Starting phenix.real_space_refine on Sun Jul 5 21:47:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r40_14250/07_2026/7r40_14250.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19449 2.51 5 N 5052 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30615 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "C" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.47, per 1000 atoms: 0.21 Number of scatterers: 30615 At special positions: 0 Unit cell: (152.52, 158.72, 230.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5982 8.00 N 5052 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.846A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.527A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.608A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 8.036A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.020A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.538A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.711A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.846A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 98 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 109 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.021A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.537A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.311A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.732A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.205A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.649A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 98 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 109 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.539A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.397A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS E 98 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE E 109 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 92 " --> pdb=" O VAL E 116 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2505 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 3.28 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: 16455 17.63 - 35.26: 1381 35.26 - 52.89: 263 52.89 - 70.52: 34 70.52 - 88.15: 53 Dihedral angle restraints: 18186 sinusoidal: 7077 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 18183 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.220 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 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 : 14.041 88.155 10920 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 3780 helix: -3.72 (0.09), residues: 603 sheet: -0.50 (0.18), residues: 831 loop : -1.75 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 577 TYR 0.010 0.001 TYR C 351 PHE 0.016 0.001 PHE G 49 TRP 0.006 0.001 TRP D 47 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (31317) covalent geometry : angle 0.73238 / 0.37 (42591) SS BOND : bond 0.00387 / 0.26 ( 48) SS BOND : angle 1.00020 / 0.69 ( 96) hydrogen bonds : bond 0.28524 / 18.79 ( 871) hydrogen bonds : angle 10.33944 / 7.13 ( 2505) Misc. bond : bond 0.00105 / 0.05 ( 3) link_BETA1-4 : bond 0.00740 / 0.43 ( 12) link_BETA1-4 : angle 1.28309 / 0.98 ( 36) link_NAG-ASN : bond 0.00566 / 0.36 ( 39) link_NAG-ASN : angle 2.74865 / 1.60 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6741 (m) cc_final: 0.6457 (t) REVERT: A 58 PHE cc_start: 0.7383 (m-10) cc_final: 0.7020 (m-80) REVERT: A 129 LYS cc_start: 0.6947 (mppt) cc_final: 0.6628 (mppt) REVERT: A 310 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7785 (ttpp) REVERT: A 319 ARG cc_start: 0.7123 (ptp90) cc_final: 0.6697 (ptt180) REVERT: A 374 PHE cc_start: 0.6948 (m-80) cc_final: 0.6657 (m-10) REVERT: A 511 VAL cc_start: 0.8113 (t) cc_final: 0.7891 (p) REVERT: A 572 THR cc_start: 0.8105 (t) cc_final: 0.7669 (p) REVERT: A 606 ASN cc_start: 0.8119 (m-40) cc_final: 0.7883 (m-40) REVERT: A 612 TYR cc_start: 0.8288 (m-80) cc_final: 0.7890 (m-80) REVERT: A 671 CYS cc_start: 0.5055 (m) cc_final: 0.4817 (m) REVERT: A 673 SER cc_start: 0.8365 (t) cc_final: 0.8029 (p) REVERT: A 725 GLU cc_start: 0.7325 (tt0) cc_final: 0.7069 (tt0) REVERT: A 736 VAL cc_start: 0.7929 (t) cc_final: 0.7715 (m) REVERT: A 790 LYS cc_start: 0.7401 (mmpt) cc_final: 0.7087 (mmpt) REVERT: A 933 LYS cc_start: 0.7924 (mttt) cc_final: 0.7710 (mttt) REVERT: A 936 ASP cc_start: 0.7675 (m-30) cc_final: 0.7327 (m-30) REVERT: A 947 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7615 (mtpp) REVERT: A 964 LYS cc_start: 0.7858 (mttt) cc_final: 0.7642 (mttt) REVERT: A 975 SER cc_start: 0.8576 (p) cc_final: 0.8229 (t) REVERT: A 1045 LYS cc_start: 0.7927 (mttt) cc_final: 0.7533 (mttt) REVERT: A 1082 CYS cc_start: 0.5882 (t) cc_final: 0.5446 (t) REVERT: A 1086 LYS cc_start: 0.6615 (mtmm) cc_final: 0.6110 (mtmm) REVERT: A 1092 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 1101 HIS cc_start: 0.7474 (m-70) cc_final: 0.7185 (m170) REVERT: A 1138 TYR cc_start: 0.7675 (t80) cc_final: 0.7343 (t80) REVERT: L 71 PHE cc_start: 0.5786 (t80) cc_final: 0.5218 (t80) REVERT: B 53 ASP cc_start: 0.5842 (t0) cc_final: 0.5596 (t0) REVERT: B 54 LEU cc_start: 0.7550 (mm) cc_final: 0.7343 (mm) REVERT: B 153 MET cc_start: 0.4381 (mpp) cc_final: 0.4165 (mpp) REVERT: B 192 PHE cc_start: 0.7684 (m-80) cc_final: 0.7336 (m-80) REVERT: B 269 TYR cc_start: 0.6950 (m-80) cc_final: 0.6349 (m-80) REVERT: B 319 ARG cc_start: 0.7154 (ptp90) cc_final: 0.6840 (ptt180) REVERT: B 340 GLU cc_start: 0.6812 (mp0) cc_final: 0.6420 (mp0) REVERT: B 374 PHE cc_start: 0.6793 (m-80) cc_final: 0.6207 (m-80) REVERT: B 427 ASP cc_start: 0.7460 (p0) cc_final: 0.7219 (p0) REVERT: B 511 VAL cc_start: 0.8281 (t) cc_final: 0.7950 (p) REVERT: B 541 PHE cc_start: 0.6432 (p90) cc_final: 0.6086 (p90) REVERT: B 586 ASP cc_start: 0.7245 (m-30) cc_final: 0.6991 (m-30) REVERT: B 612 TYR cc_start: 0.8224 (m-80) cc_final: 0.7990 (m-80) REVERT: B 655 HIS cc_start: 0.7519 (t70) cc_final: 0.7298 (t-170) REVERT: B 675 GLN cc_start: 0.7175 (mt0) cc_final: 0.6971 (mt0) REVERT: B 725 GLU cc_start: 0.7045 (tt0) cc_final: 0.6786 (tt0) REVERT: B 731 MET cc_start: 0.8013 (mtm) cc_final: 0.7718 (mtm) REVERT: B 764 ASN cc_start: 0.7217 (m-40) cc_final: 0.7016 (m-40) REVERT: B 772 VAL cc_start: 0.8514 (p) cc_final: 0.8196 (t) REVERT: B 790 LYS cc_start: 0.7328 (mmpt) cc_final: 0.6851 (mmmt) REVERT: B 933 LYS cc_start: 0.7898 (mttt) cc_final: 0.7306 (mmtm) REVERT: B 947 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7507 (mtpp) REVERT: B 950 ASP cc_start: 0.7513 (m-30) cc_final: 0.7108 (m-30) REVERT: B 1050 MET cc_start: 0.8046 (ptm) cc_final: 0.7769 (ptm) REVERT: B 1082 CYS cc_start: 0.5844 (t) cc_final: 0.5395 (t) REVERT: B 1138 TYR cc_start: 0.7570 (t80) cc_final: 0.7163 (t80) REVERT: F 35 TRP cc_start: 0.4773 (m-10) cc_final: 0.4558 (m-10) REVERT: F 71 PHE cc_start: 0.5833 (t80) cc_final: 0.5451 (t80) REVERT: C 29 THR cc_start: 0.7105 (m) cc_final: 0.6759 (t) REVERT: C 45 SER cc_start: 0.7750 (t) cc_final: 0.7384 (p) REVERT: C 47 VAL cc_start: 0.8166 (m) cc_final: 0.7951 (m) REVERT: C 53 ASP cc_start: 0.6313 (t0) cc_final: 0.6031 (t70) REVERT: C 54 LEU cc_start: 0.7405 (mm) cc_final: 0.7091 (mm) REVERT: C 138 ASP cc_start: 0.6414 (t0) cc_final: 0.6155 (t0) REVERT: C 192 PHE cc_start: 0.7483 (m-80) cc_final: 0.7215 (m-80) REVERT: C 237 ARG cc_start: 0.6765 (mtp85) cc_final: 0.6230 (mpp80) REVERT: C 340 GLU cc_start: 0.6712 (mp0) cc_final: 0.6468 (mp0) REVERT: C 374 PHE cc_start: 0.6729 (m-80) cc_final: 0.6323 (m-80) REVERT: C 427 ASP cc_start: 0.7512 (p0) cc_final: 0.7244 (p0) REVERT: C 453 TYR cc_start: 0.6947 (p90) cc_final: 0.5538 (p90) REVERT: C 511 VAL cc_start: 0.8263 (t) cc_final: 0.7969 (p) REVERT: C 532 ASN cc_start: 0.8300 (t0) cc_final: 0.8088 (t0) REVERT: C 541 PHE cc_start: 0.6507 (p90) cc_final: 0.5978 (p90) REVERT: C 553 THR cc_start: 0.8147 (p) cc_final: 0.7928 (p) REVERT: C 572 THR cc_start: 0.8110 (m) cc_final: 0.7857 (p) REVERT: C 612 TYR cc_start: 0.8135 (m-80) cc_final: 0.7789 (m-80) REVERT: C 725 GLU cc_start: 0.7187 (tt0) cc_final: 0.6903 (tt0) REVERT: C 772 VAL cc_start: 0.8443 (p) cc_final: 0.8235 (t) REVERT: C 773 GLU cc_start: 0.7237 (pt0) cc_final: 0.7033 (tt0) REVERT: C 790 LYS cc_start: 0.7371 (mmpt) cc_final: 0.7024 (mmpt) REVERT: C 868 GLU cc_start: 0.7122 (mp0) cc_final: 0.6829 (mp0) REVERT: C 933 LYS cc_start: 0.7927 (mttt) cc_final: 0.7419 (mptt) REVERT: C 936 ASP cc_start: 0.7347 (m-30) cc_final: 0.7138 (m-30) REVERT: C 947 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7665 (mtpp) REVERT: C 950 ASP cc_start: 0.7478 (m-30) cc_final: 0.7165 (m-30) REVERT: C 954 GLN cc_start: 0.7959 (mt0) cc_final: 0.7629 (mt0) REVERT: C 964 LYS cc_start: 0.7848 (mttt) cc_final: 0.7553 (mttt) REVERT: C 975 SER cc_start: 0.8623 (p) cc_final: 0.8323 (t) REVERT: C 1091 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7369 (mmt90) REVERT: C 1101 HIS cc_start: 0.7635 (m-70) cc_final: 0.7426 (m-70) REVERT: G 71 PHE cc_start: 0.5991 (t80) cc_final: 0.5569 (t80) REVERT: G 92 PHE cc_start: 0.6863 (m-80) cc_final: 0.6616 (m-80) REVERT: E 68 PHE cc_start: 0.7039 (m-10) cc_final: 0.6694 (m-10) outliers start: 0 outliers final: 4 residues processed: 776 average time/residue: 0.6071 time to fit residues: 563.9032 Evaluate side-chains 659 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 655 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN A 540 ASN A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1010 GLN L 27 GLN L 93 ASN B 317 ASN B 448 ASN B 540 ASN B 607 GLN B 613 GLN B 804 GLN B 935 GLN B 957 GLN B 960 ASN B 992 GLN B1101 HIS C 49 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN C 960 ASN C 992 GLN C1010 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.206319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.184571 restraints weight = 59988.727| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.79 r_work: 0.4136 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31419 Z= 0.187 Angle : 0.705 20.532 42840 Z= 0.348 Chirality : 0.049 0.563 4920 Planarity : 0.005 0.061 5448 Dihedral : 4.905 46.998 4138 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.26 % Allowed : 11.62 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3780 helix: -0.61 (0.19), residues: 615 sheet: -0.45 (0.17), residues: 870 loop : -1.61 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 995 TYR 0.023 0.002 TYR A 453 PHE 0.024 0.002 PHE A 490 TRP 0.015 0.002 TRP C 353 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (31317) covalent geometry : angle 0.67826 / 0.34 (42591) SS BOND : bond 0.00771 / 0.55 ( 48) SS BOND : angle 1.36326 / 0.93 ( 96) hydrogen bonds : bond 0.05104 / 3.32 ( 871) hydrogen bonds : angle 6.54524 / 4.52 ( 2505) Misc. bond : bond 0.00047 / 0.02 ( 3) link_BETA1-4 : bond 0.00469 / 0.30 ( 12) link_BETA1-4 : angle 1.02809 / 0.77 ( 36) link_NAG-ASN : bond 0.00823 / 0.53 ( 39) link_NAG-ASN : angle 3.55902 / 2.06 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 704 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.7787 (m-10) cc_final: 0.7425 (m-10) REVERT: A 153 MET cc_start: 0.3699 (mpp) cc_final: 0.3399 (mpp) REVERT: A 208 THR cc_start: 0.8258 (t) cc_final: 0.8014 (p) REVERT: A 319 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7211 (ptt180) REVERT: A 429 PHE cc_start: 0.5586 (t80) cc_final: 0.5355 (t80) REVERT: A 572 THR cc_start: 0.8377 (t) cc_final: 0.8089 (p) REVERT: A 612 TYR cc_start: 0.8483 (m-80) cc_final: 0.8082 (m-80) REVERT: A 651 ILE cc_start: 0.8760 (mm) cc_final: 0.8558 (mp) REVERT: A 673 SER cc_start: 0.8489 (t) cc_final: 0.8113 (p) REVERT: A 719 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 725 GLU cc_start: 0.7855 (tt0) cc_final: 0.7515 (tt0) REVERT: A 736 VAL cc_start: 0.8146 (t) cc_final: 0.7815 (m) REVERT: A 776 LYS cc_start: 0.8002 (tmmt) cc_final: 0.7738 (ttpp) REVERT: A 790 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7275 (mmpt) REVERT: A 811 LYS cc_start: 0.6928 (mmpt) cc_final: 0.6502 (mtpt) REVERT: A 933 LYS cc_start: 0.7952 (mttt) cc_final: 0.7578 (mtmm) REVERT: A 936 ASP cc_start: 0.7546 (m-30) cc_final: 0.7267 (m-30) REVERT: A 947 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7583 (mtpp) REVERT: A 975 SER cc_start: 0.8658 (p) cc_final: 0.8326 (t) REVERT: A 1038 LYS cc_start: 0.7823 (tppt) cc_final: 0.7582 (mmmt) REVERT: A 1045 LYS cc_start: 0.8396 (mttt) cc_final: 0.7923 (mttt) REVERT: A 1082 CYS cc_start: 0.7079 (t) cc_final: 0.6605 (t) REVERT: A 1086 LYS cc_start: 0.6956 (mtmm) cc_final: 0.6326 (mtmm) REVERT: A 1101 HIS cc_start: 0.8107 (m-70) cc_final: 0.7891 (m-70) REVERT: A 1141 LEU cc_start: 0.7709 (tm) cc_final: 0.7458 (tt) REVERT: L 81 GLU cc_start: 0.7768 (mp0) cc_final: 0.7405 (mp0) REVERT: H 34 MET cc_start: 0.6431 (ppp) cc_final: 0.5863 (ppp) REVERT: B 49 HIS cc_start: 0.8092 (t-90) cc_final: 0.7811 (t70) REVERT: B 53 ASP cc_start: 0.6612 (t0) cc_final: 0.6332 (t0) REVERT: B 54 LEU cc_start: 0.7964 (mm) cc_final: 0.7738 (mm) REVERT: B 61 ASN cc_start: 0.6701 (p0) cc_final: 0.6434 (p0) REVERT: B 153 MET cc_start: 0.4885 (mpp) cc_final: 0.4593 (mpp) REVERT: B 192 PHE cc_start: 0.8358 (m-80) cc_final: 0.8131 (m-80) REVERT: B 286 THR cc_start: 0.7946 (OUTLIER) cc_final: 0.7642 (t) REVERT: B 319 ARG cc_start: 0.7826 (ptp90) cc_final: 0.7372 (ptt180) REVERT: B 340 GLU cc_start: 0.7262 (mp0) cc_final: 0.6802 (mp0) REVERT: B 427 ASP cc_start: 0.7958 (p0) cc_final: 0.7730 (p0) REVERT: B 497 PHE cc_start: 0.4305 (m-10) cc_final: 0.3621 (m-10) REVERT: B 511 VAL cc_start: 0.8611 (t) cc_final: 0.8394 (p) REVERT: B 541 PHE cc_start: 0.6524 (p90) cc_final: 0.6111 (p90) REVERT: B 586 ASP cc_start: 0.7596 (m-30) cc_final: 0.7211 (m-30) REVERT: B 675 GLN cc_start: 0.7725 (mt0) cc_final: 0.7456 (mt0) REVERT: B 725 GLU cc_start: 0.7758 (tt0) cc_final: 0.7460 (tt0) REVERT: B 772 VAL cc_start: 0.8556 (p) cc_final: 0.8335 (t) REVERT: B 780 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: B 859 THR cc_start: 0.8143 (t) cc_final: 0.7896 (p) REVERT: B 931 ILE cc_start: 0.7833 (mm) cc_final: 0.7571 (tp) REVERT: B 933 LYS cc_start: 0.8040 (mttt) cc_final: 0.7345 (mmtm) REVERT: B 947 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7479 (mtpp) REVERT: B 950 ASP cc_start: 0.7749 (m-30) cc_final: 0.7282 (m-30) REVERT: B 1038 LYS cc_start: 0.7899 (tppt) cc_final: 0.7664 (tppt) REVERT: B 1055 SER cc_start: 0.8095 (t) cc_final: 0.7736 (m) REVERT: B 1082 CYS cc_start: 0.7168 (t) cc_final: 0.6698 (t) REVERT: B 1138 TYR cc_start: 0.7884 (t80) cc_final: 0.7349 (t80) REVERT: F 71 PHE cc_start: 0.6693 (t80) cc_final: 0.6140 (t80) REVERT: D 39 GLN cc_start: 0.7172 (tp40) cc_final: 0.6544 (pp30) REVERT: C 45 SER cc_start: 0.8149 (t) cc_final: 0.7885 (p) REVERT: C 53 ASP cc_start: 0.6875 (t0) cc_final: 0.6620 (t70) REVERT: C 81 ASN cc_start: 0.7367 (p0) cc_final: 0.7032 (m110) REVERT: C 84 LEU cc_start: 0.7147 (mt) cc_final: 0.6933 (mp) REVERT: C 121 ASN cc_start: 0.6176 (t0) cc_final: 0.5965 (t0) REVERT: C 138 ASP cc_start: 0.6611 (t0) cc_final: 0.6179 (t0) REVERT: C 192 PHE cc_start: 0.8297 (m-80) cc_final: 0.8067 (m-80) REVERT: C 208 THR cc_start: 0.8365 (t) cc_final: 0.8119 (p) REVERT: C 224 GLU cc_start: 0.6770 (mp0) cc_final: 0.6553 (mp0) REVERT: C 314 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7847 (tp40) REVERT: C 324 GLU cc_start: 0.6965 (pm20) cc_final: 0.6664 (pm20) REVERT: C 340 GLU cc_start: 0.6885 (mp0) cc_final: 0.6576 (mp0) REVERT: C 392 PHE cc_start: 0.7295 (m-10) cc_final: 0.7067 (m-80) REVERT: C 436 TRP cc_start: 0.6289 (p90) cc_final: 0.5934 (p90) REVERT: C 455 LEU cc_start: 0.8952 (tm) cc_final: 0.8602 (mm) REVERT: C 497 PHE cc_start: 0.4395 (m-10) cc_final: 0.3637 (m-10) REVERT: C 511 VAL cc_start: 0.8703 (t) cc_final: 0.8462 (p) REVERT: C 541 PHE cc_start: 0.6503 (p90) cc_final: 0.5954 (p90) REVERT: C 572 THR cc_start: 0.8273 (m) cc_final: 0.7862 (p) REVERT: C 725 GLU cc_start: 0.7838 (tt0) cc_final: 0.7516 (tt0) REVERT: C 754 LEU cc_start: 0.8459 (mt) cc_final: 0.8168 (mt) REVERT: C 765 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7242 (ttp80) REVERT: C 790 LYS cc_start: 0.7591 (mmpt) cc_final: 0.7326 (mmpt) REVERT: C 858 LEU cc_start: 0.8252 (mm) cc_final: 0.7995 (mp) REVERT: C 933 LYS cc_start: 0.8136 (mttt) cc_final: 0.7438 (mptt) REVERT: C 947 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7605 (mtpp) REVERT: C 964 LYS cc_start: 0.8321 (mttt) cc_final: 0.8033 (mttt) REVERT: C 995 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7784 (mtp85) REVERT: C 1038 LYS cc_start: 0.7576 (tppt) cc_final: 0.7200 (mmmm) REVERT: C 1045 LYS cc_start: 0.8082 (mttt) cc_final: 0.7783 (tttt) REVERT: C 1072 GLU cc_start: 0.7600 (pm20) cc_final: 0.7274 (pm20) REVERT: C 1101 HIS cc_start: 0.8273 (m-70) cc_final: 0.7844 (m-70) REVERT: C 1138 TYR cc_start: 0.7926 (t80) cc_final: 0.7720 (t80) REVERT: G 71 PHE cc_start: 0.6703 (t80) cc_final: 0.6044 (t80) REVERT: G 81 GLU cc_start: 0.8008 (mp0) cc_final: 0.7803 (mp0) REVERT: G 92 PHE cc_start: 0.7483 (m-80) cc_final: 0.7202 (m-80) REVERT: E 32 TYR cc_start: 0.7732 (m-80) cc_final: 0.7312 (m-80) REVERT: E 83 MET cc_start: 0.4347 (mmm) cc_final: 0.3668 (ppp) outliers start: 75 outliers final: 37 residues processed: 731 average time/residue: 0.6127 time to fit residues: 536.8367 Evaluate side-chains 700 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 659 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain L residue 93 ASN 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 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 332 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 919 ASN A1002 GLN L 27 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1101 HIS F 93 ASN C 764 ASN C1010 GLN G 93 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.202089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.180186 restraints weight = 59237.421| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 3.76 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: 0.6889 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 31419 Z= 0.208 Angle : 0.686 15.222 42840 Z= 0.343 Chirality : 0.049 0.557 4920 Planarity : 0.005 0.059 5448 Dihedral : 4.972 29.294 4130 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.25 % Allowed : 14.51 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3780 helix: 0.39 (0.20), residues: 657 sheet: -0.55 (0.17), residues: 924 loop : -1.66 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 38 TYR 0.019 0.002 TYR B 204 PHE 0.031 0.002 PHE B 329 TRP 0.018 0.002 TRP C 353 HIS 0.006 0.001 HIS G 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (31317) covalent geometry : angle 0.67194 / 0.34 (42591) SS BOND : bond 0.00358 / 0.24 ( 48) SS BOND : angle 1.45713 / 1.01 ( 96) hydrogen bonds : bond 0.04615 / 3.01 ( 871) hydrogen bonds : angle 6.08151 / 4.21 ( 2505) Misc. bond : bond 0.00289 / 0.14 ( 3) link_BETA1-4 : bond 0.00411 / 0.24 ( 12) link_BETA1-4 : angle 1.11504 / 0.79 ( 36) link_NAG-ASN : bond 0.00763 / 0.53 ( 39) link_NAG-ASN : angle 2.46150 / 1.60 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 689 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7200 (ttm-80) REVERT: A 153 MET cc_start: 0.3926 (mpp) cc_final: 0.3526 (mpp) REVERT: A 282 ASN cc_start: 0.7163 (t0) cc_final: 0.6902 (m110) REVERT: A 319 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7355 (ptt180) REVERT: A 421 TYR cc_start: 0.6814 (m-80) cc_final: 0.6346 (m-10) REVERT: A 429 PHE cc_start: 0.6002 (t80) cc_final: 0.5722 (t80) REVERT: A 490 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7787 (OUTLIER) REVERT: A 572 THR cc_start: 0.8422 (t) cc_final: 0.7807 (p) REVERT: A 588 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8288 (p) REVERT: A 651 ILE cc_start: 0.8750 (mm) cc_final: 0.8491 (mp) REVERT: A 673 SER cc_start: 0.8322 (t) cc_final: 0.7929 (p) REVERT: A 719 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8058 (p) REVERT: A 725 GLU cc_start: 0.8028 (tt0) cc_final: 0.7680 (tt0) REVERT: A 736 VAL cc_start: 0.8190 (t) cc_final: 0.7871 (m) REVERT: A 790 LYS cc_start: 0.7501 (mmpt) cc_final: 0.7225 (mmpt) REVERT: A 811 LYS cc_start: 0.7029 (mmpt) cc_final: 0.6529 (mtpp) REVERT: A 933 LYS cc_start: 0.7951 (mttt) cc_final: 0.7580 (mtmm) REVERT: A 947 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7498 (mtpp) REVERT: A 964 LYS cc_start: 0.8236 (mttt) cc_final: 0.8024 (mttt) REVERT: A 975 SER cc_start: 0.8700 (p) cc_final: 0.8391 (t) REVERT: A 1038 LYS cc_start: 0.8066 (tppt) cc_final: 0.7777 (mmpt) REVERT: A 1045 LYS cc_start: 0.8333 (mttt) cc_final: 0.7966 (mttt) REVERT: A 1072 GLU cc_start: 0.7951 (pm20) cc_final: 0.7443 (pm20) REVERT: A 1086 LYS cc_start: 0.7037 (mtmm) cc_final: 0.6415 (mtmm) REVERT: A 1101 HIS cc_start: 0.8196 (m-70) cc_final: 0.7983 (m-70) REVERT: L 81 GLU cc_start: 0.7688 (mp0) cc_final: 0.7420 (mp0) REVERT: H 34 MET cc_start: 0.6733 (ppp) cc_final: 0.6376 (ppp) REVERT: H 39 GLN cc_start: 0.7089 (tp40) cc_final: 0.6061 (tp40) REVERT: H 95 TYR cc_start: 0.5635 (m-80) cc_final: 0.5189 (m-80) REVERT: B 49 HIS cc_start: 0.8196 (t-90) cc_final: 0.7811 (t70) REVERT: B 53 ASP cc_start: 0.6751 (t0) cc_final: 0.6338 (t0) REVERT: B 54 LEU cc_start: 0.7954 (mm) cc_final: 0.7709 (mm) REVERT: B 61 ASN cc_start: 0.6774 (p0) cc_final: 0.6560 (p0) REVERT: B 81 ASN cc_start: 0.7673 (p0) cc_final: 0.7174 (p0) REVERT: B 153 MET cc_start: 0.5102 (mpp) cc_final: 0.4817 (mpp) REVERT: B 192 PHE cc_start: 0.8392 (m-80) cc_final: 0.8159 (m-80) REVERT: B 286 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7702 (t) REVERT: B 319 ARG cc_start: 0.7954 (ptp90) cc_final: 0.7561 (ptt180) REVERT: B 340 GLU cc_start: 0.7363 (mp0) cc_final: 0.6850 (mp0) REVERT: B 374 PHE cc_start: 0.7377 (m-80) cc_final: 0.7092 (m-80) REVERT: B 427 ASP cc_start: 0.8064 (p0) cc_final: 0.7850 (p0) REVERT: B 448 ASN cc_start: 0.4426 (p0) cc_final: 0.3649 (p0) REVERT: B 508 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: B 511 VAL cc_start: 0.8686 (t) cc_final: 0.8456 (p) REVERT: B 586 ASP cc_start: 0.7603 (m-30) cc_final: 0.7157 (m-30) REVERT: B 675 GLN cc_start: 0.7742 (mt0) cc_final: 0.7501 (mt0) REVERT: B 725 GLU cc_start: 0.7804 (tt0) cc_final: 0.7485 (tt0) REVERT: B 772 VAL cc_start: 0.8528 (p) cc_final: 0.8317 (t) REVERT: B 780 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: B 859 THR cc_start: 0.8167 (t) cc_final: 0.7885 (p) REVERT: B 913 GLN cc_start: 0.7997 (mt0) cc_final: 0.7791 (mt0) REVERT: B 931 ILE cc_start: 0.7651 (mm) cc_final: 0.7362 (tp) REVERT: B 933 LYS cc_start: 0.8029 (mttt) cc_final: 0.7283 (mmtm) REVERT: B 947 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7579 (mtpp) REVERT: B 950 ASP cc_start: 0.7630 (m-30) cc_final: 0.7191 (m-30) REVERT: B 1038 LYS cc_start: 0.7978 (tppt) cc_final: 0.7651 (tppt) REVERT: F 71 PHE cc_start: 0.6648 (t80) cc_final: 0.6177 (t80) REVERT: D 32 TYR cc_start: 0.7783 (m-80) cc_final: 0.7517 (m-80) REVERT: D 34 MET cc_start: 0.6814 (ppp) cc_final: 0.6366 (ppp) REVERT: D 114 THR cc_start: 0.4720 (p) cc_final: 0.4517 (m) REVERT: C 53 ASP cc_start: 0.6972 (t0) cc_final: 0.6741 (t70) REVERT: C 224 GLU cc_start: 0.6776 (mp0) cc_final: 0.6568 (mp0) REVERT: C 314 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: C 340 GLU cc_start: 0.7207 (mp0) cc_final: 0.6819 (mp0) REVERT: C 374 PHE cc_start: 0.7394 (m-80) cc_final: 0.6962 (m-80) REVERT: C 425 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7903 (mm) REVERT: C 429 PHE cc_start: 0.6509 (t80) cc_final: 0.5909 (t80) REVERT: C 436 TRP cc_start: 0.6347 (p90) cc_final: 0.6073 (p90) REVERT: C 453 TYR cc_start: 0.7261 (p90) cc_final: 0.6927 (p90) REVERT: C 541 PHE cc_start: 0.6887 (p90) cc_final: 0.6485 (p90) REVERT: C 572 THR cc_start: 0.8303 (m) cc_final: 0.7952 (p) REVERT: C 725 GLU cc_start: 0.7875 (tt0) cc_final: 0.7650 (tt0) REVERT: C 750 SER cc_start: 0.7801 (t) cc_final: 0.7472 (p) REVERT: C 773 GLU cc_start: 0.7604 (tt0) cc_final: 0.7375 (tt0) REVERT: C 776 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7767 (tmmm) REVERT: C 815 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7148 (mtm-85) REVERT: C 858 LEU cc_start: 0.8308 (mm) cc_final: 0.8067 (mp) REVERT: C 933 LYS cc_start: 0.8125 (mttt) cc_final: 0.7451 (mptt) REVERT: C 947 LYS cc_start: 0.7963 (mtpt) cc_final: 0.7688 (mtpp) REVERT: C 964 LYS cc_start: 0.8432 (mttt) cc_final: 0.8099 (mttt) REVERT: C 974 SER cc_start: 0.8608 (m) cc_final: 0.8193 (p) REVERT: C 1019 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7374 (ttp80) REVERT: C 1038 LYS cc_start: 0.7805 (tppt) cc_final: 0.7348 (mmmm) REVERT: C 1045 LYS cc_start: 0.8040 (mttt) cc_final: 0.7736 (tttt) REVERT: C 1055 SER cc_start: 0.8396 (t) cc_final: 0.8046 (m) REVERT: C 1072 GLU cc_start: 0.7659 (pm20) cc_final: 0.7386 (pm20) REVERT: C 1101 HIS cc_start: 0.8310 (m-70) cc_final: 0.7877 (m-70) REVERT: C 1138 TYR cc_start: 0.7972 (t80) cc_final: 0.7735 (t80) REVERT: G 71 PHE cc_start: 0.6816 (t80) cc_final: 0.6184 (t80) REVERT: G 92 PHE cc_start: 0.7590 (m-80) cc_final: 0.7301 (m-80) REVERT: E 32 TYR cc_start: 0.7747 (m-80) cc_final: 0.7425 (m-80) REVERT: E 34 MET cc_start: 0.6869 (ppp) cc_final: 0.6585 (pmm) outliers start: 108 outliers final: 53 residues processed: 732 average time/residue: 0.5872 time to fit residues: 517.7864 Evaluate side-chains 719 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 657 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 332 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 490 PHE 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 875 SER 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 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 286 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 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 780 GLU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain 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 314 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 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 719 THR Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 235 optimal weight: 0.0980 chunk 181 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 186 optimal weight: 0.5980 chunk 356 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 955 ASN A1010 GLN L 27 GLN L 93 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B1101 HIS C 764 ASN C1010 GLN E 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.206099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184621 restraints weight = 58891.130| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 3.83 r_work: 0.4097 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31419 Z= 0.117 Angle : 0.633 13.509 42840 Z= 0.309 Chirality : 0.046 0.403 4920 Planarity : 0.004 0.057 5448 Dihedral : 4.720 27.879 4130 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.10 % Allowed : 16.56 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3780 helix: 0.96 (0.21), residues: 654 sheet: -0.44 (0.17), residues: 903 loop : -1.61 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.017 0.001 TYR C 453 PHE 0.030 0.001 PHE B 329 TRP 0.010 0.001 TRP E 36 HIS 0.004 0.001 HIS F 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31317) covalent geometry : angle 0.62162 / 0.31 (42591) SS BOND : bond 0.00321 / 0.21 ( 48) SS BOND : angle 1.10647 / 0.74 ( 96) hydrogen bonds : bond 0.03681 / 2.42 ( 871) hydrogen bonds : angle 5.74560 / 3.96 ( 2505) Misc. bond : bond 0.00044 / 0.02 ( 3) link_BETA1-4 : bond 0.00389 / 0.25 ( 12) link_BETA1-4 : angle 1.35828 / 0.96 ( 36) link_NAG-ASN : bond 0.00525 / 0.33 ( 39) link_NAG-ASN : angle 2.06170 / 1.38 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 673 time to evaluate : 1.144 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: A 34 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: A 52 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7338 (tp-100) REVERT: A 153 MET cc_start: 0.4051 (mpp) cc_final: 0.3654 (mpp) REVERT: A 200 TYR cc_start: 0.5585 (m-10) cc_final: 0.5372 (m-10) REVERT: A 319 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7387 (ptt180) REVERT: A 429 PHE cc_start: 0.5990 (t80) cc_final: 0.5629 (t80) REVERT: A 454 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7936 (mmt90) REVERT: A 541 PHE cc_start: 0.6889 (p90) cc_final: 0.6613 (p90) REVERT: A 572 THR cc_start: 0.8309 (t) cc_final: 0.8004 (p) REVERT: A 588 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 651 ILE cc_start: 0.8749 (mm) cc_final: 0.8470 (mp) REVERT: A 673 SER cc_start: 0.8224 (t) cc_final: 0.7847 (p) REVERT: A 725 GLU cc_start: 0.7951 (tt0) cc_final: 0.7637 (tt0) REVERT: A 736 VAL cc_start: 0.8113 (t) cc_final: 0.7812 (m) REVERT: A 790 LYS cc_start: 0.7498 (mmpt) cc_final: 0.7232 (mmpt) REVERT: A 811 LYS cc_start: 0.7005 (mmpt) cc_final: 0.6523 (mtpt) REVERT: A 933 LYS cc_start: 0.7998 (mttt) cc_final: 0.7604 (mtmm) REVERT: A 949 GLN cc_start: 0.7554 (tp40) cc_final: 0.7294 (tp40) REVERT: A 1019 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7692 (ttm110) REVERT: A 1038 LYS cc_start: 0.8092 (tppt) cc_final: 0.7796 (mmpt) REVERT: A 1045 LYS cc_start: 0.8318 (mttt) cc_final: 0.7967 (mttt) REVERT: A 1072 GLU cc_start: 0.7976 (pm20) cc_final: 0.7521 (pm20) REVERT: A 1086 LYS cc_start: 0.6944 (mtmm) cc_final: 0.6301 (mtmm) REVERT: A 1101 HIS cc_start: 0.8211 (m-70) cc_final: 0.7985 (m-70) REVERT: L 81 GLU cc_start: 0.7405 (mp0) cc_final: 0.7119 (mp0) REVERT: B 49 HIS cc_start: 0.8174 (t-90) cc_final: 0.7782 (t70) REVERT: B 53 ASP cc_start: 0.6713 (t0) cc_final: 0.6292 (t0) REVERT: B 54 LEU cc_start: 0.7904 (mm) cc_final: 0.7684 (mm) REVERT: B 61 ASN cc_start: 0.6774 (p0) cc_final: 0.6559 (p0) REVERT: B 153 MET cc_start: 0.5074 (mpp) cc_final: 0.4797 (mpp) REVERT: B 200 TYR cc_start: 0.5645 (m-10) cc_final: 0.5286 (m-10) REVERT: B 206 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7174 (ttmm) REVERT: B 319 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7569 (ptt180) REVERT: B 340 GLU cc_start: 0.7317 (mp0) cc_final: 0.6861 (mp0) REVERT: B 374 PHE cc_start: 0.7427 (m-80) cc_final: 0.7158 (m-80) REVERT: B 508 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.6942 (m-10) REVERT: B 511 VAL cc_start: 0.8733 (t) cc_final: 0.8490 (p) REVERT: B 586 ASP cc_start: 0.7558 (m-30) cc_final: 0.7117 (m-30) REVERT: B 675 GLN cc_start: 0.7753 (mt0) cc_final: 0.7496 (mt0) REVERT: B 725 GLU cc_start: 0.7811 (tt0) cc_final: 0.7471 (tt0) REVERT: B 772 VAL cc_start: 0.8528 (p) cc_final: 0.8293 (t) REVERT: B 780 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: B 859 THR cc_start: 0.8130 (t) cc_final: 0.7866 (p) REVERT: B 933 LYS cc_start: 0.8030 (mttt) cc_final: 0.7289 (mmtm) REVERT: B 947 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7547 (mtpp) REVERT: B 950 ASP cc_start: 0.7609 (m-30) cc_final: 0.7176 (m-30) REVERT: B 1038 LYS cc_start: 0.7974 (tppt) cc_final: 0.7636 (tppt) REVERT: F 71 PHE cc_start: 0.6845 (t80) cc_final: 0.6300 (t80) REVERT: D 34 MET cc_start: 0.6410 (ppp) cc_final: 0.5709 (ppp) REVERT: D 36 TRP cc_start: 0.5672 (m-90) cc_final: 0.5088 (m-10) REVERT: C 53 ASP cc_start: 0.6905 (t0) cc_final: 0.6638 (t70) REVERT: C 81 ASN cc_start: 0.7825 (p0) cc_final: 0.7302 (m-40) REVERT: C 129 LYS cc_start: 0.7643 (mppt) cc_final: 0.7415 (mmmt) REVERT: C 200 TYR cc_start: 0.5287 (m-10) cc_final: 0.4966 (m-10) REVERT: C 224 GLU cc_start: 0.6815 (mp0) cc_final: 0.6603 (mp0) REVERT: C 237 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6964 (ttm-80) REVERT: C 314 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7931 (tp40) REVERT: C 340 GLU cc_start: 0.7240 (mp0) cc_final: 0.6854 (mp0) REVERT: C 374 PHE cc_start: 0.7355 (m-80) cc_final: 0.6864 (m-80) REVERT: C 392 PHE cc_start: 0.7146 (m-80) cc_final: 0.6923 (m-80) REVERT: C 402 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.6924 (mp) REVERT: C 425 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (mm) REVERT: C 429 PHE cc_start: 0.6579 (t80) cc_final: 0.6054 (t80) REVERT: C 436 TRP cc_start: 0.6225 (p90) cc_final: 0.5935 (p90) REVERT: C 541 PHE cc_start: 0.6893 (p90) cc_final: 0.6482 (p90) REVERT: C 568 ASP cc_start: 0.6419 (p0) cc_final: 0.6008 (p0) REVERT: C 572 THR cc_start: 0.8330 (m) cc_final: 0.7148 (p) REVERT: C 574 ASP cc_start: 0.7622 (t70) cc_final: 0.7389 (m-30) REVERT: C 705 VAL cc_start: 0.6512 (OUTLIER) cc_final: 0.6299 (p) REVERT: C 725 GLU cc_start: 0.7883 (tt0) cc_final: 0.7656 (tt0) REVERT: C 750 SER cc_start: 0.7701 (t) cc_final: 0.7363 (p) REVERT: C 773 GLU cc_start: 0.7568 (tt0) cc_final: 0.7367 (tt0) REVERT: C 776 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7715 (tmmm) REVERT: C 790 LYS cc_start: 0.7841 (mtmm) cc_final: 0.7237 (mmpt) REVERT: C 858 LEU cc_start: 0.8281 (mm) cc_final: 0.8017 (mp) REVERT: C 883 THR cc_start: 0.8231 (m) cc_final: 0.7781 (p) REVERT: C 933 LYS cc_start: 0.8073 (mttt) cc_final: 0.7407 (mptt) REVERT: C 947 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7710 (mtpp) REVERT: C 964 LYS cc_start: 0.8444 (mttt) cc_final: 0.8070 (mttt) REVERT: C 1019 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7377 (ttp80) REVERT: C 1038 LYS cc_start: 0.7788 (tppt) cc_final: 0.7337 (mmmm) REVERT: C 1045 LYS cc_start: 0.8055 (mttt) cc_final: 0.7756 (tttt) REVERT: C 1055 SER cc_start: 0.8377 (t) cc_final: 0.8018 (m) REVERT: C 1072 GLU cc_start: 0.7618 (pm20) cc_final: 0.7332 (pm20) REVERT: C 1101 HIS cc_start: 0.8317 (m-70) cc_final: 0.7887 (m-70) REVERT: G 71 PHE cc_start: 0.6748 (t80) cc_final: 0.6202 (t80) REVERT: G 92 PHE cc_start: 0.7148 (m-80) cc_final: 0.6662 (m-80) REVERT: E 32 TYR cc_start: 0.7764 (m-80) cc_final: 0.7447 (m-80) REVERT: E 46 GLU cc_start: 0.7176 (pm20) cc_final: 0.6921 (mp0) REVERT: E 102 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.8155 (m-10) outliers start: 103 outliers final: 54 residues processed: 709 average time/residue: 0.6161 time to fit residues: 522.7963 Evaluate side-chains 705 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 640 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 298 GLU 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 740 MET Chi-restraints excluded: chain A residue 864 LEU 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 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 47 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 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 780 GLU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 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 1130 ILE Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 218 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 371 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 804 GLN A 907 ASN A 955 ASN A1010 GLN A1101 HIS L 27 GLN H 39 GLN H 112 GLN B 658 ASN B 957 GLN B1101 HIS C 207 HIS C 764 ASN C 787 GLN C 804 GLN C1010 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.195922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173913 restraints weight = 57508.705| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 3.67 r_work: 0.4023 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 31419 Z= 0.316 Angle : 0.791 12.621 42840 Z= 0.398 Chirality : 0.052 0.366 4920 Planarity : 0.005 0.065 5448 Dihedral : 5.450 31.281 4130 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.64 % Allowed : 17.52 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3780 helix: 0.41 (0.20), residues: 684 sheet: -0.76 (0.17), residues: 897 loop : -1.83 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 346 TYR 0.034 0.002 TYR C 204 PHE 0.041 0.003 PHE L 92 TRP 0.026 0.003 TRP L 35 HIS 0.009 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.32 (31317) covalent geometry : angle 0.77522 / 0.39 (42591) SS BOND : bond 0.00475 / 0.32 ( 48) SS BOND : angle 1.90544 / 1.28 ( 96) hydrogen bonds : bond 0.04799 / 3.14 ( 871) hydrogen bonds : angle 5.98941 / 4.18 ( 2505) Misc. bond : bond 0.00504 / 0.24 ( 3) link_BETA1-4 : bond 0.00384 / 0.20 ( 12) link_BETA1-4 : angle 1.48160 / 1.12 ( 36) link_NAG-ASN : bond 0.01013 / 0.63 ( 39) link_NAG-ASN : angle 2.59186 / 1.77 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 683 time to evaluate : 1.416 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: 0.7510 (ttm-80) cc_final: 0.7277 (ttm110) REVERT: A 46 SER cc_start: 0.8082 (m) cc_final: 0.7524 (p) REVERT: A 153 MET cc_start: 0.4323 (mpp) cc_final: 0.3917 (mpp) REVERT: A 206 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7365 (ttmm) REVERT: A 274 THR cc_start: 0.8671 (t) cc_final: 0.8440 (t) REVERT: A 319 ARG cc_start: 0.7875 (ptp90) cc_final: 0.7442 (ptt180) REVERT: A 429 PHE cc_start: 0.6249 (t80) cc_final: 0.5929 (t80) REVERT: A 454 ARG cc_start: 0.8378 (mmt90) cc_final: 0.7717 (mmt90) REVERT: A 465 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5730 (pt0) REVERT: A 541 PHE cc_start: 0.7042 (p90) cc_final: 0.6373 (p90) REVERT: A 588 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 651 ILE cc_start: 0.8762 (mm) cc_final: 0.8500 (mp) REVERT: A 673 SER cc_start: 0.8349 (t) cc_final: 0.8007 (p) REVERT: A 705 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6782 (p) REVERT: A 736 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7900 (m) REVERT: A 795 LYS cc_start: 0.8456 (mptm) cc_final: 0.8168 (mptp) REVERT: A 811 LYS cc_start: 0.7296 (mmpt) cc_final: 0.6716 (mtpp) REVERT: A 933 LYS cc_start: 0.7903 (mttt) cc_final: 0.7480 (mtmm) REVERT: A 949 GLN cc_start: 0.7686 (tp40) cc_final: 0.7486 (tp40) REVERT: A 1038 LYS cc_start: 0.8161 (tppt) cc_final: 0.7888 (mmpt) REVERT: A 1045 LYS cc_start: 0.8346 (mttt) cc_final: 0.8005 (mttt) REVERT: A 1072 GLU cc_start: 0.8048 (pm20) cc_final: 0.7616 (pm20) REVERT: A 1107 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7600 (mtt-85) REVERT: H 39 GLN cc_start: 0.7478 (tp-100) cc_final: 0.6818 (tm-30) REVERT: B 49 HIS cc_start: 0.8224 (t-90) cc_final: 0.7757 (t70) REVERT: B 53 ASP cc_start: 0.6899 (t0) cc_final: 0.6473 (t0) REVERT: B 54 LEU cc_start: 0.7905 (mm) cc_final: 0.7415 (mm) REVERT: B 153 MET cc_start: 0.5358 (mpp) cc_final: 0.5016 (mpp) REVERT: B 206 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7267 (ttmm) REVERT: B 319 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7794 (ptt180) REVERT: B 340 GLU cc_start: 0.7498 (mp0) cc_final: 0.7152 (mp0) REVERT: B 421 TYR cc_start: 0.7045 (m-80) cc_final: 0.6636 (m-10) REVERT: B 427 ASP cc_start: 0.8092 (p0) cc_final: 0.7877 (p0) REVERT: B 508 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6878 (m-10) REVERT: B 511 VAL cc_start: 0.8735 (t) cc_final: 0.8522 (p) REVERT: B 586 ASP cc_start: 0.7555 (m-30) cc_final: 0.7078 (m-30) REVERT: B 675 GLN cc_start: 0.7718 (mt0) cc_final: 0.7484 (mt0) REVERT: B 725 GLU cc_start: 0.7830 (tt0) cc_final: 0.7508 (tt0) REVERT: B 772 VAL cc_start: 0.8538 (p) cc_final: 0.8302 (t) REVERT: B 859 THR cc_start: 0.8200 (t) cc_final: 0.7915 (p) REVERT: B 933 LYS cc_start: 0.8087 (mttt) cc_final: 0.7340 (mmtm) REVERT: B 947 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7506 (mtpp) REVERT: B 949 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7440 (tp40) REVERT: B 950 ASP cc_start: 0.7495 (m-30) cc_final: 0.7019 (m-30) REVERT: B 1038 LYS cc_start: 0.7970 (tppt) cc_final: 0.7644 (tppt) REVERT: F 71 PHE cc_start: 0.7058 (t80) cc_final: 0.6618 (t80) REVERT: C 53 ASP cc_start: 0.6980 (t0) cc_final: 0.6697 (t0) REVERT: C 206 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7326 (ttmm) REVERT: C 237 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7054 (ttm-80) REVERT: C 314 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: C 374 PHE cc_start: 0.7556 (m-80) cc_final: 0.7213 (m-80) REVERT: C 436 TRP cc_start: 0.6335 (p90) cc_final: 0.6055 (p90) REVERT: C 541 PHE cc_start: 0.7089 (p90) cc_final: 0.6820 (p90) REVERT: C 651 ILE cc_start: 0.8679 (mm) cc_final: 0.8432 (mt) REVERT: C 705 VAL cc_start: 0.7124 (OUTLIER) cc_final: 0.6883 (p) REVERT: C 725 GLU cc_start: 0.7866 (tt0) cc_final: 0.7620 (tt0) REVERT: C 750 SER cc_start: 0.7973 (t) cc_final: 0.7688 (p) REVERT: C 773 GLU cc_start: 0.7438 (tt0) cc_final: 0.7152 (tt0) REVERT: C 776 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: C 815 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (mtm-85) REVERT: C 883 THR cc_start: 0.8250 (m) cc_final: 0.7835 (p) REVERT: C 931 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.6955 (mp) REVERT: C 933 LYS cc_start: 0.7987 (mttt) cc_final: 0.7275 (mptt) REVERT: C 947 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7686 (mtpp) REVERT: C 964 LYS cc_start: 0.8450 (mttt) cc_final: 0.8137 (mttt) REVERT: C 1019 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.7369 (ttp80) REVERT: C 1030 SER cc_start: 0.8062 (m) cc_final: 0.7833 (p) REVERT: C 1038 LYS cc_start: 0.7948 (tppt) cc_final: 0.7553 (mmpt) REVERT: C 1045 LYS cc_start: 0.7948 (mttt) cc_final: 0.7733 (mttt) REVERT: C 1055 SER cc_start: 0.8451 (t) cc_final: 0.8161 (m) REVERT: C 1072 GLU cc_start: 0.7778 (pm20) cc_final: 0.7457 (pm20) REVERT: C 1101 HIS cc_start: 0.8293 (m-70) cc_final: 0.7785 (m-70) REVERT: C 1138 TYR cc_start: 0.7970 (t80) cc_final: 0.7767 (t80) REVERT: G 71 PHE cc_start: 0.6643 (t80) cc_final: 0.6204 (t80) REVERT: G 92 PHE cc_start: 0.7628 (m-80) cc_final: 0.7040 (m-80) REVERT: E 31 SER cc_start: 0.8196 (p) cc_final: 0.7857 (p) REVERT: E 32 TYR cc_start: 0.7812 (m-80) cc_final: 0.7356 (m-80) REVERT: E 46 GLU cc_start: 0.7159 (pm20) cc_final: 0.6958 (mp0) REVERT: E 102 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8073 (m-10) outliers start: 154 outliers final: 79 residues processed: 751 average time/residue: 0.5887 time to fit residues: 533.6813 Evaluate side-chains 757 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 662 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 515 PHE 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 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 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 A residue 1107 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 94 TRP Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 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 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 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 957 GLN Chi-restraints excluded: chain B residue 973 ILE 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 33 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 452 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 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 815 ARG Chi-restraints excluded: chain C residue 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 C residue 1141 LEU Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 TRP Chi-restraints excluded: chain E residue 28 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 323 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 129 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 352 optimal weight: 0.7980 chunk 304 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 606 ASN A 907 ASN A 955 ASN A1010 GLN A1101 HIS L 27 GLN B 61 ASN B 564 GLN B 957 GLN B1101 HIS C 764 ASN C 787 GLN C 992 GLN G 93 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.201239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179737 restraints weight = 58301.920| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.65 r_work: 0.4063 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31419 Z= 0.135 Angle : 0.677 11.985 42840 Z= 0.334 Chirality : 0.047 0.381 4920 Planarity : 0.005 0.057 5448 Dihedral : 5.028 29.174 4130 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.55 % Allowed : 19.60 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3780 helix: 0.89 (0.21), residues: 684 sheet: -0.54 (0.18), residues: 873 loop : -1.74 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 346 TYR 0.023 0.001 TYR B 453 PHE 0.033 0.002 PHE G 49 TRP 0.014 0.002 TRP E 110 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (31317) covalent geometry : angle 0.66464 / 0.33 (42591) SS BOND : bond 0.00468 / 0.32 ( 48) SS BOND : angle 1.62908 / 1.08 ( 96) hydrogen bonds : bond 0.03649 / 2.41 ( 871) hydrogen bonds : angle 5.66975 / 3.93 ( 2505) Misc. bond : bond 0.00418 / 0.20 ( 3) link_BETA1-4 : bond 0.00303 / 0.18 ( 12) link_BETA1-4 : angle 1.04937 / 0.74 ( 36) link_NAG-ASN : bond 0.00463 / 0.27 ( 39) link_NAG-ASN : angle 2.08274 / 1.42 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 666 time to evaluate : 1.383 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: 0.7494 (ttm-80) cc_final: 0.7290 (ttm110) REVERT: A 46 SER cc_start: 0.8083 (m) cc_final: 0.7551 (p) REVERT: A 52 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7394 (tp-100) REVERT: A 140 PHE cc_start: 0.7257 (p90) cc_final: 0.6562 (p90) REVERT: A 153 MET cc_start: 0.4302 (mpp) cc_final: 0.3872 (mpp) REVERT: A 177 MET cc_start: 0.0126 (mtt) cc_final: -0.0787 (mtt) REVERT: A 200 TYR cc_start: 0.5477 (m-10) cc_final: 0.5209 (m-10) REVERT: A 274 THR cc_start: 0.8666 (t) cc_final: 0.8232 (t) REVERT: A 319 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7379 (ptt180) REVERT: A 340 GLU cc_start: 0.7420 (mp0) cc_final: 0.7180 (mp0) REVERT: A 429 PHE cc_start: 0.6359 (t80) cc_final: 0.5972 (t80) REVERT: A 541 PHE cc_start: 0.7039 (p90) cc_final: 0.6335 (p90) REVERT: A 588 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8366 (p) REVERT: A 651 ILE cc_start: 0.8763 (mm) cc_final: 0.8480 (mp) REVERT: A 673 SER cc_start: 0.8189 (t) cc_final: 0.7838 (p) REVERT: A 705 VAL cc_start: 0.6981 (OUTLIER) cc_final: 0.6769 (p) REVERT: A 725 GLU cc_start: 0.7727 (tt0) cc_final: 0.7440 (tt0) REVERT: A 736 VAL cc_start: 0.8162 (t) cc_final: 0.7874 (m) REVERT: A 790 LYS cc_start: 0.7785 (mtpm) cc_final: 0.7133 (mmpt) REVERT: A 795 LYS cc_start: 0.8442 (mptm) cc_final: 0.8164 (mptp) REVERT: A 811 LYS cc_start: 0.7214 (mmpt) cc_final: 0.6652 (mtpt) REVERT: A 864 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (tt) REVERT: A 933 LYS cc_start: 0.7996 (mttt) cc_final: 0.7605 (mtmm) REVERT: A 1019 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7618 (ttm110) REVERT: A 1038 LYS cc_start: 0.8145 (tppt) cc_final: 0.7892 (mmpt) REVERT: A 1045 LYS cc_start: 0.8271 (mttt) cc_final: 0.7935 (mttt) REVERT: A 1072 GLU cc_start: 0.8032 (pm20) cc_final: 0.7635 (pm20) REVERT: A 1111 GLU cc_start: 0.7576 (tt0) cc_final: 0.7272 (tt0) REVERT: A 1141 LEU cc_start: 0.7866 (tt) cc_final: 0.7620 (tt) REVERT: H 39 GLN cc_start: 0.7207 (tp-100) cc_final: 0.6370 (pp30) REVERT: B 49 HIS cc_start: 0.8216 (t-90) cc_final: 0.7756 (t70) REVERT: B 53 ASP cc_start: 0.6860 (t0) cc_final: 0.6430 (t0) REVERT: B 54 LEU cc_start: 0.7679 (mm) cc_final: 0.7066 (mm) REVERT: B 153 MET cc_start: 0.5443 (mpp) cc_final: 0.5062 (mpp) REVERT: B 200 TYR cc_start: 0.5472 (m-10) cc_final: 0.5228 (m-10) REVERT: B 206 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7260 (ttmm) REVERT: B 319 ARG cc_start: 0.8127 (ptp90) cc_final: 0.7802 (ptt180) REVERT: B 340 GLU cc_start: 0.7520 (mp0) cc_final: 0.7020 (mp0) REVERT: B 421 TYR cc_start: 0.6778 (m-80) cc_final: 0.6425 (m-10) REVERT: B 490 PHE cc_start: 0.8118 (t80) cc_final: 0.7730 (t80) REVERT: B 508 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: B 511 VAL cc_start: 0.8769 (t) cc_final: 0.8510 (p) REVERT: B 586 ASP cc_start: 0.7539 (m-30) cc_final: 0.7015 (m-30) REVERT: B 675 GLN cc_start: 0.7716 (mt0) cc_final: 0.7475 (mt0) REVERT: B 725 GLU cc_start: 0.7792 (tt0) cc_final: 0.7535 (tt0) REVERT: B 772 VAL cc_start: 0.8564 (p) cc_final: 0.8312 (t) REVERT: B 859 THR cc_start: 0.8132 (t) cc_final: 0.7868 (p) REVERT: B 933 LYS cc_start: 0.8082 (mttt) cc_final: 0.7343 (mmtm) REVERT: B 947 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7548 (mtpp) REVERT: B 949 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7489 (tp40) REVERT: B 950 ASP cc_start: 0.7604 (m-30) cc_final: 0.7043 (m-30) REVERT: B 994 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7413 (t70) REVERT: B 1038 LYS cc_start: 0.7932 (tppt) cc_final: 0.7580 (tppt) REVERT: F 71 PHE cc_start: 0.6956 (t80) cc_final: 0.6494 (t80) REVERT: C 53 ASP cc_start: 0.6898 (t0) cc_final: 0.6679 (t0) REVERT: C 83 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.6998 (p) REVERT: C 200 TYR cc_start: 0.5512 (m-10) cc_final: 0.5250 (m-10) REVERT: C 237 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6915 (ttm-80) REVERT: C 314 GLN cc_start: 0.8192 (tt0) cc_final: 0.7944 (tp40) REVERT: C 319 ARG cc_start: 0.8083 (ptp90) cc_final: 0.7698 (ptt180) REVERT: C 340 GLU cc_start: 0.7273 (mp0) cc_final: 0.6844 (mp0) REVERT: C 374 PHE cc_start: 0.7397 (m-80) cc_final: 0.6981 (m-80) REVERT: C 436 TRP cc_start: 0.6095 (p90) cc_final: 0.5871 (p90) REVERT: C 541 PHE cc_start: 0.7072 (p90) cc_final: 0.6754 (p90) REVERT: C 574 ASP cc_start: 0.7611 (t70) cc_final: 0.7108 (t70) REVERT: C 651 ILE cc_start: 0.8663 (mm) cc_final: 0.8397 (mt) REVERT: C 705 VAL cc_start: 0.7010 (OUTLIER) cc_final: 0.6750 (p) REVERT: C 725 GLU cc_start: 0.7859 (tt0) cc_final: 0.7645 (tt0) REVERT: C 750 SER cc_start: 0.7941 (t) cc_final: 0.7664 (p) REVERT: C 776 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7856 (ttmm) REVERT: C 790 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7210 (mmpt) REVERT: C 883 THR cc_start: 0.8251 (m) cc_final: 0.7892 (p) REVERT: C 933 LYS cc_start: 0.8116 (mttt) cc_final: 0.7432 (mptt) REVERT: C 947 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7700 (mtpp) REVERT: C 964 LYS cc_start: 0.8382 (mttt) cc_final: 0.8113 (mttt) REVERT: C 994 ASP cc_start: 0.7614 (t70) cc_final: 0.7330 (m-30) REVERT: C 1030 SER cc_start: 0.7965 (m) cc_final: 0.7678 (p) REVERT: C 1038 LYS cc_start: 0.7894 (tppt) cc_final: 0.7467 (mmpt) REVERT: C 1045 LYS cc_start: 0.7978 (mttt) cc_final: 0.7766 (mttt) REVERT: C 1055 SER cc_start: 0.8378 (t) cc_final: 0.8057 (m) REVERT: C 1073 LYS cc_start: 0.7495 (pttp) cc_final: 0.7222 (ptmm) REVERT: C 1101 HIS cc_start: 0.8345 (m-70) cc_final: 0.7929 (m-70) REVERT: C 1138 TYR cc_start: 0.8001 (t80) cc_final: 0.7751 (t80) REVERT: G 71 PHE cc_start: 0.6797 (t80) cc_final: 0.6415 (t80) REVERT: G 92 PHE cc_start: 0.7333 (m-80) cc_final: 0.6803 (m-80) REVERT: E 32 TYR cc_start: 0.7725 (m-80) cc_final: 0.7452 (m-80) REVERT: E 46 GLU cc_start: 0.7140 (pm20) cc_final: 0.6889 (mp0) REVERT: E 102 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.8086 (m-80) outliers start: 118 outliers final: 65 residues processed: 719 average time/residue: 0.5966 time to fit residues: 516.6516 Evaluate side-chains 720 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 644 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 326 ILE 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 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 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 902 MET 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 5 LEU Chi-restraints excluded: chain H residue 20 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 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 957 GLN 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 60 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 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 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 163 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 901 GLN B 957 GLN B1101 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN E 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.198843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.177122 restraints weight = 58078.296| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 3.69 r_work: 0.4038 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31419 Z= 0.188 Angle : 0.715 21.163 42840 Z= 0.352 Chirality : 0.049 0.566 4920 Planarity : 0.005 0.057 5448 Dihedral : 5.160 29.439 4130 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.67 % Allowed : 20.20 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 3780 helix: 0.92 (0.21), residues: 678 sheet: -0.61 (0.17), residues: 879 loop : -1.79 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.025 0.002 TYR E 59 PHE 0.028 0.002 PHE G 49 TRP 0.020 0.002 TRP H 47 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (31317) covalent geometry : angle 0.69299 / 0.35 (42591) SS BOND : bond 0.00480 / 0.32 ( 48) SS BOND : angle 1.68247 / 1.14 ( 96) hydrogen bonds : bond 0.03810 / 2.51 ( 871) hydrogen bonds : angle 5.61378 / 3.89 ( 2505) Misc. bond : bond 0.00734 / 0.35 ( 3) link_BETA1-4 : bond 0.00342 / 0.20 ( 12) link_BETA1-4 : angle 1.01157 / 0.71 ( 36) link_NAG-ASN : bond 0.00711 / 0.49 ( 39) link_NAG-ASN : angle 3.08692 / 1.75 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 651 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 SER cc_start: 0.8095 (m) cc_final: 0.7547 (p) REVERT: A 140 PHE cc_start: 0.7277 (p90) cc_final: 0.6558 (p90) REVERT: A 153 MET cc_start: 0.4359 (mpp) cc_final: 0.3936 (mpp) REVERT: A 168 PHE cc_start: 0.5246 (t80) cc_final: 0.4813 (t80) REVERT: A 177 MET cc_start: 0.0238 (mtt) cc_final: -0.0662 (mtt) REVERT: A 274 THR cc_start: 0.8710 (t) cc_final: 0.8295 (t) REVERT: A 282 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6622 (m110) REVERT: A 319 ARG cc_start: 0.7869 (ptp90) cc_final: 0.7394 (ptt180) REVERT: A 340 GLU cc_start: 0.7563 (mp0) cc_final: 0.7272 (mp0) REVERT: A 429 PHE cc_start: 0.6422 (t80) cc_final: 0.6151 (t80) REVERT: A 454 ARG cc_start: 0.8336 (mmt90) cc_final: 0.8053 (mmt90) REVERT: A 541 PHE cc_start: 0.7042 (p90) cc_final: 0.6442 (p90) REVERT: A 588 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 651 ILE cc_start: 0.8771 (mm) cc_final: 0.8495 (mp) REVERT: A 673 SER cc_start: 0.8272 (t) cc_final: 0.7910 (p) REVERT: A 705 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6822 (p) REVERT: A 725 GLU cc_start: 0.7744 (tt0) cc_final: 0.7444 (tt0) REVERT: A 736 VAL cc_start: 0.8217 (t) cc_final: 0.7945 (m) REVERT: A 790 LYS cc_start: 0.7786 (mtpm) cc_final: 0.7119 (mmpt) REVERT: A 795 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (mptp) REVERT: A 811 LYS cc_start: 0.7241 (mmpt) cc_final: 0.6713 (mtpt) REVERT: A 864 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 933 LYS cc_start: 0.7933 (mttt) cc_final: 0.7564 (mtmm) REVERT: A 1019 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7612 (ttm110) REVERT: A 1029 MET cc_start: 0.8283 (tpp) cc_final: 0.8058 (ttp) REVERT: A 1038 LYS cc_start: 0.8173 (tppt) cc_final: 0.7931 (mmpt) REVERT: A 1045 LYS cc_start: 0.8247 (mttt) cc_final: 0.7896 (mttt) REVERT: A 1072 GLU cc_start: 0.8080 (pm20) cc_final: 0.7672 (pm20) REVERT: A 1141 LEU cc_start: 0.7817 (tt) cc_final: 0.7568 (tt) REVERT: H 39 GLN cc_start: 0.7288 (tp-100) cc_final: 0.6451 (pp30) REVERT: B 49 HIS cc_start: 0.8220 (t-90) cc_final: 0.7796 (t70) REVERT: B 53 ASP cc_start: 0.6891 (t0) cc_final: 0.6466 (t0) REVERT: B 54 LEU cc_start: 0.7667 (mm) cc_final: 0.7040 (mm) REVERT: B 153 MET cc_start: 0.5500 (mpp) cc_final: 0.5092 (mpp) REVERT: B 206 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7310 (ttmm) REVERT: B 319 ARG cc_start: 0.8144 (ptp90) cc_final: 0.7835 (ptt180) REVERT: B 340 GLU cc_start: 0.7577 (mp0) cc_final: 0.7107 (mp0) REVERT: B 421 TYR cc_start: 0.6790 (m-80) cc_final: 0.6392 (m-10) REVERT: B 490 PHE cc_start: 0.8108 (t80) cc_final: 0.7685 (t80) REVERT: B 508 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6862 (m-10) REVERT: B 511 VAL cc_start: 0.8772 (t) cc_final: 0.8527 (p) REVERT: B 586 ASP cc_start: 0.7580 (m-30) cc_final: 0.7051 (m-30) REVERT: B 606 ASN cc_start: 0.8490 (m-40) cc_final: 0.8266 (m-40) REVERT: B 675 GLN cc_start: 0.7727 (mt0) cc_final: 0.7483 (mt0) REVERT: B 725 GLU cc_start: 0.7819 (tt0) cc_final: 0.7552 (tt0) REVERT: B 772 VAL cc_start: 0.8572 (p) cc_final: 0.8318 (t) REVERT: B 859 THR cc_start: 0.8155 (t) cc_final: 0.7877 (p) REVERT: B 933 LYS cc_start: 0.8077 (mttt) cc_final: 0.7323 (mmtm) REVERT: B 935 GLN cc_start: 0.8022 (mt0) cc_final: 0.7691 (mt0) REVERT: B 947 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7536 (mtpp) REVERT: B 949 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7449 (mm-40) REVERT: B 950 ASP cc_start: 0.7578 (m-30) cc_final: 0.7023 (m-30) REVERT: B 994 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7435 (t70) REVERT: F 71 PHE cc_start: 0.7047 (t80) cc_final: 0.6570 (t80) REVERT: C 53 ASP cc_start: 0.6962 (t0) cc_final: 0.6680 (t0) REVERT: C 83 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7056 (p) REVERT: C 200 TYR cc_start: 0.5662 (m-10) cc_final: 0.5380 (m-10) REVERT: C 206 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7263 (ttmm) REVERT: C 237 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6901 (ttm-80) REVERT: C 314 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7962 (tp40) REVERT: C 319 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7795 (ptt180) REVERT: C 329 PHE cc_start: 0.6392 (m-80) cc_final: 0.6032 (m-80) REVERT: C 340 GLU cc_start: 0.7427 (mp0) cc_final: 0.6982 (mp0) REVERT: C 421 TYR cc_start: 0.6835 (m-80) cc_final: 0.6597 (m-10) REVERT: C 541 PHE cc_start: 0.7091 (p90) cc_final: 0.6805 (p90) REVERT: C 574 ASP cc_start: 0.7581 (t70) cc_final: 0.7082 (t70) REVERT: C 651 ILE cc_start: 0.8713 (mm) cc_final: 0.8467 (mt) REVERT: C 705 VAL cc_start: 0.7093 (OUTLIER) cc_final: 0.6831 (p) REVERT: C 725 GLU cc_start: 0.7868 (tt0) cc_final: 0.7651 (tt0) REVERT: C 750 SER cc_start: 0.7947 (t) cc_final: 0.7638 (p) REVERT: C 776 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7873 (ttmm) REVERT: C 790 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7210 (mmpt) REVERT: C 883 THR cc_start: 0.8277 (m) cc_final: 0.7858 (p) REVERT: C 933 LYS cc_start: 0.8090 (mttt) cc_final: 0.7397 (mptt) REVERT: C 947 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7748 (mtpp) REVERT: C 964 LYS cc_start: 0.8389 (mttt) cc_final: 0.8126 (mttt) REVERT: C 994 ASP cc_start: 0.7644 (t70) cc_final: 0.7365 (m-30) REVERT: C 1019 ARG cc_start: 0.7698 (ttp-170) cc_final: 0.7434 (ttp80) REVERT: C 1030 SER cc_start: 0.7977 (m) cc_final: 0.7707 (p) REVERT: C 1038 LYS cc_start: 0.7937 (tppt) cc_final: 0.7467 (mmpt) REVERT: C 1045 LYS cc_start: 0.7986 (mttt) cc_final: 0.7774 (mttt) REVERT: C 1055 SER cc_start: 0.8386 (t) cc_final: 0.8071 (m) REVERT: C 1101 HIS cc_start: 0.8358 (m-70) cc_final: 0.7888 (m-70) REVERT: C 1138 TYR cc_start: 0.7992 (t80) cc_final: 0.7701 (t80) REVERT: C 1141 LEU cc_start: 0.7926 (tp) cc_final: 0.7664 (tm) REVERT: G 71 PHE cc_start: 0.6728 (t80) cc_final: 0.6272 (t80) REVERT: E 32 TYR cc_start: 0.7697 (m-80) cc_final: 0.7441 (m-80) outliers start: 122 outliers final: 73 residues processed: 712 average time/residue: 0.5659 time to fit residues: 486.8116 Evaluate side-chains 723 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 636 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE 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 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 168 PHE 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 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 69 THR 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 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 76 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 133 optimal weight: 0.0770 chunk 132 optimal weight: 0.0980 chunk 367 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 216 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 422 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 957 GLN B1101 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN C 919 ASN G 93 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.205740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.184124 restraints weight = 57062.735| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 3.85 r_work: 0.4072 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3990 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= 0.123 Angle : 0.681 16.459 42840 Z= 0.333 Chirality : 0.047 0.431 4920 Planarity : 0.004 0.057 5448 Dihedral : 4.952 28.033 4130 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.34 % Allowed : 20.75 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3780 helix: 1.16 (0.21), residues: 675 sheet: -0.59 (0.17), residues: 900 loop : -1.72 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.027 0.001 TYR E 60 PHE 0.025 0.001 PHE B 490 TRP 0.019 0.002 TRP E 110 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (31317) covalent geometry : angle 0.66468 / 0.33 (42591) SS BOND : bond 0.00450 / 0.31 ( 48) SS BOND : angle 1.39381 / 0.95 ( 96) hydrogen bonds : bond 0.03346 / 2.21 ( 871) hydrogen bonds : angle 5.45771 / 3.77 ( 2505) Misc. bond : bond 0.00180 / 0.09 ( 3) link_BETA1-4 : bond 0.00351 / 0.20 ( 12) link_BETA1-4 : angle 0.96567 / 0.68 ( 36) link_NAG-ASN : bond 0.00554 / 0.38 ( 39) link_NAG-ASN : angle 2.62381 / 1.54 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 661 time to evaluate : 0.995 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 46 SER cc_start: 0.8056 (m) cc_final: 0.7523 (p) REVERT: A 52 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7432 (tp-100) REVERT: A 140 PHE cc_start: 0.7263 (p90) cc_final: 0.6534 (p90) REVERT: A 153 MET cc_start: 0.4281 (mpp) cc_final: 0.3871 (mpp) REVERT: A 168 PHE cc_start: 0.5265 (t80) cc_final: 0.4766 (t80) REVERT: A 177 MET cc_start: 0.0178 (mtt) cc_final: -0.0739 (mtt) REVERT: A 200 TYR cc_start: 0.5290 (m-10) cc_final: 0.5041 (m-10) REVERT: A 206 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7252 (ttmm) REVERT: A 282 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6589 (m110) REVERT: A 319 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7407 (ptt180) REVERT: A 340 GLU cc_start: 0.7483 (mp0) cc_final: 0.7242 (mp0) REVERT: A 429 PHE cc_start: 0.6426 (t80) cc_final: 0.6152 (t80) REVERT: A 454 ARG cc_start: 0.8277 (mmt90) cc_final: 0.8005 (mmt90) REVERT: A 541 PHE cc_start: 0.7025 (p90) cc_final: 0.6358 (p90) REVERT: A 651 ILE cc_start: 0.8754 (mm) cc_final: 0.8475 (mp) REVERT: A 673 SER cc_start: 0.8212 (t) cc_final: 0.7833 (p) REVERT: A 705 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6759 (p) REVERT: A 736 VAL cc_start: 0.8205 (t) cc_final: 0.7937 (m) REVERT: A 790 LYS cc_start: 0.7787 (mtpm) cc_final: 0.7149 (mmpt) REVERT: A 795 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8187 (mptp) REVERT: A 811 LYS cc_start: 0.7176 (mmpt) cc_final: 0.6679 (mtpt) REVERT: A 864 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 933 LYS cc_start: 0.7926 (mttt) cc_final: 0.7558 (mtmm) REVERT: A 947 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7355 (mtmt) REVERT: A 1019 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7629 (ttm110) REVERT: A 1045 LYS cc_start: 0.8261 (mttt) cc_final: 0.7930 (mttt) REVERT: A 1072 GLU cc_start: 0.7973 (pm20) cc_final: 0.7643 (pm20) REVERT: A 1107 ARG cc_start: 0.7961 (mpp80) cc_final: 0.7557 (mtt-85) REVERT: A 1141 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7558 (tt) REVERT: H 39 GLN cc_start: 0.7218 (tp-100) cc_final: 0.6412 (pp30) REVERT: H 102 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 49 HIS cc_start: 0.8208 (t-90) cc_final: 0.7778 (t70) REVERT: B 53 ASP cc_start: 0.6845 (t0) cc_final: 0.6578 (t0) REVERT: B 54 LEU cc_start: 0.7627 (mm) cc_final: 0.7017 (mm) REVERT: B 153 MET cc_start: 0.5455 (mpp) cc_final: 0.5079 (mpp) REVERT: B 200 TYR cc_start: 0.5609 (m-10) cc_final: 0.5390 (m-10) REVERT: B 206 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7232 (ttmm) REVERT: B 319 ARG cc_start: 0.8119 (ptp90) cc_final: 0.7765 (ptt180) REVERT: B 340 GLU cc_start: 0.7546 (mp0) cc_final: 0.7015 (mp0) REVERT: B 421 TYR cc_start: 0.6814 (m-80) cc_final: 0.6391 (m-10) REVERT: B 490 PHE cc_start: 0.8085 (t80) cc_final: 0.7683 (t80) REVERT: B 508 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: B 511 VAL cc_start: 0.8805 (t) cc_final: 0.8529 (p) REVERT: B 586 ASP cc_start: 0.7586 (m-30) cc_final: 0.7061 (m-30) REVERT: B 675 GLN cc_start: 0.7674 (mt0) cc_final: 0.7429 (mt0) REVERT: B 725 GLU cc_start: 0.7797 (tt0) cc_final: 0.7525 (tt0) REVERT: B 772 VAL cc_start: 0.8587 (p) cc_final: 0.8333 (t) REVERT: B 859 THR cc_start: 0.8128 (t) cc_final: 0.7855 (p) REVERT: B 933 LYS cc_start: 0.8023 (mttt) cc_final: 0.7244 (mmtm) REVERT: B 935 GLN cc_start: 0.8016 (mt0) cc_final: 0.7724 (mt0) REVERT: B 947 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7515 (mtpp) REVERT: B 949 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7443 (mm-40) REVERT: B 950 ASP cc_start: 0.7578 (m-30) cc_final: 0.7006 (m-30) REVERT: B 957 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: F 71 PHE cc_start: 0.6895 (t80) cc_final: 0.6416 (t80) REVERT: D 62 ASP cc_start: 0.8575 (p0) cc_final: 0.8307 (p0) REVERT: C 53 ASP cc_start: 0.6921 (t0) cc_final: 0.6655 (t0) REVERT: C 83 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7079 (p) REVERT: C 200 TYR cc_start: 0.5580 (m-10) cc_final: 0.5315 (m-10) REVERT: C 206 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7091 (ttmm) REVERT: C 237 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6894 (ttm-80) REVERT: C 267 VAL cc_start: 0.8134 (t) cc_final: 0.7805 (p) REVERT: C 314 GLN cc_start: 0.8173 (tt0) cc_final: 0.7887 (tp40) REVERT: C 319 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7769 (ptt180) REVERT: C 340 GLU cc_start: 0.7336 (mp0) cc_final: 0.6882 (mp0) REVERT: C 421 TYR cc_start: 0.6765 (m-80) cc_final: 0.6461 (m-10) REVERT: C 453 TYR cc_start: 0.7378 (p90) cc_final: 0.6985 (p90) REVERT: C 541 PHE cc_start: 0.7098 (p90) cc_final: 0.6791 (p90) REVERT: C 574 ASP cc_start: 0.7559 (t70) cc_final: 0.7004 (t70) REVERT: C 651 ILE cc_start: 0.8654 (mm) cc_final: 0.8407 (mt) REVERT: C 705 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6696 (p) REVERT: C 725 GLU cc_start: 0.7862 (tt0) cc_final: 0.7642 (tt0) REVERT: C 750 SER cc_start: 0.7845 (t) cc_final: 0.7551 (p) REVERT: C 776 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7716 (tmmm) REVERT: C 790 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7293 (mmpt) REVERT: C 868 GLU cc_start: 0.7261 (mp0) cc_final: 0.7056 (mp0) REVERT: C 883 THR cc_start: 0.8236 (m) cc_final: 0.7825 (p) REVERT: C 933 LYS cc_start: 0.8045 (mttt) cc_final: 0.7370 (mptt) REVERT: C 947 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7670 (mtpp) REVERT: C 964 LYS cc_start: 0.8372 (mttt) cc_final: 0.8105 (mttt) REVERT: C 994 ASP cc_start: 0.7620 (t70) cc_final: 0.7359 (m-30) REVERT: C 1019 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7460 (ttp80) REVERT: C 1030 SER cc_start: 0.7916 (m) cc_final: 0.7649 (p) REVERT: C 1038 LYS cc_start: 0.7906 (tppt) cc_final: 0.7441 (mmpt) REVERT: C 1045 LYS cc_start: 0.7995 (mttt) cc_final: 0.7737 (mttt) REVERT: C 1055 SER cc_start: 0.8312 (t) cc_final: 0.7993 (m) REVERT: C 1072 GLU cc_start: 0.7564 (pm20) cc_final: 0.7288 (pm20) REVERT: C 1073 LYS cc_start: 0.7526 (pttp) cc_final: 0.7217 (ptmm) REVERT: C 1101 HIS cc_start: 0.8330 (m-70) cc_final: 0.7851 (m-70) REVERT: C 1141 LEU cc_start: 0.7885 (tp) cc_final: 0.7635 (tm) REVERT: G 71 PHE cc_start: 0.6830 (t80) cc_final: 0.6325 (t80) REVERT: E 32 TYR cc_start: 0.7690 (m-80) cc_final: 0.7420 (m-80) REVERT: E 46 GLU cc_start: 0.7102 (pm20) cc_final: 0.6865 (mp0) REVERT: E 68 PHE cc_start: 0.7863 (m-10) cc_final: 0.7222 (m-10) outliers start: 111 outliers final: 67 residues processed: 714 average time/residue: 0.5523 time to fit residues: 474.1987 Evaluate side-chains 726 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 644 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 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 168 PHE 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 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 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 753 LEU Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 29 PHE 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 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 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 G residue 72 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 247 optimal weight: 0.5980 chunk 351 optimal weight: 2.9990 chunk 318 optimal weight: 0.2980 chunk 186 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1101 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN G 93 ASN E 77 ASN E 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.201492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.180013 restraints weight = 58367.283| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.67 r_work: 0.4063 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31419 Z= 0.143 Angle : 0.694 15.350 42840 Z= 0.340 Chirality : 0.047 0.438 4920 Planarity : 0.005 0.074 5448 Dihedral : 4.953 28.351 4130 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.07 % Allowed : 21.38 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3780 helix: 1.20 (0.21), residues: 675 sheet: -0.58 (0.17), residues: 900 loop : -1.73 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 346 TYR 0.026 0.001 TYR B 453 PHE 0.027 0.002 PHE C 490 TRP 0.048 0.002 TRP D 36 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (31317) covalent geometry : angle 0.67861 / 0.34 (42591) SS BOND : bond 0.00456 / 0.31 ( 48) SS BOND : angle 1.43230 / 0.98 ( 96) hydrogen bonds : bond 0.03408 / 2.24 ( 871) hydrogen bonds : angle 5.38669 / 3.72 ( 2505) Misc. bond : bond 0.00046 / 0.02 ( 3) link_BETA1-4 : bond 0.00346 / 0.21 ( 12) link_BETA1-4 : angle 0.96652 / 0.69 ( 36) link_NAG-ASN : bond 0.00558 / 0.37 ( 39) link_NAG-ASN : angle 2.54829 / 1.53 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 644 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7361 (tp-100) REVERT: A 140 PHE cc_start: 0.7313 (p90) cc_final: 0.6593 (p90) REVERT: A 153 MET cc_start: 0.4284 (mpp) cc_final: 0.3844 (mpp) REVERT: A 177 MET cc_start: 0.0376 (mtt) cc_final: -0.0554 (mtt) REVERT: A 206 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7285 (ttmm) REVERT: A 274 THR cc_start: 0.8711 (t) cc_final: 0.8284 (t) REVERT: A 282 ASN cc_start: 0.7234 (OUTLIER) cc_final: 0.6625 (m110) REVERT: A 319 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7360 (ptt180) REVERT: A 340 GLU cc_start: 0.7492 (mp0) cc_final: 0.7243 (mp0) REVERT: A 429 PHE cc_start: 0.6443 (t80) cc_final: 0.6157 (t80) REVERT: A 454 ARG cc_start: 0.8287 (mmt90) cc_final: 0.7997 (mmt90) REVERT: A 500 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 541 PHE cc_start: 0.7067 (p90) cc_final: 0.6395 (p90) REVERT: A 673 SER cc_start: 0.8264 (t) cc_final: 0.7877 (p) REVERT: A 705 VAL cc_start: 0.7011 (OUTLIER) cc_final: 0.6806 (p) REVERT: A 736 VAL cc_start: 0.8201 (t) cc_final: 0.7930 (m) REVERT: A 790 LYS cc_start: 0.7789 (mtpm) cc_final: 0.7124 (mmpt) REVERT: A 795 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8206 (mptp) REVERT: A 811 LYS cc_start: 0.7193 (mmpt) cc_final: 0.6706 (mtpt) REVERT: A 864 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (tt) REVERT: A 933 LYS cc_start: 0.7939 (mttt) cc_final: 0.7564 (mtmm) REVERT: A 947 LYS cc_start: 0.7611 (mtpt) cc_final: 0.7403 (mtmt) REVERT: A 1019 ARG cc_start: 0.7902 (ttp-110) cc_final: 0.7617 (ttm110) REVERT: A 1045 LYS cc_start: 0.8266 (mttt) cc_final: 0.7938 (mttt) REVERT: A 1072 GLU cc_start: 0.7971 (pm20) cc_final: 0.7644 (pm20) REVERT: A 1107 ARG cc_start: 0.7986 (mpp80) cc_final: 0.7607 (mtt-85) REVERT: A 1111 GLU cc_start: 0.7595 (tt0) cc_final: 0.7296 (tt0) REVERT: A 1141 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (tt) REVERT: H 34 MET cc_start: 0.6393 (ppp) cc_final: 0.5818 (ppp) REVERT: H 39 GLN cc_start: 0.7197 (tp-100) cc_final: 0.6405 (pp30) REVERT: H 102 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7563 (t80) REVERT: B 49 HIS cc_start: 0.8210 (t-90) cc_final: 0.7775 (t70) REVERT: B 153 MET cc_start: 0.5479 (mpp) cc_final: 0.5107 (mpp) REVERT: B 206 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7260 (ttmm) REVERT: B 319 ARG cc_start: 0.8153 (ptp90) cc_final: 0.7801 (ptt180) REVERT: B 340 GLU cc_start: 0.7574 (mp0) cc_final: 0.7094 (mp0) REVERT: B 421 TYR cc_start: 0.6747 (m-80) cc_final: 0.6412 (m-10) REVERT: B 490 PHE cc_start: 0.7980 (t80) cc_final: 0.7536 (t80) REVERT: B 493 GLN cc_start: 0.7891 (tp40) cc_final: 0.7689 (tm-30) REVERT: B 508 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6940 (m-10) REVERT: B 511 VAL cc_start: 0.8789 (t) cc_final: 0.8513 (p) REVERT: B 586 ASP cc_start: 0.7570 (m-30) cc_final: 0.7050 (m-30) REVERT: B 606 ASN cc_start: 0.8465 (m-40) cc_final: 0.8235 (m-40) REVERT: B 675 GLN cc_start: 0.7714 (mt0) cc_final: 0.7489 (mt0) REVERT: B 725 GLU cc_start: 0.7804 (tt0) cc_final: 0.7456 (tt0) REVERT: B 772 VAL cc_start: 0.8584 (p) cc_final: 0.8339 (t) REVERT: B 859 THR cc_start: 0.8124 (t) cc_final: 0.7860 (p) REVERT: B 933 LYS cc_start: 0.8064 (mttt) cc_final: 0.7286 (mmtm) REVERT: B 935 GLN cc_start: 0.8056 (mt0) cc_final: 0.7783 (mt0) REVERT: B 947 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7542 (mtpp) REVERT: B 949 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7441 (mm-40) REVERT: B 950 ASP cc_start: 0.7591 (m-30) cc_final: 0.7036 (m-30) REVERT: B 991 VAL cc_start: 0.8206 (t) cc_final: 0.7976 (p) REVERT: F 71 PHE cc_start: 0.6910 (t80) cc_final: 0.6527 (t80) REVERT: D 4 LEU cc_start: 0.8762 (pp) cc_final: 0.8541 (tm) REVERT: D 39 GLN cc_start: 0.7386 (tp40) cc_final: 0.6883 (pp30) REVERT: C 53 ASP cc_start: 0.6910 (t0) cc_final: 0.6624 (t0) REVERT: C 83 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7083 (p) REVERT: C 200 TYR cc_start: 0.5629 (m-10) cc_final: 0.5360 (m-10) REVERT: C 206 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7141 (ttmm) REVERT: C 237 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6924 (ttm-80) REVERT: C 267 VAL cc_start: 0.8134 (t) cc_final: 0.7780 (p) REVERT: C 314 GLN cc_start: 0.8159 (tt0) cc_final: 0.7888 (tp40) REVERT: C 319 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7806 (ptt180) REVERT: C 340 GLU cc_start: 0.7442 (mp0) cc_final: 0.6963 (mp0) REVERT: C 421 TYR cc_start: 0.6750 (m-80) cc_final: 0.6379 (m-10) REVERT: C 453 TYR cc_start: 0.7427 (p90) cc_final: 0.7005 (p90) REVERT: C 541 PHE cc_start: 0.7109 (p90) cc_final: 0.6811 (p90) REVERT: C 574 ASP cc_start: 0.7477 (t70) cc_final: 0.7015 (t70) REVERT: C 651 ILE cc_start: 0.8708 (mm) cc_final: 0.8459 (mt) REVERT: C 705 VAL cc_start: 0.7022 (OUTLIER) cc_final: 0.6764 (p) REVERT: C 725 GLU cc_start: 0.7833 (tt0) cc_final: 0.7614 (tt0) REVERT: C 750 SER cc_start: 0.7843 (t) cc_final: 0.7554 (p) REVERT: C 776 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7746 (tmmm) REVERT: C 790 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7229 (mmpt) REVERT: C 883 THR cc_start: 0.8266 (m) cc_final: 0.7816 (p) REVERT: C 933 LYS cc_start: 0.8091 (mttt) cc_final: 0.7425 (mptt) REVERT: C 947 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7716 (mtpp) REVERT: C 964 LYS cc_start: 0.8405 (mttt) cc_final: 0.8148 (mttt) REVERT: C 994 ASP cc_start: 0.7606 (t70) cc_final: 0.7358 (m-30) REVERT: C 1019 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7483 (ttp80) REVERT: C 1030 SER cc_start: 0.7914 (m) cc_final: 0.7670 (p) REVERT: C 1038 LYS cc_start: 0.7930 (tppt) cc_final: 0.7401 (mmmm) REVERT: C 1045 LYS cc_start: 0.8005 (mttt) cc_final: 0.7778 (mttt) REVERT: C 1055 SER cc_start: 0.8361 (t) cc_final: 0.8019 (m) REVERT: C 1072 GLU cc_start: 0.7576 (pm20) cc_final: 0.7316 (pm20) REVERT: C 1101 HIS cc_start: 0.8373 (m-70) cc_final: 0.7907 (m-70) REVERT: C 1141 LEU cc_start: 0.7887 (tp) cc_final: 0.7642 (tm) REVERT: G 71 PHE cc_start: 0.6898 (t80) cc_final: 0.6427 (t80) REVERT: E 32 TYR cc_start: 0.7674 (m-80) cc_final: 0.7440 (m-80) outliers start: 102 outliers final: 68 residues processed: 694 average time/residue: 0.5882 time to fit residues: 492.5984 Evaluate side-chains 717 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 634 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 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 805 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 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 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 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 G residue 93 ASN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 16 optimal weight: 7.9990 chunk 132 optimal weight: 0.0570 chunk 202 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 230 optimal weight: 0.0570 chunk 264 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1101 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** G 93 ASN ** 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 = 0.4493 r_free = 0.4493 target = 0.202763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.180920 restraints weight = 57519.813| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.80 r_work: 0.4062 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 31419 Z= 0.175 Angle : 0.816 59.199 42840 Z= 0.432 Chirality : 0.048 0.530 4920 Planarity : 0.005 0.145 5448 Dihedral : 4.945 29.125 4130 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 2.77 % Allowed : 21.89 % Favored : 75.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3780 helix: 1.20 (0.21), residues: 675 sheet: -0.58 (0.17), residues: 900 loop : -1.72 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 42 TYR 0.025 0.001 TYR B 453 PHE 0.245 0.002 PHE B 168 TRP 0.077 0.002 TRP D 36 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (31317) covalent geometry : angle 0.80337 / 0.43 (42591) SS BOND : bond 0.00553 / 0.39 ( 48) SS BOND : angle 1.68202 / 1.18 ( 96) hydrogen bonds : bond 0.03411 / 2.24 ( 871) hydrogen bonds : angle 5.39010 / 3.72 ( 2505) Misc. bond : bond 0.00052 / 0.03 ( 3) link_BETA1-4 : bond 0.00317 / 0.17 ( 12) link_BETA1-4 : angle 1.05738 / 0.76 ( 36) link_NAG-ASN : bond 0.00558 / 0.37 ( 39) link_NAG-ASN : angle 2.54218 / 1.52 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 639 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7376 (tp-100) REVERT: A 140 PHE cc_start: 0.7329 (p90) cc_final: 0.6602 (p90) REVERT: A 153 MET cc_start: 0.4295 (mpp) cc_final: 0.3876 (mpp) REVERT: A 168 PHE cc_start: 0.5034 (t80) cc_final: 0.4435 (t80) REVERT: A 177 MET cc_start: 0.0327 (mtt) cc_final: -0.0592 (mtt) REVERT: A 206 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7267 (ttmm) REVERT: A 274 THR cc_start: 0.8699 (t) cc_final: 0.8273 (t) REVERT: A 282 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6605 (m110) REVERT: A 319 ARG cc_start: 0.7815 (ptp90) cc_final: 0.7369 (ptt180) REVERT: A 340 GLU cc_start: 0.7549 (mp0) cc_final: 0.7253 (mp0) REVERT: A 429 PHE cc_start: 0.6427 (t80) cc_final: 0.6154 (t80) REVERT: A 454 ARG cc_start: 0.8303 (mmt90) cc_final: 0.8011 (mmt90) REVERT: A 500 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 541 PHE cc_start: 0.7052 (p90) cc_final: 0.6375 (p90) REVERT: A 673 SER cc_start: 0.8259 (t) cc_final: 0.7867 (p) REVERT: A 705 VAL cc_start: 0.7003 (OUTLIER) cc_final: 0.6799 (p) REVERT: A 736 VAL cc_start: 0.8205 (t) cc_final: 0.7934 (m) REVERT: A 790 LYS cc_start: 0.7791 (mtpm) cc_final: 0.7127 (mmpt) REVERT: A 795 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8203 (mptp) REVERT: A 811 LYS cc_start: 0.7184 (mmpt) cc_final: 0.6696 (mtpt) REVERT: A 864 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 933 LYS cc_start: 0.7911 (mttt) cc_final: 0.7539 (mtmm) REVERT: A 947 LYS cc_start: 0.7590 (mtpt) cc_final: 0.7375 (mtmt) REVERT: A 1019 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7572 (ttm110) REVERT: A 1045 LYS cc_start: 0.8269 (mttt) cc_final: 0.7939 (mttt) REVERT: A 1072 GLU cc_start: 0.7978 (pm20) cc_final: 0.7642 (pm20) REVERT: A 1107 ARG cc_start: 0.7988 (mpp80) cc_final: 0.7658 (mtt-85) REVERT: A 1111 GLU cc_start: 0.7584 (tt0) cc_final: 0.7276 (tt0) REVERT: A 1141 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7577 (tt) REVERT: H 34 MET cc_start: 0.6380 (ppp) cc_final: 0.5778 (ppp) REVERT: H 39 GLN cc_start: 0.7205 (tp-100) cc_final: 0.6405 (pp30) REVERT: H 102 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 49 HIS cc_start: 0.8217 (t-90) cc_final: 0.7784 (t70) REVERT: B 153 MET cc_start: 0.5492 (mpp) cc_final: 0.5110 (mpp) REVERT: B 206 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7259 (ttmm) REVERT: B 319 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7783 (ptt180) REVERT: B 340 GLU cc_start: 0.7615 (mp0) cc_final: 0.7261 (mp0) REVERT: B 421 TYR cc_start: 0.6748 (m-80) cc_final: 0.6412 (m-10) REVERT: B 490 PHE cc_start: 0.8013 (t80) cc_final: 0.7559 (t80) REVERT: B 508 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6928 (m-10) REVERT: B 511 VAL cc_start: 0.8800 (t) cc_final: 0.8520 (p) REVERT: B 586 ASP cc_start: 0.7583 (m-30) cc_final: 0.7061 (m-30) REVERT: B 606 ASN cc_start: 0.8472 (m-40) cc_final: 0.8240 (m-40) REVERT: B 675 GLN cc_start: 0.7705 (mt0) cc_final: 0.7478 (mt0) REVERT: B 725 GLU cc_start: 0.7818 (tt0) cc_final: 0.7464 (tt0) REVERT: B 772 VAL cc_start: 0.8574 (p) cc_final: 0.8327 (t) REVERT: B 859 THR cc_start: 0.8128 (t) cc_final: 0.7857 (p) REVERT: B 933 LYS cc_start: 0.8036 (mttt) cc_final: 0.7257 (mmtm) REVERT: B 935 GLN cc_start: 0.8042 (mt0) cc_final: 0.7761 (mt0) REVERT: B 947 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7510 (mtpp) REVERT: B 949 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7423 (mm-40) REVERT: B 950 ASP cc_start: 0.7579 (m-30) cc_final: 0.7018 (m-30) REVERT: B 991 VAL cc_start: 0.8193 (t) cc_final: 0.7961 (p) REVERT: F 71 PHE cc_start: 0.6913 (t80) cc_final: 0.6513 (t80) REVERT: D 4 LEU cc_start: 0.8698 (pp) cc_final: 0.8483 (tm) REVERT: D 39 GLN cc_start: 0.7361 (tp40) cc_final: 0.6866 (pp30) REVERT: C 53 ASP cc_start: 0.6899 (t0) cc_final: 0.6621 (t0) REVERT: C 83 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7092 (p) REVERT: C 200 TYR cc_start: 0.5649 (m-10) cc_final: 0.5363 (m-10) REVERT: C 206 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7123 (ttmm) REVERT: C 237 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6914 (ttm-80) REVERT: C 267 VAL cc_start: 0.8129 (t) cc_final: 0.7771 (p) REVERT: C 314 GLN cc_start: 0.8166 (tt0) cc_final: 0.7888 (tp40) REVERT: C 319 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7782 (ptt180) REVERT: C 340 GLU cc_start: 0.7492 (mp0) cc_final: 0.6990 (mp0) REVERT: C 421 TYR cc_start: 0.6739 (m-80) cc_final: 0.6370 (m-10) REVERT: C 453 TYR cc_start: 0.7437 (p90) cc_final: 0.7005 (p90) REVERT: C 541 PHE cc_start: 0.7100 (p90) cc_final: 0.6799 (p90) REVERT: C 574 ASP cc_start: 0.7487 (t70) cc_final: 0.7023 (t70) REVERT: C 651 ILE cc_start: 0.8700 (mm) cc_final: 0.8450 (mt) REVERT: C 705 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6758 (p) REVERT: C 725 GLU cc_start: 0.7842 (tt0) cc_final: 0.7620 (tt0) REVERT: C 740 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7138 (mtt) REVERT: C 750 SER cc_start: 0.7823 (t) cc_final: 0.7536 (p) REVERT: C 776 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7734 (tmmm) REVERT: C 790 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7230 (mmpt) REVERT: C 883 THR cc_start: 0.8256 (m) cc_final: 0.7803 (p) REVERT: C 933 LYS cc_start: 0.8051 (mttt) cc_final: 0.7378 (mptt) REVERT: C 947 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7708 (mtpp) REVERT: C 964 LYS cc_start: 0.8404 (mttt) cc_final: 0.8148 (mttt) REVERT: C 994 ASP cc_start: 0.7609 (t70) cc_final: 0.7355 (m-30) REVERT: C 1019 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7450 (ttp80) REVERT: C 1030 SER cc_start: 0.7908 (m) cc_final: 0.7662 (p) REVERT: C 1038 LYS cc_start: 0.7920 (tppt) cc_final: 0.7388 (mmmm) REVERT: C 1045 LYS cc_start: 0.7993 (mttt) cc_final: 0.7762 (mttt) REVERT: C 1055 SER cc_start: 0.8356 (t) cc_final: 0.8003 (m) REVERT: C 1072 GLU cc_start: 0.7578 (pm20) cc_final: 0.7309 (pm20) REVERT: C 1101 HIS cc_start: 0.8384 (m-70) cc_final: 0.7897 (m-70) REVERT: C 1141 LEU cc_start: 0.7879 (tp) cc_final: 0.7630 (tm) REVERT: G 71 PHE cc_start: 0.6900 (t80) cc_final: 0.6392 (t80) REVERT: E 32 TYR cc_start: 0.7681 (m-80) cc_final: 0.7447 (m-80) outliers start: 92 outliers final: 67 residues processed: 683 average time/residue: 0.5777 time to fit residues: 476.5424 Evaluate side-chains 712 residues out of total 3321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 629 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 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 805 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain F residue 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 116 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 740 MET 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 G residue 72 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 102 TYR Chi-restraints excluded: chain E residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 0.4980 chunk 301 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 291 optimal weight: 0.3980 chunk 346 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN A 764 ASN A 907 ASN A1010 GLN A1101 HIS L 27 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B1101 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** E 112 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 = 0.4489 r_free = 0.4489 target = 0.201032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.179483 restraints weight = 58509.308| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.67 r_work: 0.4065 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 31419 Z= 0.177 Angle : 0.818 59.199 42840 Z= 0.432 Chirality : 0.048 0.530 4920 Planarity : 0.005 0.145 5448 Dihedral : 4.945 29.124 4130 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.37 % Rotamer: Outliers : 2.56 % Allowed : 22.10 % Favored : 75.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 3780 helix: 1.20 (0.21), residues: 675 sheet: -0.58 (0.17), residues: 900 loop : -1.72 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 42 TYR 0.025 0.001 TYR B 453 PHE 0.245 0.002 PHE B 168 TRP 0.077 0.002 TRP D 36 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (31317) covalent geometry : angle 0.80338 / 0.43 (42591) SS BOND : bond 0.01511 / 1.02 ( 48) SS BOND : angle 1.93629 / 1.36 ( 96) hydrogen bonds : bond 0.03411 / 2.24 ( 871) hydrogen bonds : angle 5.39010 / 3.72 ( 2505) Misc. bond : bond 0.00052 / 0.03 ( 3) link_BETA1-4 : bond 0.00317 / 0.17 ( 12) link_BETA1-4 : angle 1.05738 / 0.76 ( 36) link_NAG-ASN : bond 0.00558 / 0.37 ( 39) link_NAG-ASN : angle 2.54218 / 1.52 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12992.79 seconds wall clock time: 221 minutes 46.43 seconds (13306.43 seconds total)