Starting phenix.real_space_refine on Sun Jul 5 17:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnd_32039/07_2026/7vnd_32039.map" } resolution = 3.6 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2442 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 17563 2.51 5 N 4549 2.21 5 O 5394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27632 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 4 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1015} Chain breaks: 4 Chain: "V" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 111} 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 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 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.14, per 1000 atoms: 0.19 Number of scatterers: 27632 At special positions: 0 Unit cell: (187.59, 172.38, 164.268, 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 126 16.00 O 5394 8.00 N 4549 7.00 C 17563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " 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 A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=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 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 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 C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 122 " " NAG A1306 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 616 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 149 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 616 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN C 282 " " NAG R 1 " - " ASN C1074 " " NAG T 1 " - " ASN C 331 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 976.6 milliseconds 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6422 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 54 sheets defined 22.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.075A pdb=" N ARG B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.546A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.192A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.149A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.608A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.691A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 761 through 783 removed outlier: 3.811A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 4.106A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.739A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 869 Processing helix chain 'B' and resid 870 through 882 removed outlier: 3.994A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.704A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 4.208A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.601A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.945A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.763A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 3.527A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.518A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.566A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 782 removed outlier: 3.508A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 866 through 884 removed outlier: 4.057A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 removed outlier: 3.980A pdb=" N PHE A 888 " --> pdb=" O GLY A 885 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.376A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.537A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.826A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.573A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.741A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.684A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A1010 " --> pdb=" O THR A1006 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.785A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.032A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.617A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.099A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.742A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 773 removed outlier: 3.513A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 783 removed outlier: 3.725A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 4.133A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.980A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.722A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 909 removed outlier: 3.719A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.662A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.641A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.976A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 3.937A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.652A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.338A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.760A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 64 removed outlier: 3.839A pdb=" N LYS V 64 " --> pdb=" O PRO V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 Processing helix chain 'V' and resid 98 through 102 removed outlier: 4.056A pdb=" N GLY V 102 " --> pdb=" O TRP V 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 4.112A pdb=" N TYR D 30 " --> pdb=" O PHE D 27 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP D 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.896A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 99 through 102 removed outlier: 4.202A pdb=" N GLY D 102 " --> pdb=" O TRP D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.595A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.600A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.775A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 317 removed outlier: 7.041A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.985A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.852A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 584 through 586 removed outlier: 3.605A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.982A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.142A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.490A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.550A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.486A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AC1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.512A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.990A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.267A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.610A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC7, first strand: chain 'A' and resid 225 through 229 removed outlier: 6.998A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.466A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.543A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.851A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.643A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.646A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.299A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AD7, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AD8, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.608A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.808A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.579A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 49 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 92 through 94 removed outlier: 3.659A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.176A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N LEU C 141 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU C 242 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 143 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 244 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 126 through 133 removed outlier: 8.055A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.890A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.607A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.133A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.575A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF5, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AF6, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.644A pdb=" N ASP V 72 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR V 79 " --> pdb=" O SER V 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER V 70 " --> pdb=" O TYR V 79 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN V 81 " --> pdb=" O THR V 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR V 68 " --> pdb=" O GLN V 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 35 through 39 Processing sheet with id=AF8, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.743A pdb=" N CYS D 22 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 57 through 59 removed outlier: 5.130A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER D 35 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 96 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 39 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N MET D 92 " --> pdb=" O GLN D 39 " (cutoff:3.500A) 742 hydrogen bonds defined for protein. 1974 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: 5.79 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4477 1.31 - 1.44: 7786 1.44 - 1.57: 15831 1.57 - 1.70: 1 1.70 - 1.83: 164 Bond restraints: 28259 Sorted by residual: bond pdb=" C7 NAG C1302 " pdb=" N2 NAG C1302 " ideal model delta sigma weight residual 1.346 1.487 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C7 NAG S 2 " pdb=" N2 NAG S 2 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C7 NAG R 2 " pdb=" N2 NAG R 2 " ideal model delta sigma weight residual 1.346 1.482 -0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 28254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 37209 1.91 - 3.83: 964 3.83 - 5.74: 244 5.74 - 7.65: 20 7.65 - 9.56: 15 Bond angle restraints: 38452 Sorted by residual: angle pdb=" CA CYS C 336 " pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " ideal model delta sigma weight residual 114.40 122.10 -7.70 2.30e+00 1.89e-01 1.12e+01 angle pdb=" C GLN C 613 " pdb=" N ASP C 614 " pdb=" CA ASP C 614 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C8 NAG J 1 " pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 115.06 124.62 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C8 NAG R 2 " pdb=" C7 NAG R 2 " pdb=" N2 NAG R 2 " ideal model delta sigma weight residual 115.06 124.54 -9.48 3.00e+00 1.11e-01 9.99e+00 angle pdb=" C8 NAG K 2 " pdb=" C7 NAG K 2 " pdb=" N2 NAG K 2 " ideal model delta sigma weight residual 115.06 124.40 -9.34 3.00e+00 1.11e-01 9.69e+00 ... (remaining 38447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14652 17.82 - 35.64: 1390 35.64 - 53.47: 229 53.47 - 71.29: 36 71.29 - 89.11: 28 Dihedral angle restraints: 16335 sinusoidal: 6331 harmonic: 10004 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -174.99 88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 95 " pdb=" CB CYS D 95 " ideal model delta sinusoidal sigma weight residual 93.00 166.23 -73.23 1 1.00e+01 1.00e-02 6.83e+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 -14.31 -71.69 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 16332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4108 0.093 - 0.187: 356 0.187 - 0.280: 7 0.280 - 0.373: 5 0.373 - 0.466: 4 Chirality restraints: 4480 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 4477 not shown) Planarity restraints: 4947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " 0.067 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO C 384 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 271 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 272 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A 987 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.031 5.00e-02 4.00e+02 ... (remaining 4944 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1015 2.72 - 3.26: 27098 3.26 - 3.81: 41338 3.81 - 4.35: 53029 4.35 - 4.90: 88766 Nonbonded interactions: 211246 Sorted by model distance: nonbonded pdb=" O GLN C 580 " pdb=" O3 NAG T 1 " model vdw 2.170 3.040 nonbonded pdb=" OE2 GLU C 281 " pdb=" O3 NAG P 1 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR A1076 " pdb=" OG SER A1097 " model vdw 2.185 3.040 nonbonded pdb=" O SER B 937 " pdb=" OG1 THR B 941 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.201 3.040 ... (remaining 211241 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' selection = chain 'B' selection = (chain 'C' and resid 14 through 1306) } ncs_group { reference = chain 'D' selection = chain 'V' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.060 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.009 0.141 28333 Z= 0.444 Angle : 0.782 12.524 38649 Z= 0.353 Chirality : 0.051 0.466 4480 Planarity : 0.004 0.099 4914 Dihedral : 14.151 89.109 9838 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3408 helix: -1.63 (0.20), residues: 615 sheet: -0.22 (0.22), residues: 578 loop : -2.24 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 158 TYR 0.020 0.001 TYR A1067 PHE 0.024 0.001 PHE C 106 TRP 0.026 0.002 TRP C 886 HIS 0.005 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00899 / 0.44 (28259) covalent geometry : angle 0.75101 / 0.34 (38452) SS BOND : bond 0.00244 / 0.15 ( 25) SS BOND : angle 1.67277 / 1.06 ( 50) hydrogen bonds : bond 0.28318 / 19.16 ( 730) hydrogen bonds : angle 10.22636 / 7.13 ( 1974) link_BETA1-4 : bond 0.00542 / 0.36 ( 16) link_BETA1-4 : angle 2.07398 / 1.21 ( 48) link_NAG-ASN : bond 0.00758 / 0.48 ( 33) link_NAG-ASN : angle 4.03294 / 2.72 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7773 (m-80) cc_final: 0.7492 (m-80) REVERT: C 106 PHE cc_start: 0.7661 (m-80) cc_final: 0.7424 (m-80) REVERT: C 457 ARG cc_start: 0.2105 (mtt180) cc_final: 0.1740 (mmm160) REVERT: C 645 THR cc_start: 0.8719 (p) cc_final: 0.8515 (p) REVERT: C 1081 ILE cc_start: 0.9231 (mm) cc_final: 0.8946 (mm) REVERT: V 82 MET cc_start: 0.3986 (mmt) cc_final: 0.2092 (ptt) REVERT: D 92 MET cc_start: 0.0667 (pmm) cc_final: 0.0426 (pmm) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1677 time to fit residues: 73.6842 Evaluate side-chains 210 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0060 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 935 GLN A 949 GLN A 953 ASN C 211 ASN C 717 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.173211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133270 restraints weight = 46597.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125958 restraints weight = 60406.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122907 restraints weight = 52952.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122199 restraints weight = 44546.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122706 restraints weight = 38074.102| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28333 Z= 0.147 Angle : 0.700 12.866 38649 Z= 0.336 Chirality : 0.052 0.462 4480 Planarity : 0.004 0.054 4914 Dihedral : 4.989 28.414 3700 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.63 % Allowed : 5.94 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.14), residues: 3408 helix: -1.11 (0.20), residues: 652 sheet: -0.21 (0.21), residues: 635 loop : -2.20 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 158 TYR 0.023 0.001 TYR C 37 PHE 0.032 0.002 PHE C 643 TRP 0.031 0.002 TRP C 436 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (28259) covalent geometry : angle 0.66595 / 0.33 (38452) SS BOND : bond 0.00321 / 0.17 ( 25) SS BOND : angle 1.28595 / 0.89 ( 50) hydrogen bonds : bond 0.05490 / 3.75 ( 730) hydrogen bonds : angle 6.65821 / 4.63 ( 1974) link_BETA1-4 : bond 0.00713 / 0.48 ( 16) link_BETA1-4 : angle 2.36391 / 1.52 ( 48) link_NAG-ASN : bond 0.00747 / 0.47 ( 33) link_NAG-ASN : angle 3.93839 / 2.66 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: B 32 PHE cc_start: 0.8000 (m-10) cc_final: 0.7770 (m-10) REVERT: C 457 ARG cc_start: 0.2468 (mtt180) cc_final: 0.1546 (mmm160) REVERT: C 1081 ILE cc_start: 0.9290 (mm) cc_final: 0.8930 (mm) REVERT: V 82 MET cc_start: 0.3043 (mmt) cc_final: 0.1074 (ptt) REVERT: D 34 MET cc_start: 0.4876 (tpp) cc_final: 0.2841 (ttm) outliers start: 19 outliers final: 12 residues processed: 236 average time/residue: 0.1795 time to fit residues: 69.7823 Evaluate side-chains 212 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 272 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 338 optimal weight: 0.0670 chunk 70 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 751 ASN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 717 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132989 restraints weight = 46445.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126829 restraints weight = 58893.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123449 restraints weight = 43393.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122099 restraints weight = 45902.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122870 restraints weight = 39071.585| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28333 Z= 0.121 Angle : 0.651 12.681 38649 Z= 0.310 Chirality : 0.050 0.448 4480 Planarity : 0.004 0.047 4914 Dihedral : 4.821 27.395 3700 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.77 % Allowed : 8.04 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.14), residues: 3408 helix: -0.64 (0.21), residues: 655 sheet: -0.29 (0.21), residues: 604 loop : -2.17 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 905 TYR 0.020 0.001 TYR C 37 PHE 0.023 0.001 PHE C 643 TRP 0.028 0.002 TRP C 436 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (28259) covalent geometry : angle 0.61856 / 0.30 (38452) SS BOND : bond 0.00252 / 0.14 ( 25) SS BOND : angle 0.97191 / 0.67 ( 50) hydrogen bonds : bond 0.04545 / 3.10 ( 730) hydrogen bonds : angle 6.02375 / 4.17 ( 1974) link_BETA1-4 : bond 0.00832 / 0.56 ( 16) link_BETA1-4 : angle 2.18694 / 1.40 ( 48) link_NAG-ASN : bond 0.00787 / 0.50 ( 33) link_NAG-ASN : angle 3.71572 / 2.49 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.7998 (m-10) cc_final: 0.7771 (m-10) REVERT: B 92 PHE cc_start: 0.6780 (t80) cc_final: 0.6545 (t80) REVERT: B 483 VAL cc_start: 0.7970 (m) cc_final: 0.7746 (p) REVERT: B 1010 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7659 (tp40) REVERT: A 737 ASP cc_start: 0.8156 (t0) cc_final: 0.7725 (t0) REVERT: A 957 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 457 ARG cc_start: 0.2464 (mtt180) cc_final: 0.1550 (mmm160) REVERT: C 1081 ILE cc_start: 0.9279 (mm) cc_final: 0.8933 (mm) REVERT: V 82 MET cc_start: 0.2790 (mmt) cc_final: 0.0858 (ptt) REVERT: D 34 MET cc_start: 0.4442 (tpp) cc_final: 0.2685 (ttm) outliers start: 23 outliers final: 11 residues processed: 238 average time/residue: 0.1689 time to fit residues: 67.8908 Evaluate side-chains 214 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 13 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 150 optimal weight: 50.0000 chunk 293 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 HIS B 99 ASN B 125 ASN B 409 GLN B 957 GLN B1088 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 498 GLN A 935 GLN A1101 HIS C1098 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.169624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127530 restraints weight = 46188.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121571 restraints weight = 68630.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117820 restraints weight = 43539.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116926 restraints weight = 42129.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117471 restraints weight = 39289.031| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 28333 Z= 0.230 Angle : 0.739 12.910 38649 Z= 0.355 Chirality : 0.053 0.454 4480 Planarity : 0.005 0.075 4914 Dihedral : 5.181 30.755 3700 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 1.57 % Allowed : 10.90 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.14), residues: 3408 helix: -0.73 (0.20), residues: 658 sheet: -0.46 (0.21), residues: 652 loop : -2.27 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1039 TYR 0.052 0.002 TYR A1067 PHE 0.031 0.002 PHE B 238 TRP 0.021 0.002 TRP B 886 HIS 0.009 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (28259) covalent geometry : angle 0.70790 / 0.35 (38452) SS BOND : bond 0.00440 / 0.24 ( 25) SS BOND : angle 1.40232 / 0.96 ( 50) hydrogen bonds : bond 0.04944 / 3.36 ( 730) hydrogen bonds : angle 5.97272 / 4.15 ( 1974) link_BETA1-4 : bond 0.00788 / 0.53 ( 16) link_BETA1-4 : angle 2.32072 / 1.46 ( 48) link_NAG-ASN : bond 0.00722 / 0.44 ( 33) link_NAG-ASN : angle 3.87597 / 2.59 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.8153 (m-10) cc_final: 0.7868 (m-10) REVERT: B 483 VAL cc_start: 0.7894 (m) cc_final: 0.7654 (p) REVERT: B 1010 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7793 (tp40) REVERT: A 129 LYS cc_start: 0.7487 (ttmt) cc_final: 0.7250 (ttpt) REVERT: A 558 LYS cc_start: 0.7187 (tppp) cc_final: 0.6954 (mmtm) REVERT: A 878 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9114 (tt) REVERT: A 1130 ILE cc_start: 0.9205 (pt) cc_final: 0.8938 (pt) REVERT: C 457 ARG cc_start: 0.2504 (mtt180) cc_final: 0.2073 (mtt180) REVERT: V 82 MET cc_start: 0.2767 (mmt) cc_final: 0.0768 (ptt) REVERT: D 34 MET cc_start: 0.4559 (tpp) cc_final: 0.2815 (ttm) outliers start: 47 outliers final: 26 residues processed: 244 average time/residue: 0.1673 time to fit residues: 69.1865 Evaluate side-chains 228 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain V residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 263 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 259 optimal weight: 30.0000 chunk 291 optimal weight: 9.9990 chunk 296 optimal weight: 0.5980 chunk 208 optimal weight: 0.0770 chunk 204 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 762 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1106 GLN ** 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 = 0.4125 r_free = 0.4125 target = 0.173474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134143 restraints weight = 46391.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.127346 restraints weight = 63552.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123829 restraints weight = 47067.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122963 restraints weight = 45555.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123705 restraints weight = 39457.645| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28333 Z= 0.111 Angle : 0.637 12.582 38649 Z= 0.304 Chirality : 0.050 0.448 4480 Planarity : 0.004 0.049 4914 Dihedral : 4.810 27.600 3700 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.53 % Allowed : 11.74 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3408 helix: -0.20 (0.21), residues: 646 sheet: -0.32 (0.21), residues: 606 loop : -2.18 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.020 0.001 TYR V 52 PHE 0.025 0.001 PHE B 238 TRP 0.027 0.002 TRP C 886 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (28259) covalent geometry : angle 0.60615 / 0.30 (38452) SS BOND : bond 0.00233 / 0.14 ( 25) SS BOND : angle 0.96794 / 0.68 ( 50) hydrogen bonds : bond 0.03740 / 2.55 ( 730) hydrogen bonds : angle 5.56188 / 3.85 ( 1974) link_BETA1-4 : bond 0.00839 / 0.57 ( 16) link_BETA1-4 : angle 2.10498 / 1.33 ( 48) link_NAG-ASN : bond 0.00804 / 0.51 ( 33) link_NAG-ASN : angle 3.60841 / 2.41 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8380 (tp) cc_final: 0.8179 (tt) REVERT: B 126 VAL cc_start: 0.3558 (OUTLIER) cc_final: 0.3069 (m) REVERT: B 160 TYR cc_start: 0.5180 (m-80) cc_final: 0.4565 (m-80) REVERT: B 483 VAL cc_start: 0.8009 (m) cc_final: 0.7804 (p) REVERT: B 1010 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7666 (tp40) REVERT: A 129 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7325 (ttpt) REVERT: A 208 THR cc_start: 0.8475 (p) cc_final: 0.8212 (t) REVERT: A 558 LYS cc_start: 0.7269 (tppp) cc_final: 0.7028 (mmtm) REVERT: A 737 ASP cc_start: 0.8186 (t0) cc_final: 0.7839 (t0) REVERT: A 902 MET cc_start: 0.8935 (mmm) cc_final: 0.8701 (tpt) REVERT: A 957 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 78 ARG cc_start: 0.3971 (mmt180) cc_final: 0.3309 (mtt-85) REVERT: C 905 ARG cc_start: 0.7852 (mpt-90) cc_final: 0.7604 (mtt90) REVERT: C 1081 ILE cc_start: 0.9275 (mm) cc_final: 0.8948 (mm) REVERT: V 82 MET cc_start: 0.2845 (mmt) cc_final: 0.0872 (ptt) REVERT: D 34 MET cc_start: 0.4692 (tpp) cc_final: 0.2919 (ttm) outliers start: 46 outliers final: 22 residues processed: 266 average time/residue: 0.1714 time to fit residues: 76.6198 Evaluate side-chains 228 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 249 optimal weight: 40.0000 chunk 277 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 394 ASN A 81 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 439 ASN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.127279 restraints weight = 46140.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119713 restraints weight = 67393.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116656 restraints weight = 43235.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115730 restraints weight = 45816.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116343 restraints weight = 37328.560| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28333 Z= 0.243 Angle : 0.744 12.681 38649 Z= 0.356 Chirality : 0.053 0.458 4480 Planarity : 0.005 0.068 4914 Dihedral : 5.138 29.304 3700 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.13 % Allowed : 12.74 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.14), residues: 3408 helix: -0.53 (0.21), residues: 658 sheet: -0.51 (0.21), residues: 647 loop : -2.28 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1039 TYR 0.050 0.002 TYR C1067 PHE 0.026 0.002 PHE C 643 TRP 0.025 0.002 TRP C 886 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 (28259) covalent geometry : angle 0.71398 / 0.35 (38452) SS BOND : bond 0.00657 / 0.34 ( 25) SS BOND : angle 1.38407 / 0.95 ( 50) hydrogen bonds : bond 0.04652 / 3.15 ( 730) hydrogen bonds : angle 5.76313 / 4.01 ( 1974) link_BETA1-4 : bond 0.00809 / 0.55 ( 16) link_BETA1-4 : angle 2.26486 / 1.41 ( 48) link_NAG-ASN : bond 0.00708 / 0.43 ( 33) link_NAG-ASN : angle 3.83722 / 2.56 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 126 VAL cc_start: 0.3803 (OUTLIER) cc_final: 0.3259 (m) REVERT: B 483 VAL cc_start: 0.7894 (m) cc_final: 0.7656 (p) REVERT: B 1010 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7789 (tp40) REVERT: A 129 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7232 (ttpt) REVERT: A 208 THR cc_start: 0.8654 (p) cc_final: 0.8377 (t) REVERT: A 558 LYS cc_start: 0.7236 (tppp) cc_final: 0.6937 (mmtm) REVERT: A 737 ASP cc_start: 0.8163 (t0) cc_final: 0.7801 (t0) REVERT: A 902 MET cc_start: 0.9039 (mmm) cc_final: 0.8627 (tpt) REVERT: C 78 ARG cc_start: 0.4096 (mmt180) cc_final: 0.3579 (mtt-85) REVERT: C 457 ARG cc_start: 0.3007 (mtt180) cc_final: 0.2703 (mtt180) REVERT: V 82 MET cc_start: 0.2613 (mmt) cc_final: 0.2381 (mmt) REVERT: D 34 MET cc_start: 0.4462 (tpp) cc_final: 0.2764 (ttm) outliers start: 64 outliers final: 39 residues processed: 251 average time/residue: 0.1569 time to fit residues: 67.0795 Evaluate side-chains 232 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 166 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 255 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131343 restraints weight = 45936.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122410 restraints weight = 60306.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121283 restraints weight = 48577.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120095 restraints weight = 41676.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120589 restraints weight = 40842.932| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28333 Z= 0.122 Angle : 0.659 12.520 38649 Z= 0.313 Chirality : 0.051 0.448 4480 Planarity : 0.004 0.047 4914 Dihedral : 4.882 28.269 3700 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.60 % Allowed : 13.80 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3408 helix: -0.18 (0.21), residues: 650 sheet: -0.36 (0.20), residues: 637 loop : -2.22 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE A 888 TRP 0.026 0.002 TRP C 886 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (28259) covalent geometry : angle 0.62876 / 0.31 (38452) SS BOND : bond 0.00309 / 0.17 ( 25) SS BOND : angle 1.07735 / 0.75 ( 50) hydrogen bonds : bond 0.03837 / 2.61 ( 730) hydrogen bonds : angle 5.52602 / 3.83 ( 1974) link_BETA1-4 : bond 0.00813 / 0.55 ( 16) link_BETA1-4 : angle 2.09727 / 1.31 ( 48) link_NAG-ASN : bond 0.00784 / 0.49 ( 33) link_NAG-ASN : angle 3.65060 / 2.43 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.8397 (tp) cc_final: 0.8190 (tp) REVERT: B 483 VAL cc_start: 0.7981 (m) cc_final: 0.7763 (p) REVERT: B 1010 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7734 (tp40) REVERT: A 129 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7348 (ttpt) REVERT: A 208 THR cc_start: 0.8495 (p) cc_final: 0.8236 (t) REVERT: A 558 LYS cc_start: 0.7223 (tppp) cc_final: 0.6945 (mmtm) REVERT: A 737 ASP cc_start: 0.8181 (t0) cc_final: 0.7885 (t0) REVERT: A 902 MET cc_start: 0.8975 (mmm) cc_final: 0.8693 (tpt) REVERT: C 43 PHE cc_start: 0.3990 (m-80) cc_final: 0.2864 (m-10) REVERT: C 78 ARG cc_start: 0.4137 (mmt180) cc_final: 0.3379 (mtt-85) REVERT: C 457 ARG cc_start: 0.2837 (mtt180) cc_final: 0.1941 (mmm160) REVERT: C 905 ARG cc_start: 0.8020 (mpt-90) cc_final: 0.7322 (mpt180) REVERT: V 82 MET cc_start: 0.2804 (mmt) cc_final: 0.0869 (ptt) REVERT: D 34 MET cc_start: 0.4671 (tpp) cc_final: 0.2958 (ttm) outliers start: 48 outliers final: 35 residues processed: 248 average time/residue: 0.1531 time to fit residues: 63.7116 Evaluate side-chains 235 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 152 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 225 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 217 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.170935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130689 restraints weight = 46248.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123562 restraints weight = 62141.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120268 restraints weight = 50686.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119250 restraints weight = 49339.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119954 restraints weight = 39750.319| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28333 Z= 0.145 Angle : 0.662 12.457 38649 Z= 0.314 Chirality : 0.051 0.448 4480 Planarity : 0.004 0.047 4914 Dihedral : 4.847 28.311 3700 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.73 % Allowed : 14.10 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3408 helix: -0.13 (0.21), residues: 653 sheet: -0.50 (0.20), residues: 674 loop : -2.18 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.022 0.001 TYR C1067 PHE 0.020 0.001 PHE A 888 TRP 0.025 0.002 TRP C 886 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (28259) covalent geometry : angle 0.63143 / 0.31 (38452) SS BOND : bond 0.00318 / 0.18 ( 25) SS BOND : angle 1.08479 / 0.74 ( 50) hydrogen bonds : bond 0.03878 / 2.64 ( 730) hydrogen bonds : angle 5.46284 / 3.78 ( 1974) link_BETA1-4 : bond 0.00796 / 0.54 ( 16) link_BETA1-4 : angle 2.09542 / 1.30 ( 48) link_NAG-ASN : bond 0.00744 / 0.46 ( 33) link_NAG-ASN : angle 3.64688 / 2.43 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 483 VAL cc_start: 0.8002 (m) cc_final: 0.7782 (p) REVERT: B 1010 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7662 (tp40) REVERT: A 129 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7319 (ttpt) REVERT: A 208 THR cc_start: 0.8512 (p) cc_final: 0.8267 (t) REVERT: A 558 LYS cc_start: 0.7258 (tppp) cc_final: 0.7013 (mmtm) REVERT: A 737 ASP cc_start: 0.8220 (t0) cc_final: 0.7883 (t0) REVERT: A 902 MET cc_start: 0.8926 (mmm) cc_final: 0.8637 (tpt) REVERT: C 44 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8611 (mmt90) REVERT: C 78 ARG cc_start: 0.4202 (mmt180) cc_final: 0.3665 (mtt-85) REVERT: C 457 ARG cc_start: 0.2868 (mtt180) cc_final: 0.1998 (mmm160) REVERT: V 82 MET cc_start: 0.2842 (mmt) cc_final: 0.0917 (ptt) REVERT: D 34 MET cc_start: 0.4672 (tpp) cc_final: 0.2959 (ttm) outliers start: 52 outliers final: 40 residues processed: 245 average time/residue: 0.1479 time to fit residues: 61.2135 Evaluate side-chains 239 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130075 restraints weight = 45976.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123832 restraints weight = 63319.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119735 restraints weight = 42749.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119121 restraints weight = 47066.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120153 restraints weight = 37006.088| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28333 Z= 0.137 Angle : 0.654 12.400 38649 Z= 0.311 Chirality : 0.051 0.445 4480 Planarity : 0.004 0.046 4914 Dihedral : 4.800 28.290 3700 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.67 % Allowed : 14.34 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.98 (0.14), residues: 3408 helix: 0.01 (0.21), residues: 648 sheet: -0.47 (0.20), residues: 674 loop : -2.16 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.031 0.001 TYR B 160 PHE 0.020 0.001 PHE A 888 TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (28259) covalent geometry : angle 0.62429 / 0.30 (38452) SS BOND : bond 0.00301 / 0.16 ( 25) SS BOND : angle 1.07308 / 0.74 ( 50) hydrogen bonds : bond 0.03781 / 2.57 ( 730) hydrogen bonds : angle 5.40398 / 3.74 ( 1974) link_BETA1-4 : bond 0.00804 / 0.54 ( 16) link_BETA1-4 : angle 2.06790 / 1.28 ( 48) link_NAG-ASN : bond 0.00748 / 0.46 ( 33) link_NAG-ASN : angle 3.60852 / 2.40 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 483 VAL cc_start: 0.7972 (m) cc_final: 0.7752 (p) REVERT: B 901 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: B 1010 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7708 (tp40) REVERT: A 129 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7174 (ttpt) REVERT: A 208 THR cc_start: 0.8554 (p) cc_final: 0.8315 (t) REVERT: A 558 LYS cc_start: 0.7250 (tppp) cc_final: 0.6947 (mmtm) REVERT: A 737 ASP cc_start: 0.8185 (t0) cc_final: 0.7849 (t0) REVERT: A 902 MET cc_start: 0.8983 (mmm) cc_final: 0.8731 (tpt) REVERT: C 44 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8532 (mmt90) REVERT: C 78 ARG cc_start: 0.4107 (mmt180) cc_final: 0.3370 (mtt-85) REVERT: C 457 ARG cc_start: 0.2742 (mtt180) cc_final: 0.1785 (mmm160) REVERT: C 1081 ILE cc_start: 0.9219 (mm) cc_final: 0.8867 (mm) REVERT: V 82 MET cc_start: 0.2716 (mmt) cc_final: 0.0844 (ptt) REVERT: D 34 MET cc_start: 0.4590 (tpp) cc_final: 0.2902 (ttm) outliers start: 50 outliers final: 41 residues processed: 240 average time/residue: 0.1688 time to fit residues: 68.5033 Evaluate side-chains 238 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 152 optimal weight: 0.4980 chunk 280 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.170297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130834 restraints weight = 46260.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121994 restraints weight = 64135.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118984 restraints weight = 45299.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118866 restraints weight = 42748.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119100 restraints weight = 38274.995| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28333 Z= 0.156 Angle : 0.669 12.412 38649 Z= 0.318 Chirality : 0.051 0.444 4480 Planarity : 0.004 0.047 4914 Dihedral : 4.856 29.047 3700 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.53 % Allowed : 14.64 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.14), residues: 3408 helix: -0.00 (0.21), residues: 650 sheet: -0.53 (0.20), residues: 647 loop : -2.17 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 357 TYR 0.031 0.001 TYR C1067 PHE 0.020 0.001 PHE C 643 TRP 0.025 0.002 TRP C 886 HIS 0.004 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (28259) covalent geometry : angle 0.63904 / 0.31 (38452) SS BOND : bond 0.00339 / 0.18 ( 25) SS BOND : angle 1.13633 / 0.78 ( 50) hydrogen bonds : bond 0.03911 / 2.66 ( 730) hydrogen bonds : angle 5.41096 / 3.75 ( 1974) link_BETA1-4 : bond 0.00794 / 0.54 ( 16) link_BETA1-4 : angle 2.07296 / 1.28 ( 48) link_NAG-ASN : bond 0.00736 / 0.45 ( 33) link_NAG-ASN : angle 3.63754 / 2.42 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 483 VAL cc_start: 0.8006 (m) cc_final: 0.7782 (p) REVERT: B 1010 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7706 (tp40) REVERT: A 129 LYS cc_start: 0.7430 (ttmt) cc_final: 0.7118 (ttpt) REVERT: A 208 THR cc_start: 0.8452 (p) cc_final: 0.8200 (t) REVERT: A 558 LYS cc_start: 0.7264 (tppp) cc_final: 0.7009 (mmtm) REVERT: A 737 ASP cc_start: 0.8185 (t0) cc_final: 0.7852 (t0) REVERT: A 902 MET cc_start: 0.9202 (mmm) cc_final: 0.8852 (tpt) REVERT: C 44 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8589 (mmt90) REVERT: C 78 ARG cc_start: 0.4019 (mmt180) cc_final: 0.3287 (mtt-85) REVERT: C 357 ARG cc_start: 0.6347 (mtp-110) cc_final: 0.5647 (ttp80) REVERT: D 34 MET cc_start: 0.4407 (tpp) cc_final: 0.2723 (ttm) outliers start: 46 outliers final: 40 residues processed: 233 average time/residue: 0.1593 time to fit residues: 62.6783 Evaluate side-chains 234 residues out of total 2999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain D residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 199 optimal weight: 5.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.172158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132433 restraints weight = 46006.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123536 restraints weight = 62467.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120725 restraints weight = 49702.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119720 restraints weight = 46049.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120530 restraints weight = 39721.730| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28333 Z= 0.111 Angle : 0.636 12.251 38649 Z= 0.302 Chirality : 0.050 0.441 4480 Planarity : 0.004 0.045 4914 Dihedral : 4.680 27.748 3700 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.37 % Allowed : 14.90 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.84 (0.14), residues: 3408 helix: 0.28 (0.22), residues: 647 sheet: -0.39 (0.20), residues: 650 loop : -2.10 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 319 TYR 0.017 0.001 TYR C1067 PHE 0.020 0.001 PHE A 888 TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (28259) covalent geometry : angle 0.60686 / 0.30 (38452) SS BOND : bond 0.00237 / 0.14 ( 25) SS BOND : angle 0.97674 / 0.67 ( 50) hydrogen bonds : bond 0.03491 / 2.38 ( 730) hydrogen bonds : angle 5.23747 / 3.63 ( 1974) link_BETA1-4 : bond 0.00814 / 0.55 ( 16) link_BETA1-4 : angle 1.99762 / 1.24 ( 48) link_NAG-ASN : bond 0.00779 / 0.49 ( 33) link_NAG-ASN : angle 3.51422 / 2.34 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4442.99 seconds wall clock time: 77 minutes 59.84 seconds (4679.84 seconds total)