_start: 0.8628 (t) cc_final: 0.8399 (p) REVERT: B 586 ASP cc_start: 0.7571 (m-30) cc_final: 0.7164 (m-30) REVERT: B 675 GLN cc_start: 0.7739 (mt0) cc_final: 0.7504 (mt0) REVERT: B 725 GLU cc_start: 0.7793 (tt0) cc_final: 0.7498 (tt0) REVERT: B 772 VAL cc_start: 0.8574 (p) cc_final: 0.8350 (t) REVERT: B 780 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: B 859 THR cc_start: 0.8129 (t) cc_final: 0.7872 (p) REVERT: B 931 ILE cc_start: 0.7812 (mm) cc_final: 0.7535 (tp) REVERT: B 933 LYS cc_start: 0.8021 (mttt) cc_final: 0.7309 (mmtm) REVERT: B 947 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7573 (mtpp) REVERT: B 950 ASP cc_start: 0.7691 (m-30) cc_final: 0.7225 (m-30) REVERT: B 1038 LYS cc_start: 0.7946 (tppt) cc_final: 0.7688 (tppt) REVERT: B 1055 SER cc_start: 0.8044 (t) cc_final: 0.7759 (m) REVERT: B 1082 CYS cc_start: 0.7156 (t) cc_final: 0.6677 (t) REVERT: B 1118 ASP cc_start: 0.7742 (m-30) cc_final: 0.7509 (m-30) REVERT: B 1138 TYR cc_start: 0.7907 (t80) cc_final: 0.7374 (t80) REVERT: F 71 PHE cc_start: 0.6492 (t80) cc_final: 0.6046 (t80) REVERT: D 36 TRP cc_start: 0.5315 (m-90) cc_final: 0.4766 (m-10) REVERT: D 39 GLN cc_start: 0.7220 (tp40) cc_final: 0.6661 (pp30) REVERT: C 45 SER cc_start: 0.8141 (t) cc_final: 0.7923 (p) REVERT: C 53 ASP cc_start: 0.6960 (t0) cc_final: 0.6700 (t70) REVERT: C 81 ASN cc_start: 0.7536 (p0) cc_final: 0.7173 (m110) REVERT: C 83 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6637 (p) REVERT: C 129 LYS cc_start: 0.7318 (mppt) cc_final: 0.7087 (mmtm) REVERT: C 192 PHE cc_start: 0.8294 (m-80) cc_final: 0.8060 (m-80) REVERT: C 208 THR cc_start: 0.8335 (t) cc_final: 0.8099 (p) REVERT: C 224 GLU cc_start: 0.6795 (mp0) cc_final: 0.6560 (mp0) REVERT: C 237 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7046 (ttt-90) REVERT: C 314 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: C 324 GLU cc_start: 0.6935 (pm20) cc_final: 0.6677 (pm20) REVERT: C 340 GLU cc_start: 0.6941 (mp0) cc_final: 0.6613 (mp0) REVERT: C 392 PHE cc_start: 0.7170 (m-80) cc_final: 0.6965 (m-80) REVERT: C 436 TRP cc_start: 0.6359 (p90) cc_final: 0.5951 (p90) REVERT: C 490 PHE cc_start: 0.8122 (t80) cc_final: 0.7911 (t80) REVERT: C 508 TYR cc_start: 0.7701 (m-80) cc_final: 0.6845 (m-80) REVERT: C 511 VAL cc_start: 0.8702 (t) cc_final: 0.8465 (p) REVERT: C 541 PHE cc_start: 0.6587 (p90) cc_final: 0.6053 (p90) REVERT: C 572 THR cc_start: 0.8350 (m) cc_final: 0.7940 (p) REVERT: C 725 GLU cc_start: 0.7822 (tt0) cc_final: 0.7588 (tt0) REVERT: C 750 SER cc_start: 0.7734 (t) cc_final: 0.7314 (p) REVERT: C 765 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7146 (ttp80) REVERT: C 815 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7190 (mtm-85) REVERT: C 918 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: C 933 LYS cc_start: 0.8164 (mttt) cc_final: 0.7462 (mptt) REVERT: C 947 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7599 (mtpp) REVERT: C 964 LYS cc_start: 0.8343 (mttt) cc_final: 0.8059 (mttt) REVERT: C 1038 LYS cc_start: 0.7629 (tppt) cc_final: 0.7257 (mmmm) REVERT: C 1045 LYS cc_start: 0.8084 (mttt) cc_final: 0.7773 (tttt) REVERT: C 1072 GLU cc_start: 0.7583 (pm20) cc_final: 0.7328 (pm20) REVERT: C 1101 HIS cc_start: 0.8309 (m-70) cc_final: 0.7898 (m-70) REVERT: C 1114 ILE cc_start: 0.7956 (mm) cc_final: 0.7742 (mt) REVERT: C 1138 TYR cc_start: 0.7931 (t80) cc_final: 0.7681 (t80) REVERT: G 71 PHE cc_start: 0.6672 (t80) cc_final: 0.6099 (t80) REVERT: G 92 PHE cc_start: 0.7536 (m-80) cc_final: 0.7327 (m-80) REVERT: E 32 TYR cc_start: 0.7668 (m-80) cc_final: 0.7272 (m-80) outliers start: 99 outliers final: 74 residues processed: 684 average time/residue: 1.2524 time to fit residues: 1036.2021 Evaluate side-chains 730 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 648 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 396 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 495 TYR 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 719 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 922 LEU 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 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 41 LYS Chi-restraints excluded: chain B residue 127 VAL 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 278 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR 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 651 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 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 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1041 ASP 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 237 ARG Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 396 TYR 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 551 VAL Chi-restraints excluded: chain C residue 553 THR 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 815 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 918 GLU 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 1029 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 348 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 198 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 919 ASN A1101 HIS L 27 GLN L 93 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B1101 HIS C 207 HIS C 764 ASN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.205129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.183369 restraints weight = 59656.877| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.76 r_work: 0.4118 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31419 Z= 0.134 Angle : 0.680 15.204 42840 Z= 0.329 Chirality : 0.047 0.362 4920 Planarity : 0.005 0.075 5448 Dihedral : 7.298 115.048 5201 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.56 % Allowed : 17.34 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3780 helix: 1.05 (0.21), residues: 639 sheet: -0.48 (0.17), residues: 897 loop : -1.66 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 47 HIS 0.004 0.001 HIS F 30 PHE 0.027 0.002 PHE B 490 TYR 0.030 0.001 TYR H 103 ARG 0.009 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 39) link_NAG-ASN : angle 2.68415 ( 117) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 1.22699 ( 36) hydrogen bonds : bond 0.03907 ( 871) hydrogen bonds : angle 5.82840 ( 2505) SS BOND : bond 0.00322 ( 48) SS BOND : angle 1.22449 ( 96) covalent geometry : bond 0.00310 (31317) covalent geometry : angle 0.66417 (42591) Misc. bond : bond 0.00099 ( 3) *********************** 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 746 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 661 time to evaluate : 3.248 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 34 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6719 (ttm-80) REVERT: A 52 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7303 (tp-100) REVERT: A 58 PHE cc_start: 0.7866 (m-10) cc_final: 0.7503 (m-10) REVERT: A 153 MET cc_start: 0.4020 (mpp) cc_final: 0.3582 (mpp) REVERT: A 319 ARG cc_start: 0.7863 (ptp90) cc_final: 0.7392 (ptt180) REVERT: A 429 PHE cc_start: 0.5929 (t80) cc_final: 0.5603 (t80) REVERT: A 486 PHE cc_start: 0.6181 (t80) cc_final: 0.5540 (t80) REVERT: A 572 THR cc_start: 0.8376 (t) cc_final: 0.7812 (p) REVERT: A 588 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 651 ILE cc_start: 0.8771 (mm) cc_final: 0.8490 (mp) REVERT: A 673 SER cc_start: 0.8227 (t) cc_final: 0.7841 (p) REVERT: A 725 GLU cc_start: 0.7866 (tt0) cc_final: 0.7560 (tt0) REVERT: A 736 VAL cc_start: 0.8191 (t) cc_final: 0.7900 (m) REVERT: A 780 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: A 790 LYS cc_start: 0.7902 (mtpm) cc_final: 0.7291 (mmpt) REVERT: A 811 LYS cc_start: 0.7009 (mmpt) cc_final: 0.6551 (mtpt) REVERT: A 933 LYS cc_start: 0.8058 (mttt) cc_final: 0.7675 (mtmm) REVERT: A 975 SER cc_start: 0.8666 (p) cc_final: 0.8361 (t) REVERT: A 1038 LYS cc_start: 0.8036 (tppt) cc_final: 0.7758 (mmpt) REVERT: A 1045 LYS cc_start: 0.8320 (mttt) cc_final: 0.7964 (mttt) REVERT: A 1072 GLU cc_start: 0.7945 (pm20) cc_final: 0.7479 (pm20) REVERT: A 1086 LYS cc_start: 0.6958 (mtmm) cc_final: 0.6263 (mtmm) REVERT: A 1141 LEU cc_start: 0.7689 (tm) cc_final: 0.7428 (tt) REVERT: L 37 GLN cc_start: 0.6813 (pm20) cc_final: 0.6561 (pm20) REVERT: L 81 GLU cc_start: 0.7614 (mp0) cc_final: 0.7404 (mp0) REVERT: H 39 GLN cc_start: 0.7068 (tp40) cc_final: 0.6024 (tp40) REVERT: H 95 TYR cc_start: 0.5356 (m-80) cc_final: 0.5072 (m-80) REVERT: B 49 HIS cc_start: 0.8141 (t-90) cc_final: 0.7797 (t70) REVERT: B 53 ASP cc_start: 0.6668 (t0) cc_final: 0.6275 (t0) REVERT: B 54 LEU cc_start: 0.7936 (mm) cc_final: 0.7725 (mm) REVERT: B 61 ASN cc_start: 0.6744 (p0) cc_final: 0.6519 (p0) REVERT: B 153 MET cc_start: 0.5016 (mpp) cc_final: 0.4729 (mpp) REVERT: B 192 PHE cc_start: 0.8374 (m-80) cc_final: 0.8135 (m-80) REVERT: B 200 TYR cc_start: 0.5592 (m-10) cc_final: 0.5344 (m-10) REVERT: B 206 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7143 (ttmm) REVERT: B 286 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7637 (t) REVERT: B 319 ARG cc_start: 0.7920 (ptp90) cc_final: 0.7549 (ptt180) REVERT: B 340 GLU cc_start: 0.7183 (mp0) cc_final: 0.6679 (mp0) REVERT: B 374 PHE cc_start: 0.7234 (m-80) cc_final: 0.6772 (m-80) REVERT: B 421 TYR cc_start: 0.6889 (m-80) cc_final: 0.6446 (m-10) REVERT: B 427 ASP cc_start: 0.8105 (p0) cc_final: 0.7898 (p0) REVERT: B 508 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6760 (m-10) REVERT: B 511 VAL cc_start: 0.8708 (t) cc_final: 0.8480 (p) REVERT: B 541 PHE cc_start: 0.6639 (p90) cc_final: 0.6301 (p90) REVERT: B 586 ASP cc_start: 0.7579 (m-30) cc_final: 0.7158 (m-30) REVERT: B 675 GLN cc_start: 0.7754 (mt0) cc_final: 0.7519 (mt0) REVERT: B 725 GLU cc_start: 0.7766 (tt0) cc_final: 0.7474 (tt0) REVERT: B 772 VAL cc_start: 0.8570 (p) cc_final: 0.8335 (t) REVERT: B 780 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: B 859 THR cc_start: 0.8102 (t) cc_final: 0.7871 (p) REVERT: B 931 ILE cc_start: 0.7706 (mm) cc_final: 0.7422 (tp) REVERT: B 933 LYS cc_start: 0.8084 (mttt) cc_final: 0.7331 (mmtm) REVERT: B 947 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7608 (mtpp) REVERT: B 949 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7497 (tp-100) REVERT: B 950 ASP cc_start: 0.7593 (m-30) cc_final: 0.7232 (m-30) REVERT: B 1038 LYS cc_start: 0.7918 (tppt) cc_final: 0.7638 (tppt) REVERT: B 1055 SER cc_start: 0.7978 (t) cc_final: 0.7744 (m) REVERT: B 1118 ASP cc_start: 0.7779 (m-30) cc_final: 0.7549 (m-30) REVERT: F 71 PHE cc_start: 0.6680 (t80) cc_final: 0.6155 (t80) REVERT: D 36 TRP cc_start: 0.5672 (m-90) cc_final: 0.5209 (m-10) REVERT: D 83 MET cc_start: 0.4265 (tmt) cc_final: 0.3925 (tmt) REVERT: C 45 SER cc_start: 0.8102 (t) cc_final: 0.7900 (p) REVERT: C 53 ASP cc_start: 0.6934 (t0) cc_final: 0.6661 (t70) REVERT: C 83 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.5953 (p) REVERT: C 84 LEU cc_start: 0.7145 (mp) cc_final: 0.6918 (mm) REVERT: C 129 LYS cc_start: 0.7368 (mppt) cc_final: 0.7149 (mmtm) REVERT: C 200 TYR cc_start: 0.5307 (m-10) cc_final: 0.4971 (m-10) REVERT: C 224 GLU cc_start: 0.6805 (mp0) cc_final: 0.6593 (mp0) REVERT: C 237 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6453 (ttm-80) REVERT: C 312 ILE cc_start: 0.7774 (tt) cc_final: 0.7534 (tp) REVERT: C 314 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: C 340 GLU cc_start: 0.7047 (mp0) cc_final: 0.6753 (mp0) REVERT: C 374 PHE cc_start: 0.7509 (m-80) cc_final: 0.7037 (m-80) REVERT: C 421 TYR cc_start: 0.6860 (m-80) cc_final: 0.6582 (m-10) REVERT: C 436 TRP cc_start: 0.6276 (p90) cc_final: 0.6056 (p90) REVERT: C 511 VAL cc_start: 0.8738 (t) cc_final: 0.8503 (p) REVERT: C 541 PHE cc_start: 0.6875 (p90) cc_final: 0.6462 (p90) REVERT: C 725 GLU cc_start: 0.7863 (tt0) cc_final: 0.7636 (tt0) REVERT: C 750 SER cc_start: 0.7704 (t) cc_final: 0.7235 (p) REVERT: C 765 ARG cc_start: 0.7260 (ttp-110) cc_final: 0.7055 (ttp80) REVERT: C 790 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7205 (mmmt) REVERT: C 933 LYS cc_start: 0.8115 (mttt) cc_final: 0.7432 (mptt) REVERT: C 947 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7670 (mtpp) REVERT: C 964 LYS cc_start: 0.8435 (mttt) cc_final: 0.8087 (mttt) REVERT: C 974 SER cc_start: 0.8571 (m) cc_final: 0.8216 (p) REVERT: C 1014 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8230 (ttm110) REVERT: C 1038 LYS cc_start: 0.7776 (tppt) cc_final: 0.7346 (mmmm) REVERT: C 1045 LYS cc_start: 0.8057 (mttt) cc_final: 0.7767 (tttt) REVERT: C 1072 GLU cc_start: 0.7640 (pm20) cc_final: 0.7354 (pm20) REVERT: C 1101 HIS cc_start: 0.8313 (m-70) cc_final: 0.7889 (m-70) REVERT: C 1138 TYR cc_start: 0.7948 (t80) cc_final: 0.7720 (t80) REVERT: G 71 PHE cc_start: 0.6670 (t80) cc_final: 0.6095 (t80) REVERT: E 32 TYR cc_start: 0.7708 (m-80) cc_final: 0.7357 (m-80) REVERT: E 46 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: E 68 PHE cc_start: 0.7839 (m-10) cc_final: 0.7591 (m-10) REVERT: E 102 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (m-10) outliers start: 85 outliers final: 56 residues processed: 694 average time/residue: 1.4252 time to fit residues: 1203.1135 Evaluate side-chains 710 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 643 time to evaluate : 4.046 ------------------------------------------------------------------------------- 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 332 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 478 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 780 GLU 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 33 LEU Chi-restraints excluded: chain L residue 93 ASN 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 127 VAL Chi-restraints excluded: chain B residue 206 LYS 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 332 ILE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 60 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 206 LYS Chi-restraints excluded: chain C residue 237 ARG 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 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 900 MET 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 1001 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 46 GLU 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 127 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 955 ASN A1010 GLN A1101 HIS L 27 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B1101 HIS C 764 ASN C 787 GLN C1010 GLN ** G 30 HIS ** 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 = 0.4437 r_free = 0.4437 target = 0.195975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.174490 restraints weight = 57653.571| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.61 r_work: 0.3981 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.122 31419 Z= 0.350 Angle : 0.845 15.792 42840 Z= 0.425 Chirality : 0.053 0.335 4920 Planarity : 0.006 0.105 5448 Dihedral : 7.546 116.172 5201 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.82 % Allowed : 17.80 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3780 helix: 0.36 (0.20), residues: 675 sheet: -0.67 (0.18), residues: 855 loop : -1.88 (0.12), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 886 HIS 0.009 0.002 HIS A1083 PHE 0.030 0.003 PHE C 86 TYR 0.042 0.003 TYR C 204 ARG 0.029 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.01126 ( 39) link_NAG-ASN : angle 3.15503 ( 117) link_BETA1-4 : bond 0.00387 ( 12) link_BETA1-4 : angle 1.21383 ( 36) hydrogen bonds : bond 0.04957 ( 871) hydrogen bonds : angle 6.03296 ( 2505) SS BOND : bond 0.00522 ( 48) SS BOND : angle 2.07712 ( 96) covalent geometry : bond 0.00811 (31317) covalent geometry : angle 0.82499 (42591) Misc. bond : bond 0.00048 ( 3) *********************** 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 818 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 691 time to evaluate : 3.434 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 34 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7374 (ttm110) REVERT: A 46 SER cc_start: 0.8111 (m) cc_final: 0.7608 (t) REVERT: A 153 MET cc_start: 0.4350 (mpp) cc_final: 0.3887 (mpp) REVERT: A 206 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7421 (ttmm) REVERT: A 274 THR cc_start: 0.8673 (t) cc_final: 0.8467 (t) REVERT: A 319 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7436 (ptt180) REVERT: A 429 PHE cc_start: 0.6346 (t80) cc_final: 0.6001 (t80) REVERT: A 441 LEU cc_start: 0.7425 (tt) cc_final: 0.7200 (tm) REVERT: A 453 TYR cc_start: 0.7233 (p90) cc_final: 0.6769 (p90) REVERT: A 454 ARG cc_start: 0.8216 (mmt90) cc_final: 0.8005 (mmt180) REVERT: A 541 PHE cc_start: 0.6987 (p90) cc_final: 0.6709 (p90) REVERT: A 588 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 651 ILE cc_start: 0.8813 (mm) cc_final: 0.8549 (mp) REVERT: A 673 SER cc_start: 0.8330 (t) cc_final: 0.7990 (p) REVERT: A 725 GLU cc_start: 0.7839 (tt0) cc_final: 0.7585 (tt0) REVERT: A 736 VAL cc_start: 0.8208 (t) cc_final: 0.7926 (m) REVERT: A 748 GLU cc_start: 0.7928 (pt0) cc_final: 0.7689 (pp20) REVERT: A 780 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: A 790 LYS cc_start: 0.7738 (mtpm) cc_final: 0.7196 (mmpt) REVERT: A 795 LYS cc_start: 0.8491 (mptm) cc_final: 0.8260 (mptp) REVERT: A 811 LYS cc_start: 0.7157 (mmpt) cc_final: 0.6592 (mtpp) REVERT: A 933 LYS cc_start: 0.7952 (mttt) cc_final: 0.7564 (mtmm) REVERT: A 949 GLN cc_start: 0.7646 (tp40) cc_final: 0.7364 (tp40) REVERT: A 1045 LYS cc_start: 0.8330 (mttt) cc_final: 0.7978 (mttt) REVERT: A 1072 GLU cc_start: 0.8068 (pm20) cc_final: 0.7637 (pm20) REVERT: A 1141 LEU cc_start: 0.7694 (tm) cc_final: 0.7467 (tt) REVERT: L 36 TYR cc_start: 0.5691 (m-10) cc_final: 0.5356 (m-10) REVERT: L 37 GLN cc_start: 0.6660 (pm20) cc_final: 0.6191 (pm20) REVERT: H 34 MET cc_start: 0.6920 (ppp) cc_final: 0.6370 (ppp) REVERT: B 49 HIS cc_start: 0.8229 (t-90) cc_final: 0.7800 (t70) REVERT: B 53 ASP cc_start: 0.6917 (t0) cc_final: 0.6507 (t0) REVERT: B 54 LEU cc_start: 0.7922 (mm) cc_final: 0.7496 (mm) REVERT: B 153 MET cc_start: 0.5315 (mpp) cc_final: 0.4984 (mpp) REVERT: B 206 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7252 (ttmm) REVERT: B 319 ARG cc_start: 0.8122 (ptp90) cc_final: 0.7772 (ptt180) REVERT: B 340 GLU cc_start: 0.7538 (mp0) cc_final: 0.7171 (mp0) REVERT: B 508 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: B 511 VAL cc_start: 0.8787 (t) cc_final: 0.8566 (p) REVERT: B 541 PHE cc_start: 0.6907 (p90) cc_final: 0.6520 (p90) REVERT: B 586 ASP cc_start: 0.7622 (m-30) cc_final: 0.7176 (m-30) REVERT: B 675 GLN cc_start: 0.7735 (mt0) cc_final: 0.7508 (mt0) REVERT: B 705 VAL cc_start: 0.6625 (OUTLIER) cc_final: 0.6407 (p) REVERT: B 725 GLU cc_start: 0.7912 (tt0) cc_final: 0.7609 (tt0) REVERT: B 772 VAL cc_start: 0.8578 (p) cc_final: 0.8343 (t) REVERT: B 859 THR cc_start: 0.8177 (t) cc_final: 0.7935 (p) REVERT: B 901 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: B 933 LYS cc_start: 0.8098 (mttt) cc_final: 0.7402 (mmtm) REVERT: B 947 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7567 (mtpp) REVERT: B 949 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7489 (tp40) REVERT: B 950 ASP cc_start: 0.7539 (m-30) cc_final: 0.7137 (m-30) REVERT: B 1038 LYS cc_start: 0.7992 (tppt) cc_final: 0.7649 (tppt) REVERT: B 1073 LYS cc_start: 0.7502 (pttp) cc_final: 0.7219 (ptmt) REVERT: B 1118 ASP cc_start: 0.7926 (m-30) cc_final: 0.7715 (m-30) REVERT: F 71 PHE cc_start: 0.6876 (t80) cc_final: 0.6432 (t80) REVERT: F 93 ASN cc_start: 0.7251 (t0) cc_final: 0.7021 (t160) REVERT: D 36 TRP cc_start: 0.6158 (m-90) cc_final: 0.5391 (m-10) REVERT: D 39 GLN cc_start: 0.7560 (tp40) cc_final: 0.6942 (pp30) REVERT: C 45 SER cc_start: 0.8241 (t) cc_final: 0.8008 (p) REVERT: C 53 ASP cc_start: 0.6952 (t0) cc_final: 0.6695 (t0) REVERT: C 83 VAL cc_start: 0.7391 (OUTLIER) cc_final: 0.6360 (p) REVERT: C 206 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7283 (ttmm) REVERT: C 237 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6524 (ttm-80) REVERT: C 314 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7976 (tp40) REVERT: C 319 ARG cc_start: 0.8263 (ptp90) cc_final: 0.7959 (ptt180) REVERT: C 374 PHE cc_start: 0.7712 (m-80) cc_final: 0.7217 (m-80) REVERT: C 421 TYR cc_start: 0.6991 (m-80) cc_final: 0.6595 (m-10) REVERT: C 436 TRP cc_start: 0.6429 (p90) cc_final: 0.6088 (p90) REVERT: C 725 GLU cc_start: 0.7932 (tt0) cc_final: 0.7713 (tt0) REVERT: C 750 SER cc_start: 0.8045 (t) cc_final: 0.7663 (p) REVERT: C 776 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: C 790 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7293 (mmpt) REVERT: C 815 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7024 (mtm-85) REVERT: C 883 THR cc_start: 0.8359 (m) cc_final: 0.7998 (p) REVERT: C 933 LYS cc_start: 0.8143 (mttt) cc_final: 0.7446 (mptt) REVERT: C 947 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7726 (mtpp) REVERT: C 964 LYS cc_start: 0.8462 (mttt) cc_final: 0.8164 (mttt) REVERT: C 1019 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7355 (ttp80) REVERT: C 1030 SER cc_start: 0.8113 (m) cc_final: 0.7872 (p) REVERT: C 1038 LYS cc_start: 0.7975 (tppt) cc_final: 0.7512 (mmmm) REVERT: C 1045 LYS cc_start: 0.7987 (mttt) cc_final: 0.7778 (mttt) REVERT: C 1055 SER cc_start: 0.8482 (t) cc_final: 0.8213 (m) REVERT: C 1072 GLU cc_start: 0.7765 (pm20) cc_final: 0.7463 (pm20) REVERT: C 1073 LYS cc_start: 0.7714 (pttp) cc_final: 0.7473 (ptmm) REVERT: C 1101 HIS cc_start: 0.8388 (m-70) cc_final: 0.7917 (m-70) REVERT: G 71 PHE cc_start: 0.6679 (t80) cc_final: 0.6180 (t80) REVERT: E 31 SER cc_start: 0.8173 (p) cc_final: 0.7800 (p) REVERT: E 32 TYR cc_start: 0.7770 (m-80) cc_final: 0.7365 (m-80) REVERT: E 46 GLU cc_start: 0.7237 (pm20) cc_final: 0.6968 (mp0) REVERT: E 102 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (m-80) outliers start: 127 outliers final: 60 residues processed: 747 average time/residue: 1.1767 time to fit residues: 1061.1830 Evaluate side-chains 741 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 667 time to evaluate : 3.286 ------------------------------------------------------------------------------- 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 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 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 921 LYS 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 L residue 93 ASN 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 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 278 LYS Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 287 ASP 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 508 TYR 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 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 47 VAL 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 237 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 425 LEU 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 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 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1029 MET 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 94 TRP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 MET 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 255 optimal weight: 0.3980 chunk 214 optimal weight: 0.2980 chunk 356 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 186 optimal weight: 0.6980 chunk 380 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 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 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN B 564 GLN B1101 HIS C 764 ASN C 787 GLN C1010 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.202800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.180855 restraints weight = 58612.615| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 3.78 r_work: 0.4072 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3737 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= 0.135 Angle : 0.706 15.187 42840 Z= 0.346 Chirality : 0.048 0.345 4920 Planarity : 0.005 0.136 5448 Dihedral : 7.071 115.849 5201 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.77 % Allowed : 20.11 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3780 helix: 1.07 (0.21), residues: 654 sheet: -0.62 (0.17), residues: 903 loop : -1.76 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 110 HIS 0.007 0.001 HIS B 207 PHE 0.032 0.002 PHE G 49 TYR 0.032 0.002 TYR B 453 ARG 0.030 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 39) link_NAG-ASN : angle 2.73176 ( 117) link_BETA1-4 : bond 0.00338 ( 12) link_BETA1-4 : angle 1.08864 ( 36) hydrogen bonds : bond 0.03657 ( 871) hydrogen bonds : angle 5.69059 ( 2505) SS BOND : bond 0.00427 ( 48) SS BOND : angle 1.39321 ( 96) covalent geometry : bond 0.00315 (31317) covalent geometry : angle 0.68921 (42591) Misc. bond : bond 0.00068 ( 3) *********************** 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 774 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 682 time to evaluate : 3.411 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 34 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7308 (ttm110) REVERT: A 52 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7424 (tp-100) REVERT: A 153 MET cc_start: 0.4229 (mpp) cc_final: 0.3781 (mpp) REVERT: A 177 MET cc_start: 0.0162 (mtt) cc_final: -0.0700 (mtt) REVERT: A 200 TYR cc_start: 0.5430 (m-10) cc_final: 0.5182 (m-10) REVERT: A 319 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7333 (ptt180) REVERT: A 429 PHE cc_start: 0.6385 (t80) cc_final: 0.5973 (t80) REVERT: A 453 TYR cc_start: 0.7090 (p90) cc_final: 0.6593 (p90) REVERT: A 541 PHE cc_start: 0.6965 (p90) cc_final: 0.6199 (p90) REVERT: A 572 THR cc_start: 0.8332 (t) cc_final: 0.8005 (p) REVERT: A 588 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8328 (p) REVERT: A 651 ILE cc_start: 0.8762 (mm) cc_final: 0.8472 (mp) REVERT: A 673 SER cc_start: 0.8132 (t) cc_final: 0.7782 (p) REVERT: A 725 GLU cc_start: 0.7809 (tt0) cc_final: 0.7500 (tt0) REVERT: A 736 VAL cc_start: 0.8186 (t) cc_final: 0.7897 (m) REVERT: A 780 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: A 790 LYS cc_start: 0.7741 (mtpm) cc_final: 0.7114 (mmpt) REVERT: A 795 LYS cc_start: 0.8437 (mptm) cc_final: 0.8162 (mptp) REVERT: A 811 LYS cc_start: 0.7154 (mmpt) cc_final: 0.6583 (mtpt) REVERT: A 933 LYS cc_start: 0.7964 (mttt) cc_final: 0.7599 (mtmm) REVERT: A 1019 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7604 (ttm110) REVERT: A 1045 LYS cc_start: 0.8327 (mttt) cc_final: 0.7990 (mttt) REVERT: A 1072 GLU cc_start: 0.8012 (pm20) cc_final: 0.7596 (pm20) REVERT: A 1141 LEU cc_start: 0.7864 (tm) cc_final: 0.7631 (tt) REVERT: H 34 MET cc_start: 0.6488 (ppp) cc_final: 0.5835 (ppp) REVERT: H 39 GLN cc_start: 0.7149 (tp40) cc_final: 0.6431 (pp30) REVERT: H 102 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 49 HIS cc_start: 0.8208 (t-90) cc_final: 0.7761 (t70) REVERT: B 53 ASP cc_start: 0.6850 (t0) cc_final: 0.6404 (t0) REVERT: B 54 LEU cc_start: 0.7664 (mm) cc_final: 0.7081 (mm) REVERT: B 81 ASN cc_start: 0.7749 (p0) cc_final: 0.7161 (p0) REVERT: B 153 MET cc_start: 0.5251 (mpp) cc_final: 0.4940 (mpp) REVERT: B 206 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7230 (ttmm) REVERT: B 319 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7739 (ptt180) REVERT: B 340 GLU cc_start: 0.7398 (mp0) cc_final: 0.6970 (mp0) REVERT: B 421 TYR cc_start: 0.6817 (m-80) cc_final: 0.6428 (m-10) REVERT: B 490 PHE cc_start: 0.8164 (t80) cc_final: 0.7721 (t80) REVERT: B 508 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.6783 (m-10) REVERT: B 511 VAL cc_start: 0.8804 (t) cc_final: 0.8542 (p) REVERT: B 541 PHE cc_start: 0.6819 (p90) cc_final: 0.6431 (p90) REVERT: B 586 ASP cc_start: 0.7555 (m-30) cc_final: 0.7096 (m-30) REVERT: B 675 GLN cc_start: 0.7765 (mt0) cc_final: 0.7523 (mt0) REVERT: B 705 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6216 (p) REVERT: B 725 GLU cc_start: 0.7852 (tt0) cc_final: 0.7516 (tt0) REVERT: B 772 VAL cc_start: 0.8541 (p) cc_final: 0.8288 (t) REVERT: B 859 THR cc_start: 0.8109 (t) cc_final: 0.7860 (p) REVERT: B 933 LYS cc_start: 0.8022 (mttt) cc_final: 0.7305 (mmtm) REVERT: B 935 GLN cc_start: 0.7965 (mt0) cc_final: 0.7605 (mt0) REVERT: B 947 LYS cc_start: 0.7870 (mtpt) cc_final: 0.7565 (mtpp) REVERT: B 950 ASP cc_start: 0.7490 (m-30) cc_final: 0.7050 (m-30) REVERT: B 964 LYS cc_start: 0.8290 (mttt) cc_final: 0.7854 (mptt) REVERT: B 994 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7414 (t70) REVERT: B 1038 LYS cc_start: 0.7964 (tppt) cc_final: 0.7606 (tppt) REVERT: F 71 PHE cc_start: 0.6893 (t80) cc_final: 0.6397 (t80) REVERT: D 34 MET cc_start: 0.6200 (ppp) cc_final: 0.5597 (ppp) REVERT: D 36 TRP cc_start: 0.5680 (m-90) cc_final: 0.4793 (m-10) REVERT: D 39 GLN cc_start: 0.7431 (tp40) cc_final: 0.6823 (pp30) REVERT: D 83 MET cc_start: 0.4249 (tmt) cc_final: 0.3900 (tmt) REVERT: C 53 ASP cc_start: 0.6940 (t0) cc_final: 0.6616 (t0) REVERT: C 83 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6109 (p) REVERT: C 200 TYR cc_start: 0.5407 (m-10) cc_final: 0.5151 (m-10) REVERT: C 237 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6344 (ttm-80) REVERT: C 267 VAL cc_start: 0.8145 (t) cc_final: 0.7817 (p) REVERT: C 312 ILE cc_start: 0.8007 (tt) cc_final: 0.7689 (tp) REVERT: C 314 GLN cc_start: 0.8158 (tt0) cc_final: 0.7907 (tp40) REVERT: C 319 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7890 (ptt180) REVERT: C 340 GLU cc_start: 0.7253 (mp0) cc_final: 0.6928 (mp0) REVERT: C 374 PHE cc_start: 0.7445 (m-80) cc_final: 0.6922 (m-80) REVERT: C 421 TYR cc_start: 0.6908 (m-80) cc_final: 0.6485 (m-10) REVERT: C 436 TRP cc_start: 0.6286 (p90) cc_final: 0.6011 (p90) REVERT: C 453 TYR cc_start: 0.7450 (p90) cc_final: 0.7092 (p90) REVERT: C 651 ILE cc_start: 0.8648 (mm) cc_final: 0.8395 (mt) REVERT: C 725 GLU cc_start: 0.7871 (tt0) cc_final: 0.7641 (tt0) REVERT: C 750 SER cc_start: 0.7941 (t) cc_final: 0.7568 (p) REVERT: C 776 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7780 (tmmm) REVERT: C 790 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7221 (mmpt) REVERT: C 933 LYS cc_start: 0.8117 (mttt) cc_final: 0.7427 (mptt) REVERT: C 947 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7685 (mtpp) REVERT: C 964 LYS cc_start: 0.8416 (mttt) cc_final: 0.8131 (mttt) REVERT: C 994 ASP cc_start: 0.7658 (t70) cc_final: 0.7379 (m-30) REVERT: C 1017 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 1030 SER cc_start: 0.7960 (m) cc_final: 0.7663 (p) REVERT: C 1038 LYS cc_start: 0.7907 (tppt) cc_final: 0.7422 (mmmm) REVERT: C 1045 LYS cc_start: 0.8015 (mttt) cc_final: 0.7806 (mttt) REVERT: C 1055 SER cc_start: 0.8371 (t) cc_final: 0.8022 (m) REVERT: C 1072 GLU cc_start: 0.7703 (pm20) cc_final: 0.7406 (pm20) REVERT: C 1101 HIS cc_start: 0.8351 (m-70) cc_final: 0.7875 (m-70) REVERT: C 1123 SER cc_start: 0.8591 (t) cc_final: 0.8286 (m) REVERT: G 71 PHE cc_start: 0.6829 (t80) cc_final: 0.6335 (t80) REVERT: E 31 SER cc_start: 0.8033 (p) cc_final: 0.7760 (p) REVERT: E 32 TYR cc_start: 0.7707 (m-80) cc_final: 0.7282 (m-80) REVERT: E 46 GLU cc_start: 0.7036 (pm20) cc_final: 0.6731 (mp0) outliers start: 92 outliers final: 56 residues processed: 717 average time/residue: 1.2273 time to fit residues: 1063.7133 Evaluate side-chains 717 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 651 time to evaluate : 3.403 ------------------------------------------------------------------------------- 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 282 ASN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 780 GLU 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 5 LEU 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 61 ASN 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 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG 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 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 237 ARG Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 425 LEU 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 719 THR Chi-restraints excluded: chain C residue 743 CYS 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 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 60 TYR 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 119 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 362 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 A 992 GLN A1005 GLN A1010 GLN A1101 HIS L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 540 ASN B 564 GLN B1101 HIS C 764 ASN C 787 GLN C 919 ASN C1010 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.198479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177231 restraints weight = 58006.854| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 3.66 r_work: 0.4027 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31419 Z= 0.212 Angle : 0.755 14.726 42840 Z= 0.373 Chirality : 0.049 0.339 4920 Planarity : 0.005 0.130 5448 Dihedral : 7.102 115.960 5201 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.56 % Allowed : 21.29 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 3780 helix: 0.99 (0.21), residues: 660 sheet: -0.64 (0.17), residues: 888 loop : -1.86 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 886 HIS 0.009 0.001 HIS B 207 PHE 0.032 0.002 PHE G 49 TYR 0.032 0.002 TYR B 453 ARG 0.024 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 39) link_NAG-ASN : angle 2.80506 ( 117) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 0.99231 ( 36) hydrogen bonds : bond 0.04043 ( 871) hydrogen bonds : angle 5.69016 ( 2505) SS BOND : bond 0.00437 ( 48) SS BOND : angle 1.70646 ( 96) covalent geometry : bond 0.00498 (31317) covalent geometry : angle 0.73780 (42591) Misc. bond : bond 0.00056 ( 3) *********************** 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 754 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 669 time to evaluate : 3.177 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: A 34 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7344 (ttm110) REVERT: A 153 MET cc_start: 0.4504 (mpp) cc_final: 0.4037 (mpp) REVERT: A 168 PHE cc_start: 0.5021 (t80) cc_final: 0.4702 (t80) REVERT: A 169 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 177 MET cc_start: 0.0288 (mtt) cc_final: -0.0524 (mtt) REVERT: A 274 THR cc_start: 0.8652 (t) cc_final: 0.8320 (t) REVERT: A 319 ARG cc_start: 0.7845 (ptp90) cc_final: 0.7350 (ptt180) REVERT: A 429 PHE cc_start: 0.6455 (t80) cc_final: 0.6048 (t80) REVERT: A 453 TYR cc_start: 0.7086 (p90) cc_final: 0.6717 (p90) REVERT: A 454 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7802 (mmt90) REVERT: A 541 PHE cc_start: 0.7074 (p90) cc_final: 0.6336 (p90) REVERT: A 588 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8356 (p) REVERT: A 651 ILE cc_start: 0.8771 (mm) cc_final: 0.8499 (mp) REVERT: A 673 SER cc_start: 0.8200 (t) cc_final: 0.7839 (p) REVERT: A 725 GLU cc_start: 0.7786 (tt0) cc_final: 0.7498 (tt0) REVERT: A 736 VAL cc_start: 0.8223 (t) cc_final: 0.7926 (m) REVERT: A 780 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: A 790 LYS cc_start: 0.7714 (mtpm) cc_final: 0.7063 (mmpt) REVERT: A 795 LYS cc_start: 0.8472 (mptm) cc_final: 0.8200 (mptp) REVERT: A 811 LYS cc_start: 0.7211 (mmpt) cc_final: 0.6642 (mtpt) REVERT: A 933 LYS cc_start: 0.7957 (mttt) cc_final: 0.7594 (mtmm) REVERT: A 1019 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7606 (ttm110) REVERT: A 1045 LYS cc_start: 0.8318 (mttt) cc_final: 0.7981 (mttt) REVERT: A 1072 GLU cc_start: 0.8049 (pm20) cc_final: 0.7609 (pm20) REVERT: A 1111 GLU cc_start: 0.7550 (tt0) cc_final: 0.7254 (tt0) REVERT: A 1141 LEU cc_start: 0.7878 (tm) cc_final: 0.7629 (tt) REVERT: L 36 TYR cc_start: 0.5312 (m-10) cc_final: 0.5109 (m-10) REVERT: H 34 MET cc_start: 0.6545 (ppp) cc_final: 0.6255 (ppp) REVERT: H 39 GLN cc_start: 0.7279 (tp40) cc_final: 0.6543 (pp30) REVERT: H 102 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 53 ASP cc_start: 0.6929 (t0) cc_final: 0.6634 (t0) REVERT: B 54 LEU cc_start: 0.7828 (mm) cc_final: 0.7211 (mm) REVERT: B 153 MET cc_start: 0.5309 (mpp) cc_final: 0.4985 (mpp) REVERT: B 319 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7766 (ptt180) REVERT: B 340 GLU cc_start: 0.7583 (mp0) cc_final: 0.7140 (mp0) REVERT: B 421 TYR cc_start: 0.6774 (m-80) cc_final: 0.6346 (m-10) REVERT: B 454 ARG cc_start: 0.8427 (mmt90) cc_final: 0.8067 (mmt90) REVERT: B 490 PHE cc_start: 0.8210 (t80) cc_final: 0.7718 (t80) REVERT: B 508 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: B 511 VAL cc_start: 0.8796 (t) cc_final: 0.8557 (p) REVERT: B 541 PHE cc_start: 0.6890 (p90) cc_final: 0.6526 (p90) REVERT: B 586 ASP cc_start: 0.7565 (m-30) cc_final: 0.7109 (m-30) REVERT: B 606 ASN cc_start: 0.8478 (m-40) cc_final: 0.8257 (m-40) REVERT: B 675 GLN cc_start: 0.7734 (mt0) cc_final: 0.7506 (mt0) REVERT: B 705 VAL cc_start: 0.6627 (OUTLIER) cc_final: 0.6408 (p) REVERT: B 725 GLU cc_start: 0.7848 (tt0) cc_final: 0.7592 (tt0) REVERT: B 772 VAL cc_start: 0.8557 (p) cc_final: 0.8313 (t) REVERT: B 859 THR cc_start: 0.8139 (t) cc_final: 0.7869 (p) REVERT: B 933 LYS cc_start: 0.8054 (mttt) cc_final: 0.7310 (mmtm) REVERT: B 947 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7533 (mtpp) REVERT: B 950 ASP cc_start: 0.7595 (m-30) cc_final: 0.7043 (m-30) REVERT: B 964 LYS cc_start: 0.8313 (mttt) cc_final: 0.7823 (mptt) REVERT: B 1038 LYS cc_start: 0.7975 (tppt) cc_final: 0.7576 (tppt) REVERT: F 71 PHE cc_start: 0.6941 (t80) cc_final: 0.6437 (t80) REVERT: D 34 MET cc_start: 0.6362 (ppp) cc_final: 0.5929 (ppp) REVERT: D 36 TRP cc_start: 0.5935 (m-90) cc_final: 0.4933 (m-10) REVERT: D 39 GLN cc_start: 0.7523 (tp40) cc_final: 0.6914 (pp30) REVERT: C 53 ASP cc_start: 0.6947 (t0) cc_final: 0.6621 (t0) REVERT: C 83 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7053 (p) REVERT: C 206 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7229 (ttmm) REVERT: C 314 GLN cc_start: 0.8176 (tt0) cc_final: 0.7912 (tp40) REVERT: C 319 ARG cc_start: 0.8203 (ptp90) cc_final: 0.7881 (ptt180) REVERT: C 340 GLU cc_start: 0.7368 (mp0) cc_final: 0.6914 (mp0) REVERT: C 374 PHE cc_start: 0.7594 (m-80) cc_final: 0.7099 (m-80) REVERT: C 421 TYR cc_start: 0.6957 (m-80) cc_final: 0.6495 (m-10) REVERT: C 436 TRP cc_start: 0.6286 (p90) cc_final: 0.6024 (p90) REVERT: C 453 TYR cc_start: 0.7523 (p90) cc_final: 0.7160 (p90) REVERT: C 651 ILE cc_start: 0.8723 (mm) cc_final: 0.8479 (mt) REVERT: C 725 GLU cc_start: 0.7878 (tt0) cc_final: 0.7657 (tt0) REVERT: C 750 SER cc_start: 0.7994 (t) cc_final: 0.7639 (p) REVERT: C 776 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (tmmm) REVERT: C 790 LYS cc_start: 0.7825 (mtmm) cc_final: 0.7222 (mmpt) REVERT: C 931 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7034 (mp) REVERT: C 933 LYS cc_start: 0.8149 (mttt) cc_final: 0.7451 (mptt) REVERT: C 947 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7725 (mtpp) REVERT: C 964 LYS cc_start: 0.8418 (mttt) cc_final: 0.8141 (mttt) REVERT: C 1030 SER cc_start: 0.7960 (m) cc_final: 0.7676 (p) REVERT: C 1038 LYS cc_start: 0.7941 (tppt) cc_final: 0.7453 (mmmm) REVERT: C 1045 LYS cc_start: 0.8019 (mttt) cc_final: 0.7803 (mttt) REVERT: C 1055 SER cc_start: 0.8451 (t) cc_final: 0.8104 (m) REVERT: C 1072 GLU cc_start: 0.7736 (pm20) cc_final: 0.7434 (pm20) REVERT: C 1073 LYS cc_start: 0.7658 (pttp) cc_final: 0.7397 (ptmm) REVERT: C 1101 HIS cc_start: 0.8357 (m-70) cc_final: 0.7848 (m-70) REVERT: C 1123 SER cc_start: 0.8575 (t) cc_final: 0.8314 (m) REVERT: G 71 PHE cc_start: 0.6845 (t80) cc_final: 0.6269 (t80) REVERT: E 31 SER cc_start: 0.8041 (p) cc_final: 0.7828 (p) REVERT: E 32 TYR cc_start: 0.7709 (m-80) cc_final: 0.7365 (m-80) REVERT: E 46 GLU cc_start: 0.7143 (pm20) cc_final: 0.6810 (mp0) outliers start: 85 outliers final: 63 residues processed: 706 average time/residue: 1.2380 time to fit residues: 1052.5462 Evaluate side-chains 727 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 655 time to evaluate : 3.291 ------------------------------------------------------------------------------- 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 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 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 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 643 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 780 GLU 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 L residue 94 TRP 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 61 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 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 286 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 486 PHE 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 651 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 976 VAL 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 60 TYR 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 237 ARG 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 719 THR Chi-restraints excluded: chain C residue 743 CYS 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 1029 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 17 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 373 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 367 optimal weight: 4.9990 chunk 289 optimal weight: 0.0980 chunk 202 optimal weight: 0.7980 chunk 339 optimal weight: 0.0170 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 540 ASN B 564 GLN B1101 HIS ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN C1010 GLN ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.202434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180768 restraints weight = 58902.305| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.69 r_work: 0.4077 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31419 Z= 0.130 Angle : 0.710 14.309 42840 Z= 0.347 Chirality : 0.047 0.346 4920 Planarity : 0.005 0.093 5448 Dihedral : 6.893 115.072 5201 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.14 % Allowed : 21.92 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3780 helix: 1.23 (0.21), residues: 657 sheet: -0.50 (0.17), residues: 897 loop : -1.76 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 110 HIS 0.006 0.001 HIS B 207 PHE 0.029 0.002 PHE A 92 TYR 0.029 0.001 TYR B 453 ARG 0.018 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 39) link_NAG-ASN : angle 2.59244 ( 117) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 0.94148 ( 36) hydrogen bonds : bond 0.03393 ( 871) hydrogen bonds : angle 5.53430 ( 2505) SS BOND : bond 0.00535 ( 48) SS BOND : angle 1.50873 ( 96) covalent geometry : bond 0.00305 (31317) covalent geometry : angle 0.69526 (42591) Misc. bond : bond 0.00061 ( 3) ********************** 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 732 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 661 time to evaluate : 3.163 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 34 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7326 (ttm110) REVERT: A 52 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7287 (tp-100) REVERT: A 140 PHE cc_start: 0.7234 (p90) cc_final: 0.6544 (p90) REVERT: A 153 MET cc_start: 0.4377 (mpp) cc_final: 0.3905 (mpp) REVERT: A 177 MET cc_start: 0.0238 (mtt) cc_final: -0.0624 (mtt) REVERT: A 200 TYR cc_start: 0.5392 (m-10) cc_final: 0.5160 (m-10) REVERT: A 282 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6584 (m110) REVERT: A 319 ARG cc_start: 0.7789 (ptp90) cc_final: 0.7403 (ptt180) REVERT: A 453 TYR cc_start: 0.7104 (p90) cc_final: 0.6707 (p90) REVERT: A 454 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7660 (mmt90) REVERT: A 541 PHE cc_start: 0.7052 (p90) cc_final: 0.6273 (p90) REVERT: A 588 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 651 ILE cc_start: 0.8750 (mm) cc_final: 0.8479 (mp) REVERT: A 673 SER cc_start: 0.8088 (t) cc_final: 0.7757 (p) REVERT: A 725 GLU cc_start: 0.7842 (tt0) cc_final: 0.7561 (tt0) REVERT: A 736 VAL cc_start: 0.8155 (t) cc_final: 0.7856 (m) REVERT: A 780 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: A 795 LYS cc_start: 0.8456 (mptm) cc_final: 0.8204 (mptp) REVERT: A 811 LYS cc_start: 0.7194 (mmpt) cc_final: 0.6638 (mtpt) REVERT: A 933 LYS cc_start: 0.7964 (mttt) cc_final: 0.7594 (mtmm) REVERT: A 947 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7271 (mtmt) REVERT: A 1019 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7618 (ttm110) REVERT: A 1045 LYS cc_start: 0.8258 (mttt) cc_final: 0.7962 (mttt) REVERT: A 1072 GLU cc_start: 0.8029 (pm20) cc_final: 0.7651 (pm20) REVERT: A 1141 LEU cc_start: 0.7869 (tm) cc_final: 0.7637 (tt) REVERT: H 34 MET cc_start: 0.6386 (ppp) cc_final: 0.6101 (ppp) REVERT: H 39 GLN cc_start: 0.7095 (tp40) cc_final: 0.6366 (pp30) REVERT: H 102 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 49 HIS cc_start: 0.8093 (t-90) cc_final: 0.7677 (t70) REVERT: B 53 ASP cc_start: 0.6871 (t0) cc_final: 0.6587 (t0) REVERT: B 54 LEU cc_start: 0.7797 (mm) cc_final: 0.7207 (mm) REVERT: B 81 ASN cc_start: 0.7748 (p0) cc_final: 0.7151 (p0) REVERT: B 88 ASP cc_start: 0.6715 (m-30) cc_final: 0.6497 (m-30) REVERT: B 153 MET cc_start: 0.5435 (mpp) cc_final: 0.5075 (mpp) REVERT: B 319 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7767 (ptt180) REVERT: B 340 GLU cc_start: 0.7524 (mp0) cc_final: 0.7010 (mp0) REVERT: B 454 ARG cc_start: 0.8414 (mmt90) cc_final: 0.8106 (mmt90) REVERT: B 490 PHE cc_start: 0.8169 (t80) cc_final: 0.7775 (t80) REVERT: B 508 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6767 (m-10) REVERT: B 511 VAL cc_start: 0.8812 (t) cc_final: 0.8533 (p) REVERT: B 541 PHE cc_start: 0.6849 (p90) cc_final: 0.6448 (p90) REVERT: B 586 ASP cc_start: 0.7554 (m-30) cc_final: 0.7114 (m-30) REVERT: B 606 ASN cc_start: 0.8507 (m-40) cc_final: 0.8269 (m-40) REVERT: B 675 GLN cc_start: 0.7755 (mt0) cc_final: 0.7510 (mt0) REVERT: B 725 GLU cc_start: 0.7831 (tt0) cc_final: 0.7586 (tt0) REVERT: B 748 GLU cc_start: 0.7960 (pp20) cc_final: 0.7730 (pp20) REVERT: B 772 VAL cc_start: 0.8580 (p) cc_final: 0.8325 (t) REVERT: B 859 THR cc_start: 0.8111 (t) cc_final: 0.7845 (p) REVERT: B 933 LYS cc_start: 0.8045 (mttt) cc_final: 0.7279 (mmtm) REVERT: B 935 GLN cc_start: 0.8013 (mt0) cc_final: 0.7776 (mt0) REVERT: B 947 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7546 (mtpp) REVERT: B 950 ASP cc_start: 0.7602 (m-30) cc_final: 0.7051 (m-30) REVERT: B 964 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7808 (mptt) REVERT: B 991 VAL cc_start: 0.8207 (t) cc_final: 0.7940 (p) REVERT: B 994 ASP cc_start: 0.7623 (t70) cc_final: 0.7389 (t0) REVERT: B 1038 LYS cc_start: 0.7997 (tppt) cc_final: 0.7600 (tppt) REVERT: F 71 PHE cc_start: 0.6891 (t80) cc_final: 0.6296 (t80) REVERT: D 34 MET cc_start: 0.6667 (ppp) cc_final: 0.5907 (ppp) REVERT: D 36 TRP cc_start: 0.5609 (m-90) cc_final: 0.4726 (m-10) REVERT: D 39 GLN cc_start: 0.7428 (tp40) cc_final: 0.6868 (pp30) REVERT: D 83 MET cc_start: 0.3992 (tmt) cc_final: 0.3539 (tmt) REVERT: C 53 ASP cc_start: 0.6912 (t0) cc_final: 0.6632 (t0) REVERT: C 83 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.6128 (p) REVERT: C 129 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7405 (mmtm) REVERT: C 200 TYR cc_start: 0.5550 (m-10) cc_final: 0.5265 (m-10) REVERT: C 206 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7093 (ttmm) REVERT: C 237 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6491 (ttm-80) REVERT: C 267 VAL cc_start: 0.8114 (t) cc_final: 0.7782 (p) REVERT: C 312 ILE cc_start: 0.7990 (tt) cc_final: 0.7653 (tp) REVERT: C 314 GLN cc_start: 0.8134 (tt0) cc_final: 0.7910 (tp40) REVERT: C 319 ARG cc_start: 0.8187 (ptp90) cc_final: 0.7867 (ptt180) REVERT: C 340 GLU cc_start: 0.7268 (mp0) cc_final: 0.6839 (mp0) REVERT: C 374 PHE cc_start: 0.7473 (m-80) cc_final: 0.6941 (m-80) REVERT: C 421 TYR cc_start: 0.6846 (m-80) cc_final: 0.6373 (m-10) REVERT: C 453 TYR cc_start: 0.7398 (p90) cc_final: 0.7025 (p90) REVERT: C 541 PHE cc_start: 0.7061 (p90) cc_final: 0.6730 (p90) REVERT: C 574 ASP cc_start: 0.7581 (t70) cc_final: 0.7081 (t70) REVERT: C 651 ILE cc_start: 0.8669 (mm) cc_final: 0.8416 (mt) REVERT: C 725 GLU cc_start: 0.7888 (tt0) cc_final: 0.7679 (tt0) REVERT: C 750 SER cc_start: 0.7949 (t) cc_final: 0.7537 (p) REVERT: C 776 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7776 (tmmm) REVERT: C 933 LYS cc_start: 0.8107 (mttt) cc_final: 0.7436 (mptt) REVERT: C 947 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7669 (mtpp) REVERT: C 964 LYS cc_start: 0.8395 (mttt) cc_final: 0.8127 (mttt) REVERT: C 994 ASP cc_start: 0.7595 (t70) cc_final: 0.7341 (m-30) REVERT: C 1038 LYS cc_start: 0.7914 (tppt) cc_final: 0.7484 (mmpt) REVERT: C 1045 LYS cc_start: 0.8014 (mttt) cc_final: 0.7804 (mttt) REVERT: C 1055 SER cc_start: 0.8367 (t) cc_final: 0.8023 (m) REVERT: C 1072 GLU cc_start: 0.7579 (pm20) cc_final: 0.7323 (pm20) REVERT: C 1101 HIS cc_start: 0.8348 (m-70) cc_final: 0.7890 (m-70) REVERT: C 1123 SER cc_start: 0.8569 (t) cc_final: 0.8276 (m) REVERT: G 71 PHE cc_start: 0.6772 (t80) cc_final: 0.6253 (t80) REVERT: E 31 SER cc_start: 0.7907 (p) cc_final: 0.7674 (p) REVERT: E 32 TYR cc_start: 0.7657 (m-80) cc_final: 0.7256 (m-80) REVERT: E 46 GLU cc_start: 0.7020 (pm20) cc_final: 0.6694 (mp0) outliers start: 71 outliers final: 43 residues processed: 691 average time/residue: 1.2250 time to fit residues: 1023.5113 Evaluate side-chains 698 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 646 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 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 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 780 GLU 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 33 LEU 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 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 332 ILE 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 588 THR Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain D residue 60 TYR 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 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 719 THR Chi-restraints excluded: chain C residue 743 CYS 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 1074 ASN Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 370 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 187 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 540 ASN B 564 GLN B1101 HIS ** F 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C1010 GLN E 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.200572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.179034 restraints weight = 57955.894| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.65 r_work: 0.4052 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4067 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= 0.160 Angle : 0.724 13.848 42840 Z= 0.356 Chirality : 0.048 0.341 4920 Planarity : 0.005 0.106 5448 Dihedral : 6.885 115.178 5201 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.14 % Allowed : 22.34 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 3780 helix: 1.24 (0.21), residues: 657 sheet: -0.53 (0.17), residues: 906 loop : -1.77 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 886 HIS 0.008 0.001 HIS B 207 PHE 0.030 0.002 PHE B 168 TYR 0.030 0.001 TYR B 453 ARG 0.021 0.001 ARG L 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 39) link_NAG-ASN : angle 2.59986 ( 117) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 0.92581 ( 36) hydrogen bonds : bond 0.03563 ( 871) hydrogen bonds : angle 5.50590 ( 2505) SS BOND : bond 0.00598 ( 48) SS BOND : angle 1.96858 ( 96) covalent geometry : bond 0.00381 (31317) covalent geometry : angle 0.70686 (42591) Misc. bond : bond 0.00059 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28208.89 seconds wall clock time: 485 minutes 35.26 seconds (29135.26 seconds total)