Starting phenix.real_space_refine on Sat Aug 8 14:09:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlm_38453/08_2026/8xlm_38453.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 18244 2.51 5 N 4666 2.21 5 O 5552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28596 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7794 Classifications: {'peptide': 997} Link IDs: {'PTRANS': 53, 'TRANS': 943} Chain breaks: 8 Chain: "B" Number of atoms: 7803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7803 Classifications: {'peptide': 996} Link IDs: {'PTRANS': 53, 'TRANS': 942} Chain breaks: 9 Chain: "C" Number of atoms: 7351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7351 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 50, 'TRANS': 889} Chain breaks: 17 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.27, per 1000 atoms: 0.18 Number of scatterers: 28596 At special positions: 0 Unit cell: (137.685, 147.735, 230.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 5552 8.00 N 4666 7.00 C 18244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.03 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 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B1098 " " NAG B1310 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1098 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 165 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 53 " " NAG S 1 " - " ASN D 546 " " NAG T 1 " - " ASN D 103 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6638 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 48 sheets defined 29.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.736A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 761 through 783 removed outlier: 3.716A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.681A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.643A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.157A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.939A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.589A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.910A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 782 removed outlier: 3.874A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 4.002A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.642A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.546A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.225A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.673A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.066A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.360A pdb=" N PHE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 605 removed outlier: 3.690A pdb=" N SER C 605 " --> pdb=" O THR C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.623A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.071A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.596A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.708A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.663A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.125A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.363A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 945 removed outlier: 3.583A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.031A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.571A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.966A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.786A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.515A pdb=" N TYR D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.124A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.871A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.627A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 411 removed outlier: 4.283A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.016A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.414A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.877A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.772A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 515 through 533 removed outlier: 3.849A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 521 " --> pdb=" O THR D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.948A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.537A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.923A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.533A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 195 removed outlier: 8.071A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.432A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.546A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.144A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (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: 3.685A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.591A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASN A 703 " --> pdb=" O LYS C 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 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.893A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A 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: 4.746A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 163 through 166 removed outlier: 5.165A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 188 through 190 Processing sheet with id=AC4, first strand: chain 'B' and resid 195 through 197 Processing sheet with id=AC5, first strand: chain 'B' and resid 204 through 205 removed outlier: 3.777A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.108A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 327 removed outlier: 7.039A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 7.089A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.771A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.758A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.875A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.787A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=AE2, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.745A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR C 167 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.198A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.873A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.860A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.630A 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 1121 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.883A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.074A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2757 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: 5.93 Time building geometry restraints manager: 2.96 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: 8989 1.34 - 1.46: 6499 1.46 - 1.58: 13579 1.58 - 1.70: 4 1.70 - 1.82: 182 Bond restraints: 29253 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CB PRO B 174 " pdb=" CG PRO B 174 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.16e+00 ... (remaining 29248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 39582 3.07 - 6.14: 166 6.14 - 9.21: 13 9.21 - 12.29: 3 12.29 - 15.36: 2 Bond angle restraints: 39766 Sorted by residual: angle pdb=" CA PRO B 174 " pdb=" N PRO B 174 " pdb=" CD PRO B 174 " ideal model delta sigma weight residual 112.00 96.64 15.36 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 112.00 98.88 13.12 1.40e+00 5.10e-01 8.79e+01 angle pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" CD PRO A 217 " ideal model delta sigma weight residual 112.00 102.95 9.05 1.40e+00 5.10e-01 4.18e+01 angle pdb=" N VAL D 132 " pdb=" CA VAL D 132 " pdb=" C VAL D 132 " ideal model delta sigma weight residual 112.96 108.15 4.81 1.00e+00 1.00e+00 2.32e+01 angle pdb=" CA PRO D 258 " pdb=" N PRO D 258 " pdb=" CD PRO D 258 " ideal model delta sigma weight residual 112.00 106.19 5.81 1.40e+00 5.10e-01 1.72e+01 ... (remaining 39761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 16329 24.70 - 49.40: 1524 49.40 - 74.10: 212 74.10 - 98.80: 75 98.80 - 123.50: 30 Dihedral angle restraints: 18170 sinusoidal: 7879 harmonic: 10291 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 3.37 -89.37 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual 93.00 164.80 -71.80 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.97 57.97 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 18167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3993 0.063 - 0.126: 606 0.126 - 0.189: 24 0.189 - 0.252: 1 0.252 - 0.316: 6 Chirality restraints: 4630 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.44e+00 chirality pdb=" C1 NAG D 701 " pdb=" ND2 ASN D 322 " pdb=" C2 NAG D 701 " pdb=" O5 NAG D 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4627 not shown) Planarity restraints: 5090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " -0.113 5.00e-02 4.00e+02 1.58e-01 3.98e+01 pdb=" N PRO B 174 " 0.272 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A 217 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 257 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 258 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " -0.059 5.00e-02 4.00e+02 ... (remaining 5087 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 941 2.70 - 3.25: 27427 3.25 - 3.80: 42813 3.80 - 4.35: 53087 4.35 - 4.90: 91544 Nonbonded interactions: 215812 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.199 3.040 nonbonded pdb=" OG SER D 317 " pdb=" O SER D 545 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.252 3.040 ... (remaining 215807 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 26 through 65 or resid 86 through 108 or resid 111 through \ 113 or resid 117 through 140 or resid 155 through 177 or resid 188 through 240 \ or resid 264 through 401 or resid 404 through 426 or resid 429 through 434 or re \ sid 437 through 444 or resid 451 through 465 or resid 490 through 496 or resid 5 \ 03 through 517 or resid 520 through 675 or resid 690 through 827 or resid 854 th \ rough 1310)) selection = (chain 'B' and (resid 26 through 65 or resid 86 through 108 or resid 111 through \ 113 or resid 117 through 131 or resid 137 through 140 or resid 155 through 177 \ or resid 188 through 240 or resid 264 through 401 or resid 404 through 426 or re \ sid 429 through 434 or resid 437 through 444 or resid 451 through 465 or resid 4 \ 90 through 496 or resid 503 through 517 or resid 520 through 827 or resid 854 th \ rough 1310)) selection = (chain 'C' and (resid 26 through 65 or resid 86 through 131 or resid 137 through \ 140 or resid 155 through 675 or resid 690 through 1310)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'R' selection = chain 'S' } 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 29350 Z= 0.164 Angle : 0.617 15.356 40017 Z= 0.308 Chirality : 0.044 0.316 4630 Planarity : 0.005 0.158 5047 Dihedral : 19.127 123.499 11412 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.18 % Favored : 90.50 % Rotamer: Outliers : 0.16 % Allowed : 32.65 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.15), residues: 3453 helix: 1.89 (0.18), residues: 970 sheet: 0.16 (0.23), residues: 513 loop : -2.01 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 169 TYR 0.019 0.001 TYR C1138 PHE 0.054 0.001 PHE B 562 TRP 0.017 0.001 TRP D 168 HIS 0.003 0.000 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (29253) covalent geometry : angle 0.59865 / 0.30 (39766) SS BOND : bond 0.00211 / 0.15 ( 40) SS BOND : angle 0.71305 / 0.49 ( 80) hydrogen bonds : bond 0.13501 / 8.41 ( 991) hydrogen bonds : angle 5.50112 / 3.71 ( 2757) link_ALPHA1-3 : bond 0.00338 / 0.18 ( 1) link_ALPHA1-3 : angle 1.68223 / 0.93 ( 3) link_ALPHA1-6 : bond 0.00253 / 0.13 ( 1) link_ALPHA1-6 : angle 1.70864 / 0.95 ( 3) link_BETA1-4 : bond 0.00481 / 0.25 ( 12) link_BETA1-4 : angle 1.12930 / 0.70 ( 36) link_NAG-ASN : bond 0.00552 / 0.34 ( 43) link_NAG-ASN : angle 2.58058 / 1.80 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7076 (m) cc_final: 0.6868 (m) REVERT: A 189 LEU cc_start: 0.8231 (mp) cc_final: 0.8012 (mt) REVERT: B 174 PRO cc_start: 0.4849 (Cg_exo) cc_final: 0.4488 (Cg_endo) REVERT: B 756 TYR cc_start: 0.8585 (m-80) cc_final: 0.8299 (m-80) REVERT: C 104 TRP cc_start: 0.6788 (t-100) cc_final: 0.5984 (t-100) REVERT: C 265 TYR cc_start: 0.7744 (p90) cc_final: 0.7238 (p90) REVERT: C 356 LYS cc_start: 0.7738 (tttt) cc_final: 0.7364 (tptp) REVERT: C 365 TYR cc_start: 0.8074 (m-80) cc_final: 0.7291 (m-80) REVERT: C 453 TYR cc_start: 0.7457 (t80) cc_final: 0.7149 (t80) REVERT: C 759 PHE cc_start: 0.8659 (m-80) cc_final: 0.8343 (m-10) REVERT: D 82 MET cc_start: 0.0049 (mtt) cc_final: -0.0609 (ttm) REVERT: D 145 GLU cc_start: 0.5602 (pp20) cc_final: 0.4858 (pt0) REVERT: D 270 MET cc_start: 0.3025 (tpp) cc_final: 0.2194 (ttm) outliers start: 5 outliers final: 3 residues processed: 250 average time/residue: 0.1592 time to fit residues: 64.9354 Evaluate side-chains 163 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN A 439 ASN A1002 GLN B 907 ASN C 955 ASN C 965 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.155581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092305 restraints weight = 62397.902| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.80 r_work: 0.2860 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29350 Z= 0.241 Angle : 0.669 10.787 40017 Z= 0.335 Chirality : 0.047 0.333 4630 Planarity : 0.005 0.086 5047 Dihedral : 10.703 110.078 4958 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.53 % Favored : 90.18 % Rotamer: Outliers : 3.77 % Allowed : 29.87 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3453 helix: 1.52 (0.17), residues: 979 sheet: -0.03 (0.23), residues: 516 loop : -2.19 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.034 0.002 TYR D 587 PHE 0.027 0.002 PHE B 338 TRP 0.012 0.001 TRP D 477 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (29253) covalent geometry : angle 0.64747 / 0.33 (39766) SS BOND : bond 0.00312 / 0.23 ( 40) SS BOND : angle 0.92200 / 0.62 ( 80) hydrogen bonds : bond 0.06198 / 4.02 ( 991) hydrogen bonds : angle 4.81989 / 3.31 ( 2757) link_ALPHA1-3 : bond 0.00839 / 0.44 ( 1) link_ALPHA1-3 : angle 2.15354 / 1.13 ( 3) link_ALPHA1-6 : bond 0.00648 / 0.34 ( 1) link_ALPHA1-6 : angle 1.60368 / 0.85 ( 3) link_BETA1-4 : bond 0.00405 / 0.21 ( 12) link_BETA1-4 : angle 1.45584 / 0.84 ( 36) link_NAG-ASN : bond 0.00567 / 0.35 ( 43) link_NAG-ASN : angle 2.89564 / 1.97 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 160 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.2428 (OUTLIER) cc_final: 0.2096 (mtmm) REVERT: B 1001 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9177 (mp) REVERT: B 1002 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: B 1115 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8882 (mm) REVERT: C 104 TRP cc_start: 0.6922 (t-100) cc_final: 0.6641 (t-100) REVERT: C 356 LYS cc_start: 0.7725 (tttt) cc_final: 0.7385 (tptp) REVERT: C 453 TYR cc_start: 0.7501 (t80) cc_final: 0.7225 (t80) REVERT: C 759 PHE cc_start: 0.8718 (m-80) cc_final: 0.8492 (m-10) REVERT: D 51 ASN cc_start: -0.0679 (OUTLIER) cc_final: -0.1060 (p0) REVERT: D 152 MET cc_start: -0.1688 (mmp) cc_final: -0.2136 (mmm) REVERT: D 278 LEU cc_start: 0.4545 (pp) cc_final: 0.4134 (tp) REVERT: D 323 MET cc_start: 0.5007 (OUTLIER) cc_final: 0.4604 (tpp) outliers start: 117 outliers final: 67 residues processed: 267 average time/residue: 0.1437 time to fit residues: 64.7260 Evaluate side-chains 222 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 149 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 385 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 350 optimal weight: 0.0010 chunk 316 optimal weight: 0.0670 chunk 253 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 302 optimal weight: 40.0000 chunk 143 optimal weight: 8.9990 chunk 234 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN A 762 GLN A1002 GLN B1010 GLN D 149 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093347 restraints weight = 62987.220| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.46 r_work: 0.2994 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 29350 Z= 0.108 Angle : 0.583 13.818 40017 Z= 0.286 Chirality : 0.044 0.332 4630 Planarity : 0.004 0.073 5047 Dihedral : 8.884 106.523 4956 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.37 % Favored : 91.34 % Rotamer: Outliers : 2.61 % Allowed : 30.45 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 3453 helix: 1.90 (0.17), residues: 963 sheet: 0.07 (0.23), residues: 522 loop : -2.09 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 518 TYR 0.017 0.001 TYR D 385 PHE 0.026 0.001 PHE B 338 TRP 0.014 0.001 TRP A 353 HIS 0.003 0.000 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (29253) covalent geometry : angle 0.56105 / 0.28 (39766) SS BOND : bond 0.00384 / 0.21 ( 40) SS BOND : angle 0.74664 / 0.50 ( 80) hydrogen bonds : bond 0.04237 / 2.78 ( 991) hydrogen bonds : angle 4.42327 / 3.03 ( 2757) link_ALPHA1-3 : bond 0.01271 / 0.67 ( 1) link_ALPHA1-3 : angle 1.93126 / 1.00 ( 3) link_ALPHA1-6 : bond 0.00855 / 0.45 ( 1) link_ALPHA1-6 : angle 1.54156 / 0.81 ( 3) link_BETA1-4 : bond 0.00499 / 0.30 ( 12) link_BETA1-4 : angle 1.24240 / 0.74 ( 36) link_NAG-ASN : bond 0.00581 / 0.36 ( 43) link_NAG-ASN : angle 2.72735 / 1.88 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 166 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5843 (t80) REVERT: A 458 LYS cc_start: 0.2225 (OUTLIER) cc_final: 0.1879 (mtmm) REVERT: B 756 TYR cc_start: 0.8706 (m-80) cc_final: 0.8426 (m-80) REVERT: C 356 LYS cc_start: 0.7698 (tttt) cc_final: 0.7378 (tptp) REVERT: C 423 TYR cc_start: 0.6891 (t80) cc_final: 0.6685 (t80) REVERT: C 453 TYR cc_start: 0.7427 (t80) cc_final: 0.7151 (t80) REVERT: D 132 VAL cc_start: -0.1814 (OUTLIER) cc_final: -0.2076 (m) REVERT: D 278 LEU cc_start: 0.4591 (pp) cc_final: 0.4157 (tp) REVERT: D 323 MET cc_start: 0.4484 (OUTLIER) cc_final: 0.3518 (tpt) REVERT: D 366 MET cc_start: 0.2738 (tpt) cc_final: 0.2436 (tpt) REVERT: D 498 CYS cc_start: 0.1739 (OUTLIER) cc_final: 0.1492 (t) outliers start: 81 outliers final: 40 residues processed: 243 average time/residue: 0.1455 time to fit residues: 60.0448 Evaluate side-chains 195 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 226 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 295 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.154474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089236 restraints weight = 62741.219| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.56 r_work: 0.2894 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 29350 Z= 0.285 Angle : 0.686 10.767 40017 Z= 0.342 Chirality : 0.048 0.337 4630 Planarity : 0.005 0.068 5047 Dihedral : 8.482 105.676 4954 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.64 % Favored : 90.10 % Rotamer: Outliers : 4.38 % Allowed : 29.29 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3453 helix: 1.39 (0.17), residues: 993 sheet: -0.24 (0.23), residues: 526 loop : -2.28 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 169 TYR 0.024 0.002 TYR C1067 PHE 0.036 0.002 PHE B 338 TRP 0.019 0.001 TRP A 353 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.29 (29253) covalent geometry : angle 0.66194 / 0.34 (39766) SS BOND : bond 0.00364 / 0.26 ( 40) SS BOND : angle 1.26345 / 0.80 ( 80) hydrogen bonds : bond 0.06458 / 4.21 ( 991) hydrogen bonds : angle 4.76102 / 3.26 ( 2757) link_ALPHA1-3 : bond 0.01122 / 0.59 ( 1) link_ALPHA1-3 : angle 1.81520 / 0.97 ( 3) link_ALPHA1-6 : bond 0.01057 / 0.56 ( 1) link_ALPHA1-6 : angle 1.50501 / 0.80 ( 3) link_BETA1-4 : bond 0.00391 / 0.25 ( 12) link_BETA1-4 : angle 1.41213 / 0.85 ( 36) link_NAG-ASN : bond 0.00556 / 0.36 ( 43) link_NAG-ASN : angle 3.00952 / 2.05 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 150 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: A 458 LYS cc_start: 0.2318 (OUTLIER) cc_final: 0.1945 (mtmm) REVERT: A 1116 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 569 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7328 (tt) REVERT: B 1001 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9188 (mp) REVERT: B 1002 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 1115 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 356 LYS cc_start: 0.7764 (tttt) cc_final: 0.7413 (tptp) REVERT: C 759 PHE cc_start: 0.8578 (m-80) cc_final: 0.8358 (m-10) REVERT: D 267 LEU cc_start: 0.2022 (OUTLIER) cc_final: 0.1709 (mp) REVERT: D 323 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3682 (tpt) outliers start: 136 outliers final: 80 residues processed: 276 average time/residue: 0.1432 time to fit residues: 67.1673 Evaluate side-chains 232 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 143 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 169 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 317 optimal weight: 30.0000 chunk 289 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 170 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.5487 > 50:) chunk 256 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN C 901 GLN D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092753 restraints weight = 62500.062| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.69 r_work: 0.2953 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29350 Z= 0.113 Angle : 0.582 11.832 40017 Z= 0.287 Chirality : 0.044 0.329 4630 Planarity : 0.004 0.064 5047 Dihedral : 7.629 102.502 4954 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.46 % Rotamer: Outliers : 2.96 % Allowed : 30.49 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3453 helix: 1.71 (0.17), residues: 980 sheet: -0.08 (0.23), residues: 513 loop : -2.18 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 559 TYR 0.017 0.001 TYR C1067 PHE 0.032 0.001 PHE B 338 TRP 0.025 0.001 TRP A 353 HIS 0.002 0.000 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (29253) covalent geometry : angle 0.55867 / 0.28 (39766) SS BOND : bond 0.00227 / 0.16 ( 40) SS BOND : angle 0.82316 / 0.54 ( 80) hydrogen bonds : bond 0.04441 / 2.91 ( 991) hydrogen bonds : angle 4.39974 / 3.01 ( 2757) link_ALPHA1-3 : bond 0.00850 / 0.45 ( 1) link_ALPHA1-3 : angle 1.53536 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00997 / 0.52 ( 1) link_ALPHA1-6 : angle 1.42016 / 0.76 ( 3) link_BETA1-4 : bond 0.00472 / 0.29 ( 12) link_BETA1-4 : angle 1.10596 / 0.69 ( 36) link_NAG-ASN : bond 0.00558 / 0.35 ( 43) link_NAG-ASN : angle 2.85023 / 1.97 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 150 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5899 (t80) REVERT: A 369 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: A 458 LYS cc_start: 0.2081 (OUTLIER) cc_final: 0.1645 (mtmm) REVERT: A 528 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8128 (ptmm) REVERT: A 1116 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8692 (p) REVERT: B 347 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4067 (t80) REVERT: B 569 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7240 (tt) REVERT: B 756 TYR cc_start: 0.8731 (m-80) cc_final: 0.8526 (m-80) REVERT: C 356 LYS cc_start: 0.7702 (tttt) cc_final: 0.7346 (tptp) REVERT: C 453 TYR cc_start: 0.7462 (t80) cc_final: 0.7214 (t80) REVERT: C 759 PHE cc_start: 0.8518 (m-80) cc_final: 0.8191 (m-10) REVERT: C 988 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8226 (mp0) REVERT: D 51 ASN cc_start: -0.0636 (OUTLIER) cc_final: -0.0962 (p0) REVERT: D 144 LEU cc_start: 0.1578 (OUTLIER) cc_final: 0.1038 (pt) REVERT: D 267 LEU cc_start: 0.1871 (OUTLIER) cc_final: 0.1593 (mp) REVERT: D 323 MET cc_start: 0.3693 (ttt) cc_final: 0.3305 (tpt) outliers start: 92 outliers final: 60 residues processed: 237 average time/residue: 0.1478 time to fit residues: 60.0905 Evaluate side-chains 216 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 147 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 chunk 333 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 309 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 156 optimal weight: 0.0670 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.155886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093259 restraints weight = 62662.770| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.83 r_work: 0.2911 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29350 Z= 0.151 Angle : 0.591 11.258 40017 Z= 0.291 Chirality : 0.044 0.329 4630 Planarity : 0.004 0.062 5047 Dihedral : 7.296 101.587 4954 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.95 % Favored : 90.76 % Rotamer: Outliers : 3.54 % Allowed : 29.87 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3453 helix: 1.65 (0.17), residues: 985 sheet: -0.13 (0.23), residues: 526 loop : -2.19 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.019 0.001 TYR C1067 PHE 0.031 0.001 PHE B 338 TRP 0.027 0.001 TRP A 353 HIS 0.003 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (29253) covalent geometry : angle 0.56747 / 0.29 (39766) SS BOND : bond 0.00237 / 0.17 ( 40) SS BOND : angle 0.82602 / 0.55 ( 80) hydrogen bonds : bond 0.04886 / 3.20 ( 991) hydrogen bonds : angle 4.41136 / 3.02 ( 2757) link_ALPHA1-3 : bond 0.01106 / 0.58 ( 1) link_ALPHA1-3 : angle 1.72783 / 0.92 ( 3) link_ALPHA1-6 : bond 0.01043 / 0.55 ( 1) link_ALPHA1-6 : angle 1.23591 / 0.66 ( 3) link_BETA1-4 : bond 0.00438 / 0.27 ( 12) link_BETA1-4 : angle 1.12018 / 0.70 ( 36) link_NAG-ASN : bond 0.00516 / 0.32 ( 43) link_NAG-ASN : angle 2.87868 / 2.00 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 153 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: A 458 LYS cc_start: 0.2163 (OUTLIER) cc_final: 0.1814 (mtmm) REVERT: A 528 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8063 (ptmm) REVERT: A 1116 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8695 (p) REVERT: B 220 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6626 (t80) REVERT: B 347 PHE cc_start: 0.5416 (OUTLIER) cc_final: 0.4236 (t80) REVERT: B 569 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 1002 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: C 356 LYS cc_start: 0.7470 (tttt) cc_final: 0.7161 (tptp) REVERT: C 453 TYR cc_start: 0.7453 (t80) cc_final: 0.7215 (t80) REVERT: C 759 PHE cc_start: 0.8645 (m-80) cc_final: 0.8300 (m-10) REVERT: C 988 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8260 (mp0) REVERT: D 51 ASN cc_start: -0.0705 (OUTLIER) cc_final: -0.1001 (p0) REVERT: D 323 MET cc_start: 0.3997 (ttt) cc_final: 0.3794 (tpt) outliers start: 110 outliers final: 82 residues processed: 259 average time/residue: 0.1428 time to fit residues: 62.8390 Evaluate side-chains 236 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 146 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 316 optimal weight: 50.0000 chunk 274 optimal weight: 0.5980 chunk 345 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 339 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.154751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093372 restraints weight = 63018.366| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.15 r_work: 0.2867 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29350 Z= 0.207 Angle : 0.631 11.579 40017 Z= 0.313 Chirality : 0.045 0.339 4630 Planarity : 0.004 0.061 5047 Dihedral : 7.212 99.783 4954 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.41 % Favored : 90.30 % Rotamer: Outliers : 3.90 % Allowed : 29.75 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3453 helix: 1.46 (0.17), residues: 990 sheet: -0.32 (0.22), residues: 535 loop : -2.24 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 457 TYR 0.021 0.001 TYR C1067 PHE 0.030 0.002 PHE B 338 TRP 0.028 0.001 TRP A 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (29253) covalent geometry : angle 0.60716 / 0.31 (39766) SS BOND : bond 0.00273 / 0.20 ( 40) SS BOND : angle 0.93367 / 0.62 ( 80) hydrogen bonds : bond 0.05697 / 3.72 ( 991) hydrogen bonds : angle 4.58069 / 3.13 ( 2757) link_ALPHA1-3 : bond 0.01039 / 0.55 ( 1) link_ALPHA1-3 : angle 1.64371 / 0.89 ( 3) link_ALPHA1-6 : bond 0.01250 / 0.66 ( 1) link_ALPHA1-6 : angle 0.99815 / 0.51 ( 3) link_BETA1-4 : bond 0.00433 / 0.28 ( 12) link_BETA1-4 : angle 1.17279 / 0.73 ( 36) link_NAG-ASN : bond 0.00527 / 0.33 ( 43) link_NAG-ASN : angle 2.98201 / 2.04 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 152 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: A 458 LYS cc_start: 0.2096 (OUTLIER) cc_final: 0.1734 (mtmm) REVERT: A 528 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8048 (ptmm) REVERT: A 1116 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 220 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6693 (t80) REVERT: B 347 PHE cc_start: 0.5658 (OUTLIER) cc_final: 0.4305 (t80) REVERT: B 569 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7337 (tt) REVERT: B 1002 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: C 356 LYS cc_start: 0.7527 (tttt) cc_final: 0.7201 (tptp) REVERT: C 759 PHE cc_start: 0.8691 (m-80) cc_final: 0.8357 (m-10) REVERT: D 51 ASN cc_start: -0.0684 (OUTLIER) cc_final: -0.1010 (p0) REVERT: D 267 LEU cc_start: 0.2361 (OUTLIER) cc_final: 0.2159 (mp) REVERT: D 323 MET cc_start: 0.3941 (ttt) cc_final: 0.3320 (tpt) outliers start: 121 outliers final: 90 residues processed: 266 average time/residue: 0.1364 time to fit residues: 61.0734 Evaluate side-chains 247 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 148 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 139 optimal weight: 0.0570 chunk 308 optimal weight: 7.9990 chunk 294 optimal weight: 30.0000 chunk 203 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 314 optimal weight: 40.0000 chunk 32 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.155153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091067 restraints weight = 63143.080| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.71 r_work: 0.2915 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29350 Z= 0.169 Angle : 0.602 12.994 40017 Z= 0.298 Chirality : 0.044 0.332 4630 Planarity : 0.004 0.062 5047 Dihedral : 7.046 98.599 4954 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.06 % Favored : 90.65 % Rotamer: Outliers : 3.90 % Allowed : 29.81 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3453 helix: 1.51 (0.17), residues: 987 sheet: -0.26 (0.23), residues: 517 loop : -2.23 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.020 0.001 TYR C1067 PHE 0.032 0.001 PHE B 562 TRP 0.029 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (29253) covalent geometry : angle 0.57786 / 0.29 (39766) SS BOND : bond 0.00251 / 0.19 ( 40) SS BOND : angle 0.88384 / 0.58 ( 80) hydrogen bonds : bond 0.05144 / 3.37 ( 991) hydrogen bonds : angle 4.46422 / 3.06 ( 2757) link_ALPHA1-3 : bond 0.00996 / 0.52 ( 1) link_ALPHA1-3 : angle 1.57591 / 0.86 ( 3) link_ALPHA1-6 : bond 0.01243 / 0.65 ( 1) link_ALPHA1-6 : angle 1.04629 / 0.54 ( 3) link_BETA1-4 : bond 0.00451 / 0.28 ( 12) link_BETA1-4 : angle 1.09977 / 0.68 ( 36) link_NAG-ASN : bond 0.00548 / 0.35 ( 43) link_NAG-ASN : angle 2.93022 / 2.01 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 146 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: A 371 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.4728 (m-80) REVERT: A 458 LYS cc_start: 0.2165 (OUTLIER) cc_final: 0.1822 (mtmm) REVERT: A 528 LYS cc_start: 0.8802 (mmmt) cc_final: 0.7987 (ptmm) REVERT: B 220 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6679 (t80) REVERT: B 231 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 347 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.4347 (t80) REVERT: B 569 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7299 (tt) REVERT: B 1002 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 191 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: C 356 LYS cc_start: 0.7638 (tttt) cc_final: 0.7269 (tptp) REVERT: C 759 PHE cc_start: 0.8704 (m-80) cc_final: 0.8340 (m-10) REVERT: D 51 ASN cc_start: -0.0731 (OUTLIER) cc_final: -0.0993 (p0) REVERT: D 323 MET cc_start: 0.3750 (ttt) cc_final: 0.3038 (tpt) outliers start: 121 outliers final: 98 residues processed: 263 average time/residue: 0.1483 time to fit residues: 65.8412 Evaluate side-chains 250 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 142 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 292 optimal weight: 30.0000 chunk 155 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 317 optimal weight: 0.9980 chunk 297 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.156279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092604 restraints weight = 62679.408| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.74 r_work: 0.2937 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29350 Z= 0.115 Angle : 0.578 14.454 40017 Z= 0.285 Chirality : 0.044 0.326 4630 Planarity : 0.004 0.063 5047 Dihedral : 6.775 96.761 4954 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.43 % Favored : 91.31 % Rotamer: Outliers : 3.16 % Allowed : 30.45 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.14), residues: 3453 helix: 1.67 (0.17), residues: 985 sheet: -0.18 (0.23), residues: 529 loop : -2.16 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.018 0.001 TYR D 385 PHE 0.031 0.001 PHE B 338 TRP 0.034 0.001 TRP A 353 HIS 0.002 0.000 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (29253) covalent geometry : angle 0.55487 / 0.28 (39766) SS BOND : bond 0.00225 / 0.16 ( 40) SS BOND : angle 0.77428 / 0.52 ( 80) hydrogen bonds : bond 0.04371 / 2.87 ( 991) hydrogen bonds : angle 4.32208 / 2.96 ( 2757) link_ALPHA1-3 : bond 0.00971 / 0.51 ( 1) link_ALPHA1-3 : angle 1.54551 / 0.85 ( 3) link_ALPHA1-6 : bond 0.01198 / 0.63 ( 1) link_ALPHA1-6 : angle 1.09922 / 0.57 ( 3) link_BETA1-4 : bond 0.00479 / 0.30 ( 12) link_BETA1-4 : angle 1.01489 / 0.65 ( 36) link_NAG-ASN : bond 0.00539 / 0.34 ( 43) link_NAG-ASN : angle 2.81100 / 1.93 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 146 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: A 371 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: A 458 LYS cc_start: 0.2212 (OUTLIER) cc_final: 0.1876 (mtmm) REVERT: A 528 LYS cc_start: 0.8755 (mmmt) cc_final: 0.7869 (ptmm) REVERT: B 220 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6680 (t80) REVERT: B 231 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8064 (tp) REVERT: B 347 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.4306 (t80) REVERT: B 516 GLU cc_start: 0.7012 (pm20) cc_final: 0.6786 (pm20) REVERT: B 569 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7281 (tt) REVERT: B 1002 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: C 92 PHE cc_start: 0.7955 (t80) cc_final: 0.7577 (t80) REVERT: C 191 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: C 356 LYS cc_start: 0.7377 (tttt) cc_final: 0.7090 (tptp) REVERT: D 51 ASN cc_start: -0.0565 (OUTLIER) cc_final: -0.0858 (p0) REVERT: D 323 MET cc_start: 0.3434 (ttt) cc_final: 0.2487 (tpt) outliers start: 98 outliers final: 82 residues processed: 240 average time/residue: 0.1506 time to fit residues: 61.7373 Evaluate side-chains 233 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 141 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 GLN B 87 ASN ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100987 restraints weight = 64483.823| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.29 r_work: 0.2957 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29350 Z= 0.168 Angle : 0.604 14.707 40017 Z= 0.299 Chirality : 0.044 0.331 4630 Planarity : 0.004 0.062 5047 Dihedral : 6.795 95.833 4954 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.15 % Favored : 90.56 % Rotamer: Outliers : 3.48 % Allowed : 30.29 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3453 helix: 1.56 (0.17), residues: 990 sheet: -0.18 (0.23), residues: 516 loop : -2.20 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.020 0.001 TYR C1067 PHE 0.032 0.001 PHE B 338 TRP 0.034 0.001 TRP A 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (29253) covalent geometry : angle 0.58133 / 0.29 (39766) SS BOND : bond 0.00252 / 0.18 ( 40) SS BOND : angle 0.85587 / 0.57 ( 80) hydrogen bonds : bond 0.05123 / 3.36 ( 991) hydrogen bonds : angle 4.44942 / 3.04 ( 2757) link_ALPHA1-3 : bond 0.00849 / 0.45 ( 1) link_ALPHA1-3 : angle 1.48998 / 0.83 ( 3) link_ALPHA1-6 : bond 0.01175 / 0.62 ( 1) link_ALPHA1-6 : angle 1.09746 / 0.56 ( 3) link_BETA1-4 : bond 0.00435 / 0.27 ( 12) link_BETA1-4 : angle 1.08440 / 0.68 ( 36) link_NAG-ASN : bond 0.00522 / 0.33 ( 43) link_NAG-ASN : angle 2.86525 / 1.96 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6906 Ramachandran restraints generated. 3453 Oldfield, 0 Emsley, 3453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 140 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 371 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.4752 (m-80) REVERT: A 396 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6747 (m-80) REVERT: A 458 LYS cc_start: 0.2195 (OUTLIER) cc_final: 0.1835 (mtmm) REVERT: A 528 LYS cc_start: 0.8720 (mmmt) cc_final: 0.7870 (ptmm) REVERT: B 220 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6808 (t80) REVERT: B 231 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 347 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4490 (t80) REVERT: B 569 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7298 (tt) REVERT: B 1002 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: C 104 TRP cc_start: 0.7661 (t-100) cc_final: 0.6308 (m100) REVERT: C 191 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: C 356 LYS cc_start: 0.7658 (tttt) cc_final: 0.7322 (tptp) REVERT: D 51 ASN cc_start: -0.0569 (OUTLIER) cc_final: -0.0822 (p0) REVERT: D 323 MET cc_start: 0.3854 (ttt) cc_final: 0.3426 (tpt) outliers start: 108 outliers final: 93 residues processed: 245 average time/residue: 0.1405 time to fit residues: 58.5733 Evaluate side-chains 242 residues out of total 3103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 138 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 396 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 498 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 152 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 286 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.156579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092892 restraints weight = 62888.782| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.67 r_work: 0.2956 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29350 Z= 0.113 Angle : 0.574 14.336 40017 Z= 0.282 Chirality : 0.043 0.324 4630 Planarity : 0.004 0.064 5047 Dihedral : 6.521 94.022 4954 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.17 % Favored : 91.54 % Rotamer: Outliers : 3.32 % Allowed : 30.39 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3453 helix: 1.71 (0.17), residues: 985 sheet: -0.09 (0.23), residues: 526 loop : -2.13 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.019 0.001 TYR D 385 PHE 0.040 0.001 PHE B 562 TRP 0.035 0.001 TRP A 353 HIS 0.004 0.000 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (29253) covalent geometry : angle 0.55114 / 0.28 (39766) SS BOND : bond 0.00214 / 0.15 ( 40) SS BOND : angle 0.76489 / 0.52 ( 80) hydrogen bonds : bond 0.04218 / 2.78 ( 991) hydrogen bonds : angle 4.27971 / 2.92 ( 2757) link_ALPHA1-3 : bond 0.00735 / 0.39 ( 1) link_ALPHA1-3 : angle 1.41277 / 0.78 ( 3) link_ALPHA1-6 : bond 0.00971 / 0.51 ( 1) link_ALPHA1-6 : angle 1.10185 / 0.57 ( 3) link_BETA1-4 : bond 0.00467 / 0.28 ( 12) link_BETA1-4 : angle 0.99977 / 0.65 ( 36) link_NAG-ASN : bond 0.00529 / 0.33 ( 43) link_NAG-ASN : angle 2.77785 / 1.91 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8517.32 seconds wall clock time: 145 minutes 43.55 seconds (8743.55 seconds total)