Starting phenix.real_space_refine on Wed Aug 27 00:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.map" model { file = "/net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ify_35426/08_2025/8ify_35426.cif" } resolution = 2.55 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 Anisotropic ADP refinement not supported. Converting 11893 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 174 5.16 5 C 21871 2.51 5 N 5603 2.21 5 O 6598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34248 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7922 Classifications: {'peptide': 1011} Link IDs: {'CIS': 1, 'PTRANS': 56, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7884 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 9 Chain: "C" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7922 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 56, 'TRANS': 954} Chain breaks: 8 Chain: "E" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4888 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 4888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4888 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.79, per 1000 atoms: 0.20 Number of scatterers: 34248 At special positions: 0 Unit cell: (138.16, 169.84, 247.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 174 16.00 O 6598 8.00 N 5603 7.00 C 21871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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=1.97 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.06 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=2.02 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=2.02 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 E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 343 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A1074 " " NAG B1201 " - " ASN B 63 " " NAG B1202 " - " ASN B 282 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 709 " " NAG B1205 " - " ASN B1074 " " NAG C1201 " - " ASN C 63 " " NAG C1202 " - " ASN C 282 " " NAG C1203 " - " ASN C 331 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C1074 " " NAG E 702 " - " ASN E 432 " " NAG E 704 " - " ASN E 546 " " NAG F 701 " - " ASN F 54 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 299 " " NAG F 704 " - " ASN F 546 " " NAG F 705 " - " ASN F 91 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7948 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 45 sheets defined 36.6% alpha, 19.3% 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 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.561A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.619A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.515A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.071A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.756A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.881A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (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 976 through 984 removed outlier: 3.562A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.856A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.363A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.519A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.816A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.749A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.745A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.661A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.657A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 removed outlier: 3.780A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.578A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.936A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.937A 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 976 through 984 removed outlier: 3.514A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.923A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.684A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.940A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.998A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.038A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.510A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.667A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.546A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.095A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.688A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A 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 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.345A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.265A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 54 removed outlier: 3.752A pdb=" N THR E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 38 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN E 43 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 46 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.710A pdb=" N GLN E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N MET E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 removed outlier: 4.023A pdb=" N GLU E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN E 77 " --> pdb=" O PHE E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 removed outlier: 3.759A pdb=" N THR E 83 " --> pdb=" O MET E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 93 through 102 removed outlier: 3.885A pdb=" N ALA E 100 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.537A pdb=" N VAL E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 116 removed outlier: 4.559A pdb=" N ARG E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 122 through 130 removed outlier: 3.683A pdb=" N THR E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.868A pdb=" N GLN E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.583A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 173 removed outlier: 4.108A pdb=" N TRP E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.753A pdb=" N ARG E 177 " --> pdb=" O LYS E 174 " (cutoff:3.500A) Proline residue: E 178 - end of helix No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 179 through 194 removed outlier: 4.025A pdb=" N TYR E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL E 184 " --> pdb=" O TYR E 180 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.698A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 220 through 223 Processing helix chain 'E' and resid 224 through 230 removed outlier: 3.758A pdb=" N PHE E 230 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.615A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ASP E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 4.132A pdb=" N ASN E 299 " --> pdb=" O LYS E 296 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN E 300 " --> pdb=" O MET E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.979A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 330 removed outlier: 3.616A pdb=" N ASP E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 386 removed outlier: 4.033A pdb=" N LEU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.806A pdb=" N HIS E 401 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.466A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 removed outlier: 3.764A pdb=" N ALA E 413 " --> pdb=" O LEU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.631A pdb=" N GLY E 422 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 removed outlier: 4.961A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE E 446 " --> pdb=" O GLN E 442 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.583A pdb=" N LYS E 458 " --> pdb=" O TYR E 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 474 removed outlier: 4.849A pdb=" N MET E 474 " --> pdb=" O GLU E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.026A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 517 removed outlier: 4.074A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 532 removed outlier: 3.844A pdb=" N TYR E 521 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 524 " --> pdb=" O ILE E 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 529 " --> pdb=" O PHE E 525 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS E 530 " --> pdb=" O HIS E 526 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.782A pdb=" N LYS E 541 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 542' Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.607A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 558 " --> pdb=" O LEU E 554 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.705A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 574 " --> pdb=" O LEU E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.676A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 600 removed outlier: 3.769A pdb=" N LEU E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.605A pdb=" N THR F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE F 29 " --> pdb=" O GLN F 25 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA F 37 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP F 39 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 54 removed outlier: 4.138A pdb=" N SER F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.698A pdb=" N VAL F 60 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.944A pdb=" N ALA F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 79 removed outlier: 4.465A pdb=" N GLN F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.687A pdb=" N GLU F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 100 removed outlier: 3.523A pdb=" N LYS F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'F' and resid 110 through 113 removed outlier: 3.995A pdb=" N LYS F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 110 through 113' Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.897A pdb=" N THR F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 126 " --> pdb=" O ASN F 122 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.504A pdb=" N THR F 138 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 157 through 168 removed outlier: 3.999A pdb=" N TRP F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.903A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 194 removed outlier: 3.697A pdb=" N TYR F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 184 " --> pdb=" O TYR F 180 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N MET F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'F' and resid 219 through 229 removed outlier: 4.144A pdb=" N MET F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS F 224 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU F 227 " --> pdb=" O MET F 223 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 245 removed outlier: 3.907A pdb=" N TYR F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.529A pdb=" N LEU F 281 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR F 282 " --> pdb=" O TYR F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.556A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 325 through 330 removed outlier: 3.600A pdb=" N ASP F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 330' Processing helix chain 'F' and resid 367 through 385 removed outlier: 4.168A pdb=" N THR F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY F 377 " --> pdb=" O HIS F 373 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN F 380 " --> pdb=" O MET F 376 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 384 " --> pdb=" O GLN F 380 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 405 through 412 removed outlier: 4.305A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 removed outlier: 4.181A pdb=" N ALA F 420 " --> pdb=" O HIS F 416 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU F 421 " --> pdb=" O TYR F 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 421' Processing helix chain 'F' and resid 431 through 448 removed outlier: 3.946A pdb=" N LEU F 444 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE F 446 " --> pdb=" O GLN F 442 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 removed outlier: 3.526A pdb=" N THR F 453 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU F 456 " --> pdb=" O PHE F 452 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU F 457 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP F 459 " --> pdb=" O MET F 455 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N MET F 462 " --> pdb=" O LYS F 458 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 463 " --> pdb=" O TRP F 459 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE F 464 " --> pdb=" O ARG F 460 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS F 465 " --> pdb=" O TRP F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 482 removed outlier: 3.734A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS F 481 " --> pdb=" O TRP F 477 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 509 removed outlier: 3.750A pdb=" N ALA F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 516 removed outlier: 3.524A pdb=" N TYR F 515 " --> pdb=" O PHE F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 530 removed outlier: 4.153A pdb=" N ALA F 528 " --> pdb=" O GLN F 524 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 529 " --> pdb=" O PHE F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.964A pdb=" N LYS F 541 " --> pdb=" O ALA F 538 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS F 542 " --> pdb=" O LEU F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 542' Processing helix chain 'F' and resid 549 through 559 removed outlier: 4.108A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU F 555 " --> pdb=" O GLY F 551 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN F 556 " --> pdb=" O GLN F 552 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET F 557 " --> pdb=" O ARG F 553 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER F 559 " --> pdb=" O LEU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 571 Processing helix chain 'F' and resid 582 through 586 Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.650A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU F 595 " --> pdb=" O LEU F 591 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN F 598 " --> pdb=" O TRP F 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 3.688A pdb=" N SER A 62 " --> pdb=" O SER A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 57 removed outlier: 4.052A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.329A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.551A pdb=" N ARG A 102 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 94 removed outlier: 6.410A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.311A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.696A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.232A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.522A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.196A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.722A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.890A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.689A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 Processing sheet with id=AC1, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.087A pdb=" N VAL B 38 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 57 removed outlier: 3.923A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 225 through 229 removed outlier: 5.831A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 163 through 172 removed outlier: 7.068A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.061A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.430A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY B 431 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N CYS B 379 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.609A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.317A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.752A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 31 through 33 removed outlier: 8.155A pdb=" N ASN C 63 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR C 269 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.978A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.975A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.083A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.750A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.333A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.058A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.743A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.743A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.660A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1174 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10853 1.34 - 1.47: 8955 1.47 - 1.60: 15007 1.60 - 1.72: 8 1.72 - 1.85: 248 Bond restraints: 35071 Sorted by residual: bond pdb=" C VAL A 524 " pdb=" N CYS A 525 " ideal model delta sigma weight residual 1.332 1.461 -0.130 8.30e-03 1.45e+04 2.44e+02 bond pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 1.530 1.644 -0.114 9.10e-03 1.21e+04 1.57e+02 bond pdb=" N LYS A 529 " pdb=" CA LYS A 529 " ideal model delta sigma weight residual 1.457 1.612 -0.154 1.29e-02 6.01e+03 1.43e+02 bond pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 1.457 1.603 -0.146 1.29e-02 6.01e+03 1.27e+02 bond pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 1.515 1.654 -0.139 1.43e-02 4.89e+03 9.47e+01 ... (remaining 35066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 47581 5.54 - 11.09: 60 11.09 - 16.63: 12 16.63 - 22.17: 4 22.17 - 27.71: 1 Bond angle restraints: 47658 Sorted by residual: angle pdb=" C CYS A 525 " pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sigma weight residual 114.87 87.16 27.71 1.51e+00 4.39e-01 3.37e+02 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 108.49 129.58 -21.09 1.15e+00 7.56e-01 3.36e+02 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sigma weight residual 109.51 93.14 16.37 1.02e+00 9.61e-01 2.58e+02 angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 91.73 20.27 1.40e+00 5.10e-01 2.10e+02 angle pdb=" CA CYS A 525 " pdb=" C CYS A 525 " pdb=" N GLY A 526 " ideal model delta sigma weight residual 116.68 127.36 -10.68 8.80e-01 1.29e+00 1.47e+02 ... (remaining 47653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 19915 24.90 - 49.80: 1425 49.80 - 74.69: 181 74.69 - 99.59: 43 99.59 - 124.49: 15 Dihedral angle restraints: 21579 sinusoidal: 9241 harmonic: 12338 Sorted by residual: dihedral pdb=" C CYS A 525 " pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " ideal model delta harmonic sigma weight residual -122.60 -88.90 -33.70 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N CYS A 525 " pdb=" C CYS A 525 " pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " ideal model delta harmonic sigma weight residual 122.80 91.72 31.08 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 178.12 -85.12 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 21576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 5394 0.190 - 0.380: 10 0.380 - 0.570: 2 0.570 - 0.760: 0 0.760 - 0.950: 1 Chirality restraints: 5407 Sorted by residual: chirality pdb=" C1 NAG E 702 " pdb=" ND2 ASN E 432 " pdb=" C2 NAG E 702 " pdb=" O5 NAG E 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" CA CYS A 525 " pdb=" N CYS A 525 " pdb=" C CYS A 525 " pdb=" CB CYS A 525 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" C1 NAG F 704 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG F 704 " pdb=" O5 NAG F 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 5404 not shown) Planarity restraints: 6097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 432 " 0.096 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" CG ASN E 432 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN E 432 " -0.265 2.00e-02 2.50e+03 pdb=" ND2 ASN E 432 " 0.428 2.00e-02 2.50e+03 pdb=" C1 NAG E 702 " -0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 546 " -0.156 2.00e-02 2.50e+03 1.56e-01 3.05e+02 pdb=" CG ASN E 546 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN E 546 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN E 546 " 0.211 2.00e-02 2.50e+03 pdb=" C1 NAG E 704 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.146 5.00e-02 4.00e+02 1.95e-01 6.08e+01 pdb=" N PRO A 527 " 0.334 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.067 5.00e-02 4.00e+02 ... (remaining 6094 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 45 2.34 - 2.98: 17628 2.98 - 3.62: 47149 3.62 - 4.26: 72499 4.26 - 4.90: 120815 Nonbonded interactions: 258136 Sorted by model distance: nonbonded pdb=" O GLY E 422 " pdb=" O3 NAG E 703 " model vdw 1.700 3.040 nonbonded pdb=" ND2 ASN E 432 " pdb=" N2 NAG E 702 " model vdw 1.910 2.560 nonbonded pdb=" OG SER E 78 " pdb=" O LEU E 101 " model vdw 2.102 3.040 nonbonded pdb=" O LEU E 278 " pdb=" OG1 THR E 282 " model vdw 2.139 3.040 nonbonded pdb=" O TYR E 515 " pdb=" OG1 THR E 519 " model vdw 2.179 3.040 ... (remaining 258131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 69 or resid 83 through 329 or resid 333 through \ 827 or resid 849 through 1205)) selection = chain 'B' selection = (chain 'C' and (resid 30 through 69 or resid 83 through 329 or resid 333 through \ 827 or resid 849 through 1205)) } ncs_group { reference = (chain 'E' and resid 20 through 704) selection = (chain 'F' and resid 20 through 704) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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=1.00 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: 11.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 27.150 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:7.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5113 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 : 0.006 0.195 35147 Z= 0.325 Angle : 0.843 40.102 47847 Z= 0.450 Chirality : 0.049 0.950 5407 Planarity : 0.005 0.195 6074 Dihedral : 16.511 124.488 13514 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 1.54 % Allowed : 23.25 % Favored : 75.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.55 (0.12), residues: 4158 helix: 0.70 (0.16), residues: 1076 sheet: 0.03 (0.20), residues: 652 loop : -0.97 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 357 TYR 0.022 0.001 TYR A1067 PHE 0.020 0.001 PHE C 400 TRP 0.028 0.001 TRP F 168 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00530 (35071) covalent geometry : angle 0.77149 (47658) SS BOND : bond 0.01085 ( 39) SS BOND : angle 2.15434 ( 78) hydrogen bonds : bond 0.18425 ( 1146) hydrogen bonds : angle 7.16369 ( 3237) link_BETA1-4 : bond 0.00498 ( 14) link_BETA1-4 : angle 1.98493 ( 42) link_NAG-ASN : bond 0.07860 ( 23) link_NAG-ASN : angle 8.58742 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.6179 (tmm) cc_final: 0.5866 (tmt) REVERT: E 223 MET cc_start: 0.3475 (tmm) cc_final: 0.2753 (mmm) REVERT: E 332 MET cc_start: -0.0445 (ptt) cc_final: -0.0762 (ptm) REVERT: E 360 MET cc_start: 0.4136 (mpm) cc_final: 0.3625 (mpm) REVERT: E 455 MET cc_start: 0.3709 (ppp) cc_final: 0.3225 (tmm) REVERT: E 544 ILE cc_start: -0.2522 (OUTLIER) cc_final: -0.2893 (mm) REVERT: F 108 VAL cc_start: 0.2876 (p) cc_final: 0.2658 (p) REVERT: F 168 TRP cc_start: 0.1484 (t60) cc_final: 0.0296 (t60) REVERT: F 297 MET cc_start: 0.2268 (mmp) cc_final: 0.1668 (mmm) REVERT: F 408 MET cc_start: 0.0229 (tpp) cc_final: -0.0561 (mtp) REVERT: F 462 MET cc_start: 0.3867 (mmt) cc_final: 0.1491 (ptt) outliers start: 57 outliers final: 32 residues processed: 187 average time/residue: 0.5737 time to fit residues: 131.0004 Evaluate side-chains 139 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 611 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 422 ASN A 613 GLN A 762 GLN A 856 ASN B 414 GLN B 437 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 239 GLN E 322 HIS E 325 GLN E 330 ASN E 378 HIS E 388 GLN E 416 HIS F 300 GLN F 378 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.152480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101849 restraints weight = 103399.568| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.76 r_work: 0.3030 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 35147 Z= 0.162 Angle : 0.630 17.854 47847 Z= 0.316 Chirality : 0.045 0.318 5407 Planarity : 0.005 0.176 6074 Dihedral : 9.350 103.019 5695 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 2.94 % Allowed : 21.20 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 4158 helix: 0.93 (0.16), residues: 1153 sheet: 0.37 (0.20), residues: 639 loop : -0.91 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.019 0.001 TYR C1067 PHE 0.019 0.001 PHE C 392 TRP 0.020 0.001 TRP C 436 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00376 (35071) covalent geometry : angle 0.62149 (47658) SS BOND : bond 0.00554 ( 39) SS BOND : angle 1.17942 ( 78) hydrogen bonds : bond 0.06587 ( 1146) hydrogen bonds : angle 5.72731 ( 3237) link_BETA1-4 : bond 0.00386 ( 14) link_BETA1-4 : angle 1.38750 ( 42) link_NAG-ASN : bond 0.00413 ( 23) link_NAG-ASN : angle 2.30868 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 106 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (ttp) REVERT: A 189 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 210 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6695 (pt) REVERT: B 414 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: C 153 MET cc_start: 0.7054 (tmm) cc_final: 0.6790 (tmt) REVERT: C 398 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: C 756 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8922 (t80) REVERT: E 152 MET cc_start: -0.0507 (tpp) cc_final: -0.0811 (tpp) REVERT: E 323 MET cc_start: 0.2508 (OUTLIER) cc_final: 0.2297 (tmt) REVERT: E 332 MET cc_start: 0.0135 (ptt) cc_final: -0.0827 (ptm) REVERT: E 408 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7293 (ppp) REVERT: E 455 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5677 (tmm) REVERT: E 514 ARG cc_start: 0.2631 (OUTLIER) cc_final: 0.1527 (tpt90) REVERT: E 544 ILE cc_start: -0.3536 (OUTLIER) cc_final: -0.4244 (mm) REVERT: E 557 MET cc_start: 0.7908 (tpt) cc_final: 0.7096 (pmm) REVERT: F 80 MET cc_start: -0.0547 (ppp) cc_final: -0.1327 (mpt) REVERT: F 168 TRP cc_start: -0.0342 (t60) cc_final: -0.1317 (m-90) REVERT: F 297 MET cc_start: -0.1514 (mmp) cc_final: -0.1730 (mmm) REVERT: F 462 MET cc_start: 0.1409 (mmt) cc_final: 0.0411 (ptp) outliers start: 109 outliers final: 32 residues processed: 204 average time/residue: 0.5097 time to fit residues: 130.4070 Evaluate side-chains 147 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 611 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 611 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 410 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 396 optimal weight: 50.0000 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.148334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099338 restraints weight = 117797.912| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.15 r_work: 0.3027 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 35147 Z= 0.233 Angle : 0.630 14.333 47847 Z= 0.317 Chirality : 0.046 0.333 5407 Planarity : 0.005 0.163 6074 Dihedral : 8.271 94.332 5672 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 2.91 % Allowed : 21.10 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.29 (0.13), residues: 4158 helix: 0.96 (0.16), residues: 1143 sheet: 0.27 (0.20), residues: 658 loop : -0.92 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.021 0.001 TYR A1067 PHE 0.020 0.001 PHE A 238 TRP 0.013 0.001 TRP C 436 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00560 (35071) covalent geometry : angle 0.62034 (47658) SS BOND : bond 0.00445 ( 39) SS BOND : angle 1.38292 ( 78) hydrogen bonds : bond 0.07061 ( 1146) hydrogen bonds : angle 5.61947 ( 3237) link_BETA1-4 : bond 0.00318 ( 14) link_BETA1-4 : angle 1.50422 ( 42) link_NAG-ASN : bond 0.00462 ( 23) link_NAG-ASN : angle 2.43519 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 104 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: A 189 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 210 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6798 (pt) REVERT: A 239 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7844 (tp40) REVERT: C 153 MET cc_start: 0.7118 (tmm) cc_final: 0.6887 (tmt) REVERT: C 160 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7272 (p90) REVERT: C 740 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9025 (ttp) REVERT: C 756 TYR cc_start: 0.9371 (OUTLIER) cc_final: 0.8968 (t80) REVERT: E 152 MET cc_start: -0.0477 (tpp) cc_final: -0.0826 (tpp) REVERT: E 323 MET cc_start: 0.2909 (tmt) cc_final: 0.2543 (tmt) REVERT: E 408 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7282 (ppp) REVERT: E 455 MET cc_start: 0.6104 (ppp) cc_final: 0.5833 (ppp) REVERT: E 514 ARG cc_start: 0.2744 (OUTLIER) cc_final: 0.1534 (tpt90) REVERT: E 544 ILE cc_start: -0.3703 (OUTLIER) cc_final: -0.4345 (mm) REVERT: E 557 MET cc_start: 0.8123 (tpt) cc_final: 0.6999 (pmm) REVERT: F 80 MET cc_start: -0.0595 (ppp) cc_final: -0.1440 (mpt) REVERT: F 162 LEU cc_start: 0.3656 (OUTLIER) cc_final: 0.3446 (tm) REVERT: F 168 TRP cc_start: -0.0262 (t60) cc_final: -0.1187 (m-90) REVERT: F 293 VAL cc_start: -0.1802 (OUTLIER) cc_final: -0.2015 (p) REVERT: F 297 MET cc_start: -0.1358 (mmp) cc_final: -0.1674 (mtm) REVERT: F 462 MET cc_start: 0.1410 (mmt) cc_final: 0.0513 (ptp) outliers start: 108 outliers final: 44 residues processed: 198 average time/residue: 0.4964 time to fit residues: 122.8524 Evaluate side-chains 158 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 611 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 281 optimal weight: 0.9990 chunk 363 optimal weight: 6.9990 chunk 226 optimal weight: 0.0980 chunk 164 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 329 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 overall best weight: 0.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN C 125 ASN E 378 HIS F 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.151867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101859 restraints weight = 106026.052| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.96 r_work: 0.3075 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.116 35147 Z= 0.110 Angle : 0.561 12.210 47847 Z= 0.277 Chirality : 0.043 0.333 5407 Planarity : 0.004 0.143 6074 Dihedral : 7.141 87.104 5671 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer: Outliers : 2.91 % Allowed : 21.28 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.14 (0.13), residues: 4158 helix: 1.07 (0.16), residues: 1142 sheet: 0.47 (0.20), residues: 631 loop : -0.84 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE B1121 TRP 0.012 0.001 TRP C 436 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00242 (35071) covalent geometry : angle 0.55114 (47658) SS BOND : bond 0.00296 ( 39) SS BOND : angle 1.16583 ( 78) hydrogen bonds : bond 0.05210 ( 1146) hydrogen bonds : angle 5.24805 ( 3237) link_BETA1-4 : bond 0.00443 ( 14) link_BETA1-4 : angle 1.66657 ( 42) link_NAG-ASN : bond 0.00416 ( 23) link_NAG-ASN : angle 2.32408 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 104 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9088 (ttm) REVERT: B 173 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: C 153 MET cc_start: 0.7051 (tmm) cc_final: 0.6688 (tmt) REVERT: C 160 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7227 (p90) REVERT: C 377 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.7030 (m-80) REVERT: C 398 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: C 756 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8880 (t80) REVERT: E 79 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8330 (pmt170) REVERT: E 80 MET cc_start: 0.3956 (pp-130) cc_final: 0.2488 (pp-130) REVERT: E 152 MET cc_start: -0.0681 (tpp) cc_final: -0.1016 (tpp) REVERT: E 323 MET cc_start: 0.2626 (tmt) cc_final: 0.2298 (tmt) REVERT: E 408 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7082 (ppp) REVERT: E 514 ARG cc_start: 0.2538 (OUTLIER) cc_final: 0.1391 (tpt170) REVERT: E 544 ILE cc_start: -0.3961 (OUTLIER) cc_final: -0.4559 (mm) REVERT: E 557 MET cc_start: 0.8009 (tpt) cc_final: 0.6966 (pmm) REVERT: F 80 MET cc_start: -0.0537 (ppp) cc_final: -0.1407 (mpt) REVERT: F 150 ASP cc_start: 0.2601 (t0) cc_final: 0.1733 (p0) REVERT: F 153 GLU cc_start: 0.0091 (OUTLIER) cc_final: -0.1498 (tp30) REVERT: F 168 TRP cc_start: -0.0215 (t60) cc_final: -0.1184 (m-90) REVERT: F 297 MET cc_start: -0.1338 (mmp) cc_final: -0.1539 (mmm) REVERT: F 462 MET cc_start: 0.1435 (mmt) cc_final: 0.0528 (ptp) outliers start: 108 outliers final: 41 residues processed: 200 average time/residue: 0.5242 time to fit residues: 131.4513 Evaluate side-chains 153 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 53 optimal weight: 2.9990 chunk 361 optimal weight: 50.0000 chunk 371 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 391 optimal weight: 30.0000 chunk 268 optimal weight: 0.0670 chunk 189 optimal weight: 0.7980 chunk 358 optimal weight: 50.0000 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 ASN E 378 HIS F 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.103572 restraints weight = 114100.079| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.06 r_work: 0.3032 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35147 Z= 0.143 Angle : 0.565 10.672 47847 Z= 0.280 Chirality : 0.044 0.339 5407 Planarity : 0.004 0.059 6074 Dihedral : 6.752 76.423 5668 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.89 % Allowed : 21.28 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: -0.10 (0.13), residues: 4158 helix: 1.13 (0.16), residues: 1141 sheet: 0.49 (0.20), residues: 640 loop : -0.82 (0.12), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.019 0.001 TYR C1067 PHE 0.022 0.001 PHE A 238 TRP 0.013 0.001 TRP B 104 HIS 0.008 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00337 (35071) covalent geometry : angle 0.55423 (47658) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.04257 ( 78) hydrogen bonds : bond 0.05648 ( 1146) hydrogen bonds : angle 5.21144 ( 3237) link_BETA1-4 : bond 0.00327 ( 14) link_BETA1-4 : angle 1.74829 ( 42) link_NAG-ASN : bond 0.00384 ( 23) link_NAG-ASN : angle 2.45527 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 100 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7792 (ttp) REVERT: A 740 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9053 (ttm) REVERT: B 173 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: B 421 TYR cc_start: 0.8767 (m-80) cc_final: 0.8537 (m-80) REVERT: C 153 MET cc_start: 0.7159 (tmm) cc_final: 0.6860 (tmt) REVERT: C 160 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7284 (p90) REVERT: C 398 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: C 756 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.8981 (t80) REVERT: E 80 MET cc_start: 0.3990 (pp-130) cc_final: 0.3740 (pp-130) REVERT: E 152 MET cc_start: -0.0543 (tpp) cc_final: -0.0961 (tpp) REVERT: E 323 MET cc_start: 0.3100 (OUTLIER) cc_final: 0.2875 (tmt) REVERT: E 408 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7100 (ppp) REVERT: E 461 TRP cc_start: 0.2656 (OUTLIER) cc_final: 0.2245 (m-10) REVERT: E 514 ARG cc_start: 0.2777 (OUTLIER) cc_final: 0.1501 (tpt170) REVERT: E 544 ILE cc_start: -0.3940 (OUTLIER) cc_final: -0.4326 (mm) REVERT: E 557 MET cc_start: 0.8088 (tpt) cc_final: 0.7067 (pmm) REVERT: F 80 MET cc_start: -0.0489 (ppp) cc_final: -0.1405 (mpt) REVERT: F 150 ASP cc_start: 0.2748 (t0) cc_final: 0.1980 (p0) REVERT: F 153 GLU cc_start: -0.0148 (OUTLIER) cc_final: -0.1744 (tp30) REVERT: F 162 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4447 (mm) REVERT: F 168 TRP cc_start: -0.0282 (t60) cc_final: -0.1178 (m-90) REVERT: F 295 GLU cc_start: -0.1392 (OUTLIER) cc_final: -0.1847 (mm-30) REVERT: F 297 MET cc_start: -0.1665 (mmp) cc_final: -0.2185 (mmm) REVERT: F 298 LYS cc_start: 0.2538 (OUTLIER) cc_final: 0.2188 (mmmt) REVERT: F 462 MET cc_start: 0.1322 (mmt) cc_final: 0.0480 (ptp) REVERT: F 527 GLU cc_start: 0.1196 (OUTLIER) cc_final: 0.0817 (mm-30) outliers start: 107 outliers final: 44 residues processed: 195 average time/residue: 0.5378 time to fit residues: 130.9770 Evaluate side-chains 160 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 100 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 295 GLU Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 498 CYS Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 607 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 399 optimal weight: 50.0000 chunk 295 optimal weight: 0.9990 chunk 348 optimal weight: 50.0000 chunk 199 optimal weight: 0.5980 chunk 40 optimal weight: 40.0000 chunk 262 optimal weight: 0.8980 chunk 176 optimal weight: 0.0070 chunk 328 optimal weight: 0.5980 chunk 358 optimal weight: 40.0000 chunk 413 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.152388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.102841 restraints weight = 105879.326| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.41 r_work: 0.3074 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 35147 Z= 0.101 Angle : 0.535 10.348 47847 Z= 0.264 Chirality : 0.043 0.340 5407 Planarity : 0.004 0.057 6074 Dihedral : 6.271 58.531 5667 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 2.40 % Allowed : 21.61 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.03 (0.13), residues: 4158 helix: 1.21 (0.16), residues: 1138 sheet: 0.60 (0.20), residues: 628 loop : -0.73 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 357 TYR 0.018 0.001 TYR B1067 PHE 0.021 0.001 PHE A 238 TRP 0.010 0.001 TRP C 436 HIS 0.011 0.001 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00219 (35071) covalent geometry : angle 0.52452 (47658) SS BOND : bond 0.00222 ( 39) SS BOND : angle 0.79203 ( 78) hydrogen bonds : bond 0.04619 ( 1146) hydrogen bonds : angle 5.00462 ( 3237) link_BETA1-4 : bond 0.00516 ( 14) link_BETA1-4 : angle 1.72664 ( 42) link_NAG-ASN : bond 0.00412 ( 23) link_NAG-ASN : angle 2.48439 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 106 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: A 740 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8903 (ttm) REVERT: A 823 PHE cc_start: 0.8359 (t80) cc_final: 0.7987 (m-80) REVERT: B 173 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: B 375 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8052 (p90) REVERT: C 153 MET cc_start: 0.7242 (tmm) cc_final: 0.6838 (tmt) REVERT: C 160 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7208 (p90) REVERT: C 398 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: C 756 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8751 (t80) REVERT: E 80 MET cc_start: 0.3832 (pp-130) cc_final: 0.3491 (pp-130) REVERT: E 152 MET cc_start: -0.0694 (tpp) cc_final: -0.1098 (tpp) REVERT: E 323 MET cc_start: 0.3039 (OUTLIER) cc_final: 0.2791 (tmt) REVERT: E 408 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7065 (ppp) REVERT: E 461 TRP cc_start: 0.2813 (OUTLIER) cc_final: 0.2390 (m-10) REVERT: E 514 ARG cc_start: 0.2668 (OUTLIER) cc_final: 0.1449 (tpt170) REVERT: E 557 MET cc_start: 0.7998 (tpt) cc_final: 0.6966 (pmm) REVERT: F 80 MET cc_start: -0.0440 (ppp) cc_final: -0.1327 (mpt) REVERT: F 150 ASP cc_start: 0.2681 (t0) cc_final: 0.1931 (p0) REVERT: F 153 GLU cc_start: -0.0077 (OUTLIER) cc_final: -0.1694 (tp30) REVERT: F 168 TRP cc_start: -0.0087 (t60) cc_final: -0.1007 (m-90) REVERT: F 176 LEU cc_start: -0.0932 (OUTLIER) cc_final: -0.1414 (mm) REVERT: F 297 MET cc_start: -0.1747 (mmp) cc_final: -0.2327 (mmm) REVERT: F 298 LYS cc_start: 0.2534 (OUTLIER) cc_final: 0.2251 (mmmt) REVERT: F 462 MET cc_start: 0.1408 (mmt) cc_final: 0.0411 (ptp) outliers start: 89 outliers final: 41 residues processed: 188 average time/residue: 0.6121 time to fit residues: 143.0063 Evaluate side-chains 156 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 101 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 381 TYR Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 chunk 240 optimal weight: 4.9990 chunk 319 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 HIS ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.152389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103476 restraints weight = 104931.787| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.37 r_work: 0.3045 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35147 Z= 0.150 Angle : 0.556 9.628 47847 Z= 0.276 Chirality : 0.044 0.339 5407 Planarity : 0.004 0.056 6074 Dihedral : 6.164 59.901 5665 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.48 % Allowed : 21.77 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.01 (0.13), residues: 4158 helix: 1.20 (0.16), residues: 1146 sheet: 0.49 (0.19), residues: 668 loop : -0.74 (0.12), residues: 2344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 357 TYR 0.023 0.001 TYR E 381 PHE 0.023 0.001 PHE A 238 TRP 0.010 0.001 TRP B 104 HIS 0.010 0.001 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00355 (35071) covalent geometry : angle 0.54401 (47658) SS BOND : bond 0.00261 ( 39) SS BOND : angle 0.97487 ( 78) hydrogen bonds : bond 0.05450 ( 1146) hydrogen bonds : angle 5.08235 ( 3237) link_BETA1-4 : bond 0.00389 ( 14) link_BETA1-4 : angle 1.77762 ( 42) link_NAG-ASN : bond 0.00376 ( 23) link_NAG-ASN : angle 2.62059 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 100 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 239 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7746 (tp40) REVERT: A 740 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9082 (ttm) REVERT: A 820 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8816 (m-30) REVERT: B 173 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: B 375 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8087 (p90) REVERT: C 153 MET cc_start: 0.7324 (tmm) cc_final: 0.6955 (tmt) REVERT: C 160 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7207 (p90) REVERT: C 398 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: C 756 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8900 (t80) REVERT: E 80 MET cc_start: 0.3921 (OUTLIER) cc_final: 0.3612 (pp-130) REVERT: E 152 MET cc_start: -0.0579 (tpp) cc_final: -0.0986 (tpp) REVERT: E 323 MET cc_start: 0.3000 (OUTLIER) cc_final: 0.2731 (tmt) REVERT: E 408 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7065 (ppp) REVERT: E 461 TRP cc_start: 0.2742 (OUTLIER) cc_final: 0.2336 (m-10) REVERT: E 514 ARG cc_start: 0.2769 (OUTLIER) cc_final: 0.1508 (tpt170) REVERT: E 557 MET cc_start: 0.7954 (tpt) cc_final: 0.6964 (pmm) REVERT: F 80 MET cc_start: -0.0274 (ppp) cc_final: -0.1207 (mpt) REVERT: F 150 ASP cc_start: 0.2832 (t0) cc_final: 0.2119 (p0) REVERT: F 153 GLU cc_start: -0.0105 (OUTLIER) cc_final: -0.1699 (tm-30) REVERT: F 168 TRP cc_start: -0.0193 (t60) cc_final: -0.1062 (m-90) REVERT: F 176 LEU cc_start: -0.0916 (OUTLIER) cc_final: -0.1411 (mm) REVERT: F 223 MET cc_start: 0.4049 (mmt) cc_final: 0.3087 (ttt) REVERT: F 297 MET cc_start: -0.1738 (mmp) cc_final: -0.1938 (mmm) REVERT: F 435 GLU cc_start: -0.0120 (OUTLIER) cc_final: -0.0501 (tt0) REVERT: F 462 MET cc_start: 0.1271 (mmt) cc_final: 0.0415 (ptp) outliers start: 92 outliers final: 50 residues processed: 180 average time/residue: 0.5262 time to fit residues: 118.2839 Evaluate side-chains 167 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 100 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 381 TYR Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 346 optimal weight: 40.0000 chunk 337 optimal weight: 50.0000 chunk 129 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 285 optimal weight: 0.0470 chunk 278 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 395 optimal weight: 30.0000 chunk 403 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 378 HIS F 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.103169 restraints weight = 103141.012| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.85 r_work: 0.3056 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 35147 Z= 0.106 Angle : 0.531 10.118 47847 Z= 0.262 Chirality : 0.043 0.339 5407 Planarity : 0.004 0.055 6074 Dihedral : 5.930 59.025 5665 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.29 % Allowed : 21.99 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.09 (0.13), residues: 4158 helix: 1.28 (0.16), residues: 1140 sheet: 0.57 (0.20), residues: 648 loop : -0.70 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.020 0.001 TYR E 381 PHE 0.022 0.001 PHE A 238 TRP 0.011 0.001 TRP B 104 HIS 0.007 0.001 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00236 (35071) covalent geometry : angle 0.51942 (47658) SS BOND : bond 0.00414 ( 39) SS BOND : angle 0.94314 ( 78) hydrogen bonds : bond 0.04747 ( 1146) hydrogen bonds : angle 4.95132 ( 3237) link_BETA1-4 : bond 0.00500 ( 14) link_BETA1-4 : angle 1.71795 ( 42) link_NAG-ASN : bond 0.00399 ( 23) link_NAG-ASN : angle 2.51893 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 101 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7526 (tp40) REVERT: A 740 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8933 (ttm) REVERT: A 823 PHE cc_start: 0.8417 (t80) cc_final: 0.8009 (m-80) REVERT: B 173 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: B 375 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8020 (p90) REVERT: B 421 TYR cc_start: 0.9074 (m-80) cc_final: 0.8625 (m-80) REVERT: B 1043 CYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9222 (m) REVERT: C 153 MET cc_start: 0.7216 (tmm) cc_final: 0.6638 (tmt) REVERT: C 160 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7190 (p90) REVERT: C 398 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: C 756 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8742 (t80) REVERT: E 80 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3455 (pp-130) REVERT: E 152 MET cc_start: -0.0751 (tpp) cc_final: -0.1220 (tpp) REVERT: E 323 MET cc_start: 0.2901 (OUTLIER) cc_final: 0.2637 (tmt) REVERT: E 408 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6945 (ppp) REVERT: E 461 TRP cc_start: 0.2600 (OUTLIER) cc_final: 0.2293 (m-10) REVERT: E 514 ARG cc_start: 0.2710 (OUTLIER) cc_final: 0.1408 (tpt170) REVERT: E 544 ILE cc_start: -0.4276 (OUTLIER) cc_final: -0.4614 (mm) REVERT: E 557 MET cc_start: 0.7961 (tpt) cc_final: 0.6728 (pmt) REVERT: F 80 MET cc_start: -0.0126 (ppp) cc_final: -0.1107 (mpt) REVERT: F 150 ASP cc_start: 0.2919 (t0) cc_final: 0.2227 (p0) REVERT: F 153 GLU cc_start: -0.0022 (OUTLIER) cc_final: -0.1718 (tm-30) REVERT: F 168 TRP cc_start: -0.0153 (t60) cc_final: -0.1016 (m-90) REVERT: F 176 LEU cc_start: -0.0914 (OUTLIER) cc_final: -0.1376 (mm) REVERT: F 223 MET cc_start: 0.4146 (mmt) cc_final: 0.3228 (ttt) REVERT: F 297 MET cc_start: -0.1763 (mmp) cc_final: -0.2362 (mmm) REVERT: F 298 LYS cc_start: 0.2546 (OUTLIER) cc_final: 0.2243 (mmmt) REVERT: F 435 GLU cc_start: -0.0044 (OUTLIER) cc_final: -0.0448 (tt0) REVERT: F 462 MET cc_start: 0.1465 (mmt) cc_final: 0.0523 (ptp) outliers start: 85 outliers final: 51 residues processed: 180 average time/residue: 0.6241 time to fit residues: 139.5860 Evaluate side-chains 169 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 100 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 381 TYR Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 248 optimal weight: 1.9990 chunk 308 optimal weight: 40.0000 chunk 136 optimal weight: 9.9990 chunk 157 optimal weight: 0.6980 chunk 287 optimal weight: 0.7980 chunk 254 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 404 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 chunk 274 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.152659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103670 restraints weight = 103560.218| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.39 r_work: 0.3083 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35147 Z= 0.107 Angle : 0.537 10.683 47847 Z= 0.263 Chirality : 0.043 0.338 5407 Planarity : 0.004 0.055 6074 Dihedral : 5.781 58.896 5664 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.37 % Allowed : 21.88 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.13 (0.13), residues: 4158 helix: 1.33 (0.16), residues: 1144 sheet: 0.59 (0.20), residues: 648 loop : -0.68 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 357 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.001 PHE A 238 TRP 0.010 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00242 (35071) covalent geometry : angle 0.52548 (47658) SS BOND : bond 0.00293 ( 39) SS BOND : angle 0.97505 ( 78) hydrogen bonds : bond 0.04705 ( 1146) hydrogen bonds : angle 4.90374 ( 3237) link_BETA1-4 : bond 0.00474 ( 14) link_BETA1-4 : angle 1.70560 ( 42) link_NAG-ASN : bond 0.00391 ( 23) link_NAG-ASN : angle 2.47186 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 101 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 239 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7496 (tp40) REVERT: A 740 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8941 (ttm) REVERT: A 820 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: A 823 PHE cc_start: 0.8404 (t80) cc_final: 0.7998 (m-80) REVERT: B 173 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: B 375 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.8117 (p90) REVERT: B 421 TYR cc_start: 0.8978 (m-80) cc_final: 0.8492 (m-80) REVERT: B 1043 CYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9199 (m) REVERT: C 153 MET cc_start: 0.7324 (tmm) cc_final: 0.6771 (tmt) REVERT: C 160 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7172 (p90) REVERT: C 398 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: C 756 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8581 (t80) REVERT: E 80 MET cc_start: 0.3149 (OUTLIER) cc_final: 0.2788 (pp-130) REVERT: E 152 MET cc_start: -0.0972 (tpp) cc_final: -0.1414 (tpp) REVERT: E 323 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.2215 (tmt) REVERT: E 408 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6939 (ppp) REVERT: E 461 TRP cc_start: 0.2556 (OUTLIER) cc_final: 0.2212 (m-10) REVERT: E 514 ARG cc_start: 0.2517 (OUTLIER) cc_final: 0.1243 (tpt170) REVERT: E 544 ILE cc_start: -0.4191 (OUTLIER) cc_final: -0.4546 (mm) REVERT: E 557 MET cc_start: 0.7849 (tpt) cc_final: 0.6658 (pmt) REVERT: F 80 MET cc_start: -0.0206 (ppp) cc_final: -0.1096 (mpt) REVERT: F 150 ASP cc_start: 0.2821 (t0) cc_final: 0.2147 (p0) REVERT: F 153 GLU cc_start: 0.0062 (OUTLIER) cc_final: -0.1674 (tm-30) REVERT: F 168 TRP cc_start: -0.0116 (t60) cc_final: -0.0982 (m-90) REVERT: F 176 LEU cc_start: -0.0882 (OUTLIER) cc_final: -0.1327 (mm) REVERT: F 223 MET cc_start: 0.4153 (mmt) cc_final: 0.3197 (ttt) REVERT: F 297 MET cc_start: -0.1903 (mmp) cc_final: -0.2485 (mmm) REVERT: F 298 LYS cc_start: 0.2762 (OUTLIER) cc_final: 0.2332 (mmmt) REVERT: F 435 GLU cc_start: -0.0023 (OUTLIER) cc_final: -0.0516 (tt0) REVERT: F 462 MET cc_start: 0.1487 (mmt) cc_final: 0.0525 (ptp) outliers start: 88 outliers final: 54 residues processed: 177 average time/residue: 0.4005 time to fit residues: 88.9408 Evaluate side-chains 175 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 101 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 461 TRP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 381 TYR Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 358 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 417 optimal weight: 0.0010 chunk 305 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.102123 restraints weight = 104194.829| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.74 r_work: 0.3056 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35147 Z= 0.115 Angle : 0.538 10.583 47847 Z= 0.264 Chirality : 0.043 0.339 5407 Planarity : 0.004 0.059 6074 Dihedral : 5.735 59.217 5664 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.05 % Allowed : 22.15 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.13 (0.13), residues: 4158 helix: 1.34 (0.16), residues: 1144 sheet: 0.57 (0.20), residues: 647 loop : -0.68 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 357 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.001 PHE A 238 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00264 (35071) covalent geometry : angle 0.52679 (47658) SS BOND : bond 0.00272 ( 39) SS BOND : angle 0.97879 ( 78) hydrogen bonds : bond 0.04844 ( 1146) hydrogen bonds : angle 4.91384 ( 3237) link_BETA1-4 : bond 0.00478 ( 14) link_BETA1-4 : angle 1.68940 ( 42) link_NAG-ASN : bond 0.00396 ( 23) link_NAG-ASN : angle 2.44473 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8316 Ramachandran restraints generated. 4158 Oldfield, 0 Emsley, 4158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 100 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 239 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7603 (tp40) REVERT: A 341 VAL cc_start: 0.4758 (OUTLIER) cc_final: 0.4412 (m) REVERT: A 740 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8938 (ttm) REVERT: A 820 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: A 823 PHE cc_start: 0.8385 (t80) cc_final: 0.7984 (m-80) REVERT: B 173 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: B 375 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8035 (p90) REVERT: B 421 TYR cc_start: 0.8992 (m-80) cc_final: 0.8489 (m-80) REVERT: B 1043 CYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9178 (m) REVERT: C 153 MET cc_start: 0.7322 (tmm) cc_final: 0.6815 (tmt) REVERT: C 160 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7140 (p90) REVERT: C 398 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6431 (m-30) REVERT: C 756 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8607 (t80) REVERT: E 80 MET cc_start: 0.3472 (OUTLIER) cc_final: 0.3069 (pp-130) REVERT: E 152 MET cc_start: -0.1024 (tpp) cc_final: -0.1488 (tpp) REVERT: E 323 MET cc_start: 0.2733 (OUTLIER) cc_final: 0.2467 (tmt) REVERT: E 408 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7032 (ppp) REVERT: E 514 ARG cc_start: 0.2473 (OUTLIER) cc_final: 0.1235 (tpt170) REVERT: E 544 ILE cc_start: -0.4260 (OUTLIER) cc_final: -0.4584 (mm) REVERT: E 557 MET cc_start: 0.7913 (tpt) cc_final: 0.6692 (pmt) REVERT: F 80 MET cc_start: -0.0169 (ppp) cc_final: -0.1026 (mpt) REVERT: F 150 ASP cc_start: 0.2919 (t0) cc_final: 0.2277 (p0) REVERT: F 153 GLU cc_start: -0.0085 (OUTLIER) cc_final: -0.1727 (tm-30) REVERT: F 168 TRP cc_start: -0.0257 (t60) cc_final: -0.1030 (m-90) REVERT: F 176 LEU cc_start: -0.0926 (OUTLIER) cc_final: -0.1353 (mm) REVERT: F 223 MET cc_start: 0.4158 (mmt) cc_final: 0.3188 (ttt) REVERT: F 297 MET cc_start: -0.2080 (mmp) cc_final: -0.2656 (mmm) REVERT: F 298 LYS cc_start: 0.2589 (OUTLIER) cc_final: 0.2234 (mmmt) REVERT: F 435 GLU cc_start: -0.0090 (OUTLIER) cc_final: -0.0545 (tt0) REVERT: F 462 MET cc_start: 0.1437 (mmt) cc_final: 0.0510 (ptp) outliers start: 76 outliers final: 52 residues processed: 165 average time/residue: 0.3929 time to fit residues: 80.9123 Evaluate side-chains 171 residues out of total 3707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 99 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 514 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 298 LYS Chi-restraints excluded: chain F residue 381 TYR Chi-restraints excluded: chain F residue 435 GLU Chi-restraints excluded: chain F residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 411 optimal weight: 40.0000 chunk 257 optimal weight: 0.9980 chunk 346 optimal weight: 20.0000 chunk 290 optimal weight: 0.7980 chunk 360 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN E 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102267 restraints weight = 103754.552| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.39 r_work: 0.2998 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35147 Z= 0.122 Angle : 0.540 10.707 47847 Z= 0.266 Chirality : 0.043 0.339 5407 Planarity : 0.004 0.065 6074 Dihedral : 5.718 59.426 5664 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 22.12 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.94 % Cis-general : 0.03 % 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 aren not related in a simple way. whole: 0.14 (0.13), residues: 4158 helix: 1.35 (0.16), residues: 1144 sheet: 0.59 (0.20), residues: 645 loop : -0.68 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 357 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.001 PHE A 238 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00282 (35071) covalent geometry : angle 0.52928 (47658) SS BOND : bond 0.00288 ( 39) SS BOND : angle 1.04144 ( 78) hydrogen bonds : bond 0.04991 ( 1146) hydrogen bonds : angle 4.92612 ( 3237) link_BETA1-4 : bond 0.00456 ( 14) link_BETA1-4 : angle 1.66742 ( 42) link_NAG-ASN : bond 0.00394 ( 23) link_NAG-ASN : angle 2.43116 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17746.65 seconds wall clock time: 300 minutes 42.11 seconds (18042.11 seconds total)